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Aguilar-Rangel EJ, Savin-Gámez A, García-Maldonado JQ, Prado B, Vásquez-Murrieta MS, Siebe C, Alcántara-Hernández RJ. Increases in the soil ammonia oxidizing phylotypes and their rechange due to long-term irrigation with wastewater. PLoS One 2024; 19:e0299518. [PMID: 38603769 PMCID: PMC11008854 DOI: 10.1371/journal.pone.0299518] [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: 11/28/2023] [Accepted: 02/13/2024] [Indexed: 04/13/2024] Open
Abstract
Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.
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Affiliation(s)
- Eduardo J. Aguilar-Rangel
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - Alba Savin-Gámez
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de México, México
| | - José Q. García-Maldonado
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Merida 97310, Yucatán, México
| | - Blanca Prado
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
| | - María Soledad Vásquez-Murrieta
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340, Ciudad de México, México
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
| | - Rocío J. Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
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Ochoa-Hernández ME, Reynoso-Varela A, Martínez-Córdova LR, Rodelas B, Durán U, Alcántara-Hernández RJ, Serrano-Palacios D, Calderón K. Linking the shifts in the metabolically active microbiota in a UASB and hybrid anaerobic-aerobic bioreactor for swine wastewater treatment. J Environ Manage 2023; 344:118435. [PMID: 37379625 DOI: 10.1016/j.jenvman.2023.118435] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/20/2022] [Revised: 06/05/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.
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Affiliation(s)
- María E Ochoa-Hernández
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Andrea Reynoso-Varela
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico
| | - Luis R Martínez-Córdova
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico
| | - Belén Rodelas
- Department of Microbiology and Institute of Water Research, University of Granada, Spain
| | - Ulises Durán
- Universidad Autónoma Metropolitana, Biotechnology Dept., P.A. 55-535, 09340, Iztapalapa, Mexico City, Mexico
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, Mexico
| | - Denisse Serrano-Palacios
- Departamento de Ciencias del Agua y Medio Ambiente, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur., Ciudad Obregón, Sonora, CP.85000, Mexico.
| | - Kadiya Calderón
- Departamento de Investigaciones Científicas y Tecnológicas, Universidad de Sonora, Blvd. Luis Donaldo Colosio S/N. CP., 83000, Hermosillo, Sonora, Mexico.
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3
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Sánchez-Soto MF, Cerqueda-García D, Alcántara-Hernández RJ, Falcón LI, Pech D, Árcega-Cabrera F, Aguirre-Macedo ML, García-Maldonado JQ. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. Microb Ecol 2021; 81:908-921. [PMID: 33196853 DOI: 10.1007/s00248-020-01631-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | | | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Ma Leopoldina Aguirre-Macedo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico.
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México.
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Valdespino-Castillo PM, Bautista-García A, Favoretto F, Merino-Ibarra M, Alcántara-Hernández RJ, Pi-Puig T, Castillo FS, Espinosa-Matías S, Holman HY, Blanco-Jarvio A. Interplay of microbial communities with mineral environments in coralline algae. Sci Total Environ 2021; 757:143877. [PMID: 33316514 DOI: 10.1016/j.scitotenv.2020.143877] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 07/30/2020] [Revised: 11/12/2020] [Accepted: 11/12/2020] [Indexed: 06/12/2023]
Abstract
Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18-19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO2 world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.
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Affiliation(s)
- Patricia M Valdespino-Castillo
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Andrea Bautista-García
- Laboratorio de Bioingeniería y Ciencias Ambientales (BICA), Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, La Paz, BCS, Mexico
| | - Fabio Favoretto
- Laboratorio de Bioingeniería y Ciencias Ambientales (BICA), Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, La Paz, BCS, Mexico; Gulf of California Marine Program, Scripps Institution of Oceanography, University of California San Diego, CA, United States
| | - Martín Merino-Ibarra
- Unidad Académica de Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Teresa Pi-Puig
- Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico; Laboratorio Nacional de Geoquímica y Mineralogía (LANGEM), Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - F Sergio Castillo
- Unidad Académica de Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Silvia Espinosa-Matías
- Laboratorio de Microscopía Electrónica de Barrido, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Hoi-Ying Holman
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anidia Blanco-Jarvio
- Laboratorio de Bioingeniería y Ciencias Ambientales (BICA), Departamento Académico de Ingeniería en Pesquerías, Universidad Autónoma de Baja California Sur, La Paz, BCS, Mexico.
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Aguilar-Rangel EJ, Prado BL, Vásquez-Murrieta MS, Los Santos PED, Siebe C, Falcón LI, Santillán J, Alcántara-Hernández RJ. Temporal analysis of the microbial communities in a nitrate-contaminated aquifer and the co-occurrence of anammox, n-damo and nitrous-oxide reducing bacteria. J Contam Hydrol 2020; 234:103657. [PMID: 32777591 DOI: 10.1016/j.jconhyd.2020.103657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 01/08/2020] [Revised: 04/13/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
Groundwater-N pollution derives from agricultural and urban activities, and compromises water quality in shallow aquifers, putting human and environmental health at risk. Nonetheless, subsurface microbiota can transform dissolved inorganic nitrogen into N2. In this study, we surveyed the microbial community of a shallow aquifer by sampling one well, one piezometer and a spring within an agricultural area that receives N-inputs of more than 700 kg/ha per year through irrigation with wastewater. The survey was conducted during a year with a 16S rRNA next-gen approach. In parallel, we quantified the number of gene copies and transcripts related to anaerobic ammonium oxidation (anammox, hzo), nitrite-dependent anaerobic methane oxidation (n-damo, nod and pmoA) and nitrous oxide reduction (last step of denitrification, nosZ), during the dry and rainy seasons. Our results showed that the groundwater samples had 17.7 to 22.5 mg/L of NO3--N. The bacterial and archaeal community structure was distinctive at each site, and it remained relatively stable over time. We verified the co-occurrence of N-transforming bacteria, which was correlated with the concentration of NO2-/NO3- and ORP/DO values (DO: ~3.0 mg/L). Our analyses suggest that these conditions may allow the presence of nitrifying microorganisms which can couple with anammox, n-damo and denitrifying bacteria in interrelated biogeochemical pathways. Gene density (as the number of gene copies per litre) was lower in the rainy season than in the dry season, possibly due to dilution by rainwater infiltration. Yet, the numbers of hzo gene copies here found were similar to those reported in oceanic oxygen minimum zones and in a carbonate-rock aquifer. The transcript sequences showed that Candidatus Brocadia spp. (anammox), Candidatus Methylomirabilis spp. (n-damo) and autotrophic denitrifying Betaproteobacteria coexist in the groundwater environment, with the potential to attenuate the concentration of dissolved inorganic nitrogen by reducing it to N2 rather than N2O; delivering thus, an important ecosystem service to remove contaminants.
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Affiliation(s)
- Eduardo J Aguilar-Rangel
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Blanca L Prado
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - María Soledad Vásquez-Murrieta
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340 Ciudad de México, Mexico
| | - Paulina Estrada-de Los Santos
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Del. Miguel Hidalgo, 11340 Ciudad de México, Mexico
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, 97302, Yucatán, Mexico
| | - Jazmín Santillán
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510 Ciudad de México, Mexico.
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Valdespino-Castillo PM, Cerqueda-García D, Espinosa AC, Batista S, Merino-Ibarra M, Taş N, Alcántara-Hernández RJ, Falcón LI. Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments. FEMS Microbiol Ecol 2019; 94:5047302. [PMID: 29982398 DOI: 10.1093/femsec/fiy129] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 11/29/2017] [Accepted: 06/04/2018] [Indexed: 11/14/2022] Open
Abstract
Maritime Antarctica has shown the highest increase in temperature in the Southern Hemisphere. Under this scenario, biogeochemical cycles may be altered, resulting in rapid environmental change for Antarctic biota. Microbes that drive biogeochemical cycles often form biofilms or microbial mats in continental meltwater environments. Limnetic microbial mats from the Fildes Peninsula were studied using high-throughput 16S rRNA gene sequencing. Mat samples were collected from 15 meltwater stream sites, comprising a natural gradient from ultraoligotrophic glacier flows to meltwater streams exposed to anthropogenic activities. Our analyses show that microbial community structure differences between mats are explained by environmental NH4+, NO3-, DIN, soluble reactive silicon and conductivity. Microbial mats living under ultraoligotrophic meltwater conditions did not exhibit a dominance of cyanobacterial photoautotrophs, as has been documented for other Antarctic limnetic microbial mats. Instead, ultraoligotrophic mat communities were characterized by the presence of microbes recognized as heterotrophs and photoheterotrophs. This suggests that microbial capabilities for recycling organic matter may be a key factor to dwell in ultra-low nutrient conditions. Our analyses show that phylotype level assemblages exhibit coupled distribution patterns in environmental oligotrophic inland waters. The evaluation of these microbes suggests the relevance of reproductive and structural strategies to pioneer these psychrophilic ultraoligotrophic environments.
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Affiliation(s)
| | - Daniel Cerqueda-García
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico
| | - Ana Cecilia Espinosa
- LANCIS, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico
| | - Silvia Batista
- Unidad de Microbiología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, 11600, Uruguay
| | - Martín Merino-Ibarra
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico
| | - Neslihan Taş
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | | | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, CDMX, 04510, Mexico
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Sánchez-Sánchez J, Cerca M, Alcántara-Hernández RJ, Lozano-Flores C, Carreón-Freyre D, Levresse G, Vega M, Varela-Echavarría A, Aranda-Gómez JJ. Extant microbial communities in the partially desiccated Rincon de Parangueo maar crater lake in Mexico. FEMS Microbiol Ecol 2019; 95:5437671. [DOI: 10.1093/femsec/fiz051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 04/09/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Rincon de Parangueo is a maar where a perennial lake was present until the 1980s. A conspicuous feature of the lake’s sediments is the presence of bioherms and organo-sedimentary deposits produced by microbial communities. The gradual lake desiccation during the last 40 years has produced dramatic environmental changes inside the maar basin, which resulted in the formation of a highly saline-alkaline system with extant microorganisms. In this paper we succinctly describe the geologic setting where the microbial communities have developed inside of the maar crater and the results obtained from high-throughput sequencing methods to characterize the microbial component (Bacteria, Eukarya and Archaea) in endolithic mats of calcareous sediments, and microbial mats and free-living microorganisms in the soda ponds. The studied sites displayed different microbial communities with a diverse number of phylotypes belonging to Bacteria and Eukarya, contrasting with a much less diverse component in Archaea. The sequences here detected were related to environmental sequences from sites with extreme life conditions such as high alkalinity (alkaliphiles), high salinity (halophiles) and high temperature (thermophiles). Moreover, our results indicate an important unexplored endemic microbial biodiversity in the vestiges of the former lake that need to be studied.
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Affiliation(s)
- Janet Sánchez-Sánchez
- Posgrado en Ciencias de la Tierra, Centro de Geociencias, Universidad Nacional Autónoma de México, Blvd Juriquilla, 3001, 76230, Juriquilla, Querétaro, México
| | - Mariano Cerca
- Centro de Geociencias, Universidad Nacional Autónoma de México, Blvd Juriquilla, 3001, 76230, Juriquilla, Querétaro, México
| | - Rocío J Alcántara-Hernández
- Instituto de Geología, UNAM, Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Av. Universidad 3000, Del. Coyoacán, 04510, Ciudad de México, México
| | - Carlos Lozano-Flores
- Departamento de Biología del Desarrollo y Neurofisiología, Instituto de Neurobiología Universidad Nacional Autónoma de México, Querétaro, México
| | - Dora Carreón-Freyre
- Centro de Geociencias, Universidad Nacional Autónoma de México, Blvd Juriquilla, 3001, 76230, Juriquilla, Querétaro, México
| | - Gilles Levresse
- Centro de Geociencias, Universidad Nacional Autónoma de México, Blvd Juriquilla, 3001, 76230, Juriquilla, Querétaro, México
| | - Marina Vega
- Centro de Geociencias, Universidad Nacional Autónoma de México, Blvd Juriquilla, 3001, 76230, Juriquilla, Querétaro, México
| | - Alfredo Varela-Echavarría
- Departamento de Biología del Desarrollo y Neurofisiología, Instituto de Neurobiología Universidad Nacional Autónoma de México, Querétaro, México
| | - Jose Jorge Aranda-Gómez
- Centro de Geociencias, Universidad Nacional Autónoma de México, Blvd Juriquilla, 3001, 76230, Juriquilla, Querétaro, México
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Valdespino-Castillo PM, Alcántara-Hernández RJ, Merino-Ibarra M, Alcocer J, Macek M, Moreno-Guillén OA, Falcón LI. Phylotype Dynamics of Bacterial P Utilization Genes in Microbialites and Bacterioplankton of a Monomictic Endorheic Lake. Microb Ecol 2017; 73:296-309. [PMID: 27726035 DOI: 10.1007/s00248-016-0862-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 06/24/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
Microbes can modulate ecosystem function since they harbor a vast genetic potential for biogeochemical cycling. The spatial and temporal dynamics of this genetic diversity should be acknowledged to establish a link between ecosystem function and community structure. In this study, we analyzed the genetic diversity of bacterial phosphorus utilization genes in two microbial assemblages, microbialites and bacterioplankton of Lake Alchichica, a semiclosed (i.e., endorheic) system with marked seasonality that varies in nutrient conditions, temperature, dissolved oxygen, and water column stability. We focused on dissolved organic phosphorus (DOP) utilization gene dynamics during contrasting mixing and stratification periods. Bacterial alkaline phosphatases (phoX and phoD) and alkaline beta-propeller phytases (bpp) were surveyed. DOP utilization genes showed different dynamics evidenced by a marked change within an intra-annual period and a differential circadian pattern of expression. Although Lake Alchichica is a semiclosed system, this dynamic turnover of phylotypes (from lake circulation to stratification) points to a different potential of DOP utilization by the microbial communities within periods. DOP utilization gene dynamics was different among genetic markers and among assemblages (microbialite vs. bacterioplankton). As estimated by the system's P mass balance, P inputs and outputs were similar in magnitude (difference was <10 %). A theoretical estimation of water column P monoesters was used to calculate the potential P fraction that can be remineralized on an annual basis. Overall, bacterial groups including Proteobacteria (Alpha and Gamma) and Bacteroidetes seem to be key participants in DOP utilization responses.
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Affiliation(s)
- Patricia M Valdespino-Castillo
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Secretaría de Ciencia, Tecnología e Innovación del Distrito Federal-Centro Latino-Americano de Física, Olivo 39, Col. Florida, 01030, Mexico City, Mexico
| | | | - Martín Merino-Ibarra
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Javier Alcocer
- Proyecto de Investigación en Limnología Tropical, FES Iztacala, UNAM, Av. de los Barrios No. 1, Los Reyes Iztacala, 54090, Tlalnepantla, State of Mexico, Mexico
| | - Miroslav Macek
- Proyecto de Investigación en Limnología Tropical, FES Iztacala, UNAM, Av. de los Barrios No. 1, Los Reyes Iztacala, 54090, Tlalnepantla, State of Mexico, Mexico
- Biology Centre v. v. i., Institute of Hydrobiology, Academy of Sciences of the Czech Republic, 37001, České Budějovice, Czech Republic
| | - Octavio A Moreno-Guillén
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico.
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Centeno CM, Legendre P, Beltrán Y, Alcántara-Hernández RJ, Lidström UE, Ashby MN, Falcón LI. Microbialite genetic diversity and composition relate to environmental variables. FEMS Microbiol Ecol 2012; 82:724-35. [PMID: 22775797 DOI: 10.1111/j.1574-6941.2012.01447.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 11/30/2022] Open
Abstract
Microbialites have played an important role in the early history of life on Earth. Their fossilized forms represent the oldest evidence of life on our planet dating back to 3500 Ma. Extant microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. Although their ecological and evolutionary importance has been recognized, the study of their genetic diversity is yet scanty. The main goal of this study was to analyse microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and a crater-lake. We followed a pyrosequencing approach of hypervariable regions of the 16S rRNA gene. Results showed that microbialite communities were very diverse (H' = 6-7) and showed geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explained 33% of the genetic variation. All microbialites had similar proportions of major bacterial and archaeal phyla.
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Affiliation(s)
- Carla M Centeno
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Alcántara-Hernández RJ, Rodríguez-Álvarez JA, Valenzuela-Encinas C, Gutiérrez-Miceli FA, Castañón-González H, Marsch R, Ayora-Talavera T, Dendooven L. The bacterial community in 'taberna' a traditional beverage of Southern Mexico. Lett Appl Microbiol 2010; 51:558-63. [PMID: 21039665 DOI: 10.1111/j.1472-765x.2010.02934.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To characterize the bacterial community of taberna, an alcoholic traditional beverage from the Southern part of Mexico produced by the fermentation of the coyol palm sap (Acrocomia aculeate). METHODS AND RESULTS Bacterial 16S rDNA libraries were constructed from metagenomic DNA extracted during the fermentation process at 0, 60 and 108 h. A total of 154 clones were sequenced, and 13, 10 and nine unique sequences were found at each sampling time. At the onset of the fermentation, Zymomonas mobilis, Fructobacillus spp., Pantoea agglomerans and other Gammaproteobacteria were detected. After 60 h, lactic acid bacteria were found and 30% of clones in the library were related to Lactobacillus nagelii, L. sucicola and L. sp. By the end of the experiment, i.e. after 108 h, the bacterial community included Z. mobilis, Lact. nagelii and Acetobacter pasteurianus. CONCLUSIONS Our results suggest that Z. mobilis population represented an important proportion of the bacterial community (60-80%), as well as the lactobacilli during the fermentation process. The bacterial diversity was low and decreased as the fermentation progressed. SIGNIFICANCE AND IMPACT OF THE STUDY This culture-independent study suggests that Z. mobilis and lactobacilli play an important role in the alcoholic fermentation of the taberna beverage.
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