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Gallardo-Navarro O, Aguilar-Salinas B, Rocha J, Olmedo-Álvarez G. Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology. Heliyon 2024; 10:e33896. [PMID: 39130413 PMCID: PMC11315108 DOI: 10.1016/j.heliyon.2024.e33896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 06/28/2024] [Indexed: 08/13/2024] Open
Abstract
Humans have long relied on microbial communities to create products, produce energy, and treat waste. The microbiota residing within our bodies directly impacts our health, while the soil and rhizosphere microbiomes influence the productivity of our crops. However, the complexity and diversity of microbial communities make them challenging to study and difficult to develop into applications, as they often exhibit the emergence of unpredictable higher-order phenomena. Synthetic ecology aims at simplifying complexity by constituting synthetic or semi-natural microbial communities with reduced diversity that become easier to study and analyze. This strategy combines methodologies that simplify existing complex systems (top-down approach) or build the system from its constituent components (bottom-up approach). Simplified communities are studied to understand how interactions among populations shape the behavior of the community and to model and predict their response to external stimuli. By harnessing the potential of synthetic microbial communities through a multidisciplinary approach, we can advance knowledge of ecological concepts and address critical public health, agricultural, and environmental issues more effectively.
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Affiliation(s)
- Oscar Gallardo-Navarro
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Bernardo Aguilar-Salinas
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
| | - Jorge Rocha
- Centro de Investigaciones Biológicas del Noroeste, S. C., La Paz, Mexico
| | - Gabriela Olmedo-Álvarez
- Centro de Investigación y de Estudios Avanzado del Instituto Politécnico Nacional, Unidad Irapuato, Mexico
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2
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Viladomat Jasso M, García-Ulloa M, Zapata-Peñasco I, Eguiarte LE, Souza V. Metagenomic insight into taxonomic composition, environmental filtering and functional redundancy for shaping worldwide modern non-lithifying microbial mats. PeerJ 2024; 12:e17412. [PMID: 38827283 PMCID: PMC11144394 DOI: 10.7717/peerj.17412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Modern microbial mats are relictual communities mostly found in extreme environments worldwide. Despite their significance as representatives of the ancestral Earth and their important roles in biogeochemical cycling, research on microbial mats has largely been localized, focusing on site-specific descriptions and environmental change experiments. Here, we present a global comparative analysis of non-lithifying microbial mats, integrating environmental measurements with metagenomic data from 62 samples across eight sites, including two new samples from the recently discovered Archaean Domes from Cuatro Ciénegas, Mexico. Our results revealed a notable influence of environmental filtering on both taxonomic and functional compositions of microbial mats. Functional redundancy appears to confer resilience to mats, with essential metabolic pathways conserved across diverse and highly contrasting habitats. We identified six highly correlated clusters of taxa performing similar ecological functions, suggesting niche partitioning and functional specialization as key mechanisms shaping community structure. Our findings provide insights into the ecological principles governing microbial mats, and lay the foundation for future research elucidating the intricate interplay between environmental factors and microbial community dynamics.
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Affiliation(s)
- Mariette Viladomat Jasso
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Icoquih Zapata-Peñasco
- Dirección de Investigación en Transformación de Hidrocarburos, Instituto Mexicano del Petróleo, Ciudad de México, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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3
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Cubillos CF, Aguilar P, Moreira D, Bertolino P, Iniesto M, Dorador C, López-García P. Exploring the prokaryote-eukaryote interplay in microbial mats from an Andean athalassohaline wetland. Microbiol Spectr 2024; 12:e0007224. [PMID: 38456669 PMCID: PMC10986560 DOI: 10.1128/spectrum.00072-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/28/2024] [Indexed: 03/09/2024] Open
Abstract
Microbial community assembly results from the interaction between biotic and abiotic factors. However, environmental selection is thought to predominantly shape communities in extreme ecosystems. Salar de Huasco, situated in the high-altitude Andean Altiplano, represents a poly-extreme ecosystem displaying spatial gradients of physicochemical conditions. To disentangle the influence of abiotic and biotic factors, we studied prokaryotic and eukaryotic communities from microbial mats and underlying sediments across contrasting areas of this athalassohaline ecosystem. The prokaryotic communities were primarily composed of bacteria, notably including a significant proportion of photosynthetic organisms like Cyanobacteria and anoxygenic photosynthetic members of Alpha- and Gammaproteobacteria and Chloroflexi. Additionally, Bacteroidetes, Verrucomicrobia, and Deltaproteobacteria were abundantly represented. Among eukaryotes, photosynthetic organisms (Ochrophyta and Archaeplastida) were predominant, alongside relatively abundant ciliates, cercozoans, and flagellated fungi. Salinity emerged as a key driver for the assembly of prokaryotic communities. Collectively, abiotic factors influenced both prokaryotic and eukaryotic communities, particularly those of algae. However, prokaryotic communities strongly correlated with photosynthetic eukaryotes, suggesting a pivotal role of biotic interactions in shaping these communities. Co-occurrence networks suggested potential interactions between different organisms, such as diatoms with specific photosynthetic and heterotrophic bacteria or with protist predators, indicating influences beyond environmental selection. While some associations may be explained by environmental preferences, the robust biotic correlations, alongside insights from other ecosystems and experimental studies, suggest that symbiotic and trophic interactions significantly shape microbial mat and sediment microbial communities in this athalassohaline ecosystem.IMPORTANCEHow biotic and abiotic factors influence microbial community assembly is still poorly defined. Here, we explore their influence on prokaryotic and eukaryotic community assembly within microbial mats and sediments of an Andean high-altitude polyextreme wetland system. We show that, in addition to abiotic elements, mutual interactions exist between prokaryotic and eukaryotic communities. Notably, photosynthetic eukaryotes exhibit a strong correlation with prokaryotic communities, specifically diatoms with certain bacteria and other protists. Our findings underscore the significance of biotic interactions in community assembly and emphasize the necessity of considering the complete microbial community.
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Affiliation(s)
- Carolina F. Cubillos
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pablo Aguilar
- Laboratorio de Complejidad Microbiana, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
- Millennium Nucleus of Austral Invasive Salmonids - INVASAL, Concepción, Chile
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Paola Bertolino
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Miguel Iniesto
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana, Instituto Antofagasta and Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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4
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Madrigal-Trejo D, Sánchez-Pérez J, Espinosa-Asuar L, Valdivia-Anistro JA, Eguiarte LE, Souza V. A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment. MICROBIAL ECOLOGY 2023; 86:2252-2270. [PMID: 37393557 PMCID: PMC10640475 DOI: 10.1007/s00248-023-02231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 04/23/2023] [Indexed: 07/04/2023]
Abstract
Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from [Formula: see text]1-4% to [Formula: see text]33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.
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Affiliation(s)
- David Madrigal-Trejo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional AutÓnoma de México, Mexico City, Mexico
| | - Jazmín Sánchez-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional AutÓnoma de México, Mexico City, Mexico
| | - Laura Espinosa-Asuar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional AutÓnoma de México, Mexico City, Mexico
| | - Jorge A Valdivia-Anistro
- Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional AutÓnoma de México, Mexico City, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional AutÓnoma de México, Mexico City, Mexico.
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile.
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López-García P, Gutiérrez-Preciado A, Krupovic M, Ciobanu M, Deschamps P, Jardillier L, López-Pérez M, Rodríguez-Valera F, Moreira D. Metagenome-derived virus-microbe ratios across ecosystems. THE ISME JOURNAL 2023; 17:1552-1563. [PMID: 37169871 PMCID: PMC10504350 DOI: 10.1038/s41396-023-01431-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.
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Affiliation(s)
- Purificación López-García
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France.
| | - Ana Gutiérrez-Preciado
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Maria Ciobanu
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Philippe Deschamps
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Ludwig Jardillier
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
| | - Mario López-Pérez
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Alicante, Spain
| | | | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif-sur-Yvette, France
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6
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Acosta-Grinok M, Vázquez S, Guiliani N, Marín S, Demergasso C. Looking for the mechanism of arsenate respiration of Fusibacter sp. strain 3D3, independent of ArrAB. Front Microbiol 2022; 13:1029886. [PMID: 36532432 PMCID: PMC9751042 DOI: 10.3389/fmicb.2022.1029886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022] Open
Abstract
The literature has reported the isolation of arsenate-dependent growing microorganisms which lack a canonical homolog for respiratory arsenate reductase, ArrAB. We recently isolated an arsenate-dependent growing bacterium from volcanic arsenic-bearing environments in Northern Chile, Fusibacter sp. strain 3D3 (Fas) and studied the arsenic metabolism in this Gram-positive isolate. Features of Fas deduced from genome analysis and comparative analysis with other arsenate-reducing microorganisms revealed the lack of ArrAB coding genes and the occurrence of two arsC genes encoding for putative cytoplasmic arsenate reductases named ArsC-1 and ArsC-2. Interestingly, ArsC-1 and ArsC-2 belong to the thioredoxin-coupled family (because of the redox-active disulfide protein used as reductant), but they conferred differential arsenate resistance to the E. coli WC3110 ΔarsC strain. PCR experiments confirmed the absence of arrAB genes and results obtained using uncouplers revealed that Fas growth is linked to the proton gradient. In addition, Fas harbors ferredoxin-NAD+ oxidoreductase (Rnf) and electron transfer flavoprotein (etf) coding genes. These are key molecular markers of a recently discovered flavin-based electron bifurcation mechanism involved in energy conservation, mainly in anaerobic metabolisms regulated by the cellular redox state and mostly associated with cytoplasmic enzyme complexes. At least three electron-bifurcating flavoenzyme complexes were evidenced in Fas, some of them shared in conserved genomic regions by other members of the Fusibacter genus. These physiological and genomic findings permit us to hypothesize the existence of an uncharacterized arsenate-dependent growth metabolism regulated by the cellular redox state in the Fusibacter genus.
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Affiliation(s)
| | - Susana Vázquez
- Cátedra de Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina,Instituto de Nanobiotecnología (NANOBIOTEC), Universidad de Buenos Aires (UBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nicolás Guiliani
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Antofagasta, Chile
| | - Sabrina Marín
- Biotechnology Center, Universidad Católica del Norte, Antofagasta, Chile
| | - Cecilia Demergasso
- Biotechnology Center, Universidad Católica del Norte, Antofagasta, Chile,Nucleus for the Study of Cancer at a Basic, Applied, and Clinical Level, Universidad Católica del Norte, Antofagasta, Chile,*Correspondence: Cecilia Demergasso,
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7
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Alonso-Reyes DG, Galván FS, Irazoqui JM, Amadio A, Tschoeke D, Thompson F, Albarracín VH, Farias ME. Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02112-7. [PMID: 36161499 DOI: 10.1007/s00248-022-02112-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.
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Affiliation(s)
- Daniel Gonzalo Alonso-Reyes
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - Fátima Silvina Galván
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
| | - José Matías Irazoqui
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Ariel Amadio
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Diogo Tschoeke
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Virginia Helena Albarracín
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán, Argentina.
| | - María Eugenia Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
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8
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Cai YJ, Liu ZA, Zhang S, Liu H, Nicol GW, Chen Z. Microbial community structure is stratified at the millimeter-scale across the soil-water interface. ISME COMMUNICATIONS 2022; 2:53. [PMID: 37938662 PMCID: PMC9723559 DOI: 10.1038/s43705-022-00138-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/25/2022] [Accepted: 06/14/2022] [Indexed: 08/09/2023]
Abstract
Soil-water interfaces (SWI) are biogeochemical hotspots characterized by millimeter-scale redox gradients, indicating that parallel changes are also present in microbial community structure and activity. However, soil-based analyses of microbial community structure typically examine bulk samples and seldom consider variation at a scale relevant to changes in environmental conditions. Here we presented a study that aimed to describe millimeter-scale variance in both microbial community structure and physicochemical properties in a lab flooded soil. At this fine-scale resolution, the stratification of biogeochemical properties (e.g., redox potential, nitrate concentration) was consistent with the structure of the active microbial community with clear shifts in the relative abundance of transcriptionally active populations associated with changing redox conditions. Our results demonstrate that spatial scale should be carefully considered when investigating ecological mechanisms that influence soil microbial community structures.
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Affiliation(s)
- Yu-Jia Cai
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
- Department of Geography & Planning, School of Environmental Sciences, University of Liverpool, Brownlow Hill, Liverpool, L697ZX, UK
| | - Zi-Ao Liu
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
| | - Sha Zhang
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
- Department of Geography & Planning, School of Environmental Sciences, University of Liverpool, Brownlow Hill, Liverpool, L697ZX, UK
| | - Hao Liu
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China
- Department of Geography & Planning, School of Environmental Sciences, University of Liverpool, Brownlow Hill, Liverpool, L697ZX, UK
| | - Graeme W Nicol
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134, Ecully cedex, France
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, 111 Ren'ai Road, Suzhou, Jiangsu, 215123, China.
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9
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Espinosa-Asuar L, Monroy-Guzmán C, Madrigal-Trejo D, Navarro-Miranda M, Sánchez-Pérez J, Buenrostro Muñoz J, Villar J, Cifuentes Camargo JF, Kalambokidis M, Esquivel-Hernandez DA, Viladomat Jasso M, Escalante AE, Velez P, Figueroa M, Martinez-Cardenas A, Ramirez-Barahona S, Gasca-Pineda J, Eguiarte LE, Souza V. Diversity of an uncommon elastic hypersaline microbial mat along a small-scale transect. PeerJ 2022; 10:e13579. [PMID: 35757167 PMCID: PMC9220918 DOI: 10.7717/peerj.13579] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/22/2022] [Indexed: 01/17/2023] Open
Abstract
We evaluated the microbial diversity and metabolome profile of an uncommon hypersaline elastic microbial mat from Cuatro Ciénegas Basin (CCB) in the Chihuahuan Desert of Coahuila, México. We collected ten samples on a small scale transect (1.5-m) and described its microbial diversity through NGS-based ITS and 16S rDNA gene sequencing. A very low number of taxa comprised a considerable proportion of the mat and were shared across all sampling points, whereas the rare biosphere was more phylogenetically diverse (Faith's Phylogenetic Diversity (FPD) index) and phylogenetically disperse (using a null model distribution of Phylogenetic Species Clustering (nmdPSC)) than the abundant (high read count) taxa for both analyzed libraries. We also found a distinctive metabolome profile for each sample and were able to tentatively annotate several classes of compounds with relevant biological properties.
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Affiliation(s)
- Laura Espinosa-Asuar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Camila Monroy-Guzmán
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - David Madrigal-Trejo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Marisol Navarro-Miranda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Jazmin Sánchez-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Jhoselinne Buenrostro Muñoz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Juan Villar
- Pontifica Universidad Javeriana, Bogotá D.C., Colombia
| | | | - Maria Kalambokidis
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Diego A. Esquivel-Hernandez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Mariette Viladomat Jasso
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Ana E. Escalante
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Patricia Velez
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, CdMx, México
| | - Mario Figueroa
- Facultad de Química, Universidad Nacional Autónoma de México, CdMx, México
| | | | - Santiago Ramirez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, CdMx, México
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, CdMx, México
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10
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Carrizo D, Vignale FA, Sánchez-García L, Farías ME. Ecological variability based on lipid biomarkers in astrobiologically interesting wetlands from the Argentinian central Andes. FEMS Microbiol Ecol 2022; 98:6575537. [PMID: 35482603 DOI: 10.1093/femsec/fiac049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Andean wetlands hold extremophilic communities adapted to live in harsh conditions. Here, we investigated the microbial ecology of three high-altitude hypersaline ponds from La Puna region (Argentina) showing an increasing extent of desiccation by analyzing their lipid sedimentary record. We recreated the microbial community structure and the carbon metabolisms in each lacustrine system based on the molecular distribution of lipid biomarkers and their compound-specific carbon and hydrogen isotopic signatures. We detected lipid compounds considered to be biomarkers of cyanobacteria, sulfate-reducing bacteria, purple sulfur bacteria, and archaea in the three Andean ponds, as well as diatoms in the intermediate salinity system. The relative abundance of purple sulfur and sulfate-reducing bacteria decreased with salinity, whereas cyanobacteria and archaea decreased their relative abundance in the mid-saline pond to increase it again and became both prevailing at the highest salinity. Carbon fixation in the three ponds was driven by a combination of the reductive tricarboxylic acid cycle, the reductive pentose phosphate cycle, and the reductive acetyl-CoA pathway. This work is the first to describe molecular and isotopic lipid fingerprints in wetlands from the central Andean Puna, and serves as a basis for further biogeochemical studies in the area.
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Affiliation(s)
- Daniel Carrizo
- Centro de Astrobiología (CSIC-INTA), Department of Planetology and Habitability, Madrid, Spain
| | - Federico A Vignale
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, T4001MVB, Argentina.,Laboratorio de Bioinformática Estructural, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires (UBA), Buenos Aires, C1428EHA, Argentina
| | - Laura Sánchez-García
- Centro de Astrobiología (CSIC-INTA), Department of Molecular Evolution, Madrid, Spain
| | - María E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, T4001MVB, Argentina
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11
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Berlanga M, Palau M, Guerrero R. Community homeostasis of coastal microbial mats from the Camargue during winter (cold) and summer (hot) seasons. Ecosphere 2022. [DOI: 10.1002/ecs2.3922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Mercedes Berlanga
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences University of Barcelona Barcelona Spain
| | - Montserrat Palau
- Department of Biology, Environment and Health, Section Microbiology, Faculty of Pharmacy and Food Sciences University of Barcelona Barcelona Spain
| | - Ricardo Guerrero
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, Faculty of Medicine University of Barcelona Barcelona Spain
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12
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Muñoz-Gómez SA, Susko E, Williamson K, Eme L, Slamovits CH, Moreira D, López-García P, Roger AJ. Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria. Nat Ecol Evol 2022; 6:253-262. [PMID: 35027725 DOI: 10.1038/s41559-021-01638-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/29/2021] [Indexed: 01/01/2023]
Abstract
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional heterogeneity. We applied this site-and-branch-heterogeneous model (MAM60 + GFmix) to a considerably expanded dataset that comprises 108 mitochondrial proteins of alphaproteobacterial origin, and novel metagenome-assembled genomes from microbial mats, microbialites and sediments. The MAM60 + GFmix model fits the data much better and agrees with analyses of compositionally homogenized datasets with conventional site-heterogenous models. The consilience of evidence thus suggests that mitochondria are sister to the Alphaproteobacteria to the exclusion of MarineProteo1 and Magnetococcia. We also show that the ancestral presence of the crista-developing mitochondrial contact site and cristae organizing system (a mitofilin-domain-containing Mic60 protein) in mitochondria and the Alphaproteobacteria only supports their close relationship.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.
| | - Edward Susko
- Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Kelsey Williamson
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | | | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.
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13
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Bornemann TLV, Adam PS, Turzynski V, Schreiber U, Figueroa-Gonzalez PA, Rahlff J, Köster D, Schmidt TC, Schunk R, Krauthausen B, Probst AJ. Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing. Nat Commun 2022; 13:284. [PMID: 35022403 PMCID: PMC8755723 DOI: 10.1038/s41467-021-27783-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/02/2021] [Indexed: 12/30/2022] Open
Abstract
Earth’s mantle releases 38.7 ± 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere. Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
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Affiliation(s)
- Till L V Bornemann
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Panagiotis S Adam
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Victoria Turzynski
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany
| | - Ulrich Schreiber
- Department of Geology, University Duisburg-Essen, Essen, Germany
| | | | - Janina Rahlff
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany.,Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linneaus University, Kalmar, Sweden
| | - Daniel Köster
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Torsten C Schmidt
- Instrumental Analytical Chemistry and Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany
| | | | - Bernhard Krauthausen
- Institute of Applied Geosciences, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alexander J Probst
- Environmental Microbiology and Biotechnology, Faculty of Chemistry, University Duisburg-Essen, Essen, Germany. .,Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße 5, Essen, Germany.
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14
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Vignale FA, Lencina AI, Stepanenko TM, Soria MN, Saona LA, Kurth D, Guzmán D, Foster JS, Poiré DG, Villafañe PG, Albarracín VH, Contreras M, Farías ME. Lithifying and Non-Lithifying Microbial Ecosystems in the Wetlands and Salt Flats of the Central Andes. MICROBIAL ECOLOGY 2022; 83:1-17. [PMID: 33730193 DOI: 10.1007/s00248-021-01725-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
The wetlands and salt flats of the Central Andes region are unique extreme environments as they are located in high-altitude saline deserts, largely influenced by volcanic activity. Environmental factors, such as ultraviolet (UV) radiation, arsenic content, high salinity, low dissolved oxygen content, extreme daily temperature fluctuation, and oligotrophic conditions, resemble the early Earth and potentially extraterrestrial conditions. The discovery of modern microbialites and microbial mats in the Central Andes during the past decade has increased the interest in this area as an early Earth analog. In this work, we review the current state of knowledge of Central Andes region environments found within lakes, small ponds or puquios, and salt flats of Argentina, Chile, and Bolivia, many of them harboring a diverse range of microbial communities that we have termed Andean Microbial Ecosystems (AMEs). We have integrated the data recovered from all the known AMEs and compared their biogeochemistry and microbial diversity to achieve a better understanding of them and, consequently, facilitate their protection.
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Affiliation(s)
- Federico A Vignale
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-CONICET, Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Agustina I Lencina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Tatiana M Stepanenko
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Mariana N Soria
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Luis A Saona
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Daniel Guzmán
- Centro de Biotecnología (CBT), Facultad de Ciencias y Tecnología, Universidad Mayor de San Simón (UMSS), Cochabamba, Bolivia
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Merritt Island, FL, USA
| | - Daniel G Poiré
- Centro de Investigaciones Geológicas (CIG), Universidad Nacional de La Plata (UNLP)-CONICET, La Plata, Argentina
| | - Patricio G Villafañe
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - Virginia H Albarracín
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina
- Centro Integral de Microscopía Electrónica (CIME)-CCT-CONICET, Universidad Nacional de Tucumán (UNT), Tucumán, Argentina
| | | | - María E Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI)-CCT-CONICET, San Miguel de Tucumán, Tucumán, Argentina.
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15
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Kindler GS, Wong HL, Larkum AWD, Johnson M, MacLeod FI, Burns BP. Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay. FEMS Microbiol Ecol 2021; 98:6448473. [PMID: 34865013 DOI: 10.1093/femsec/fiab158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The present study describes for the first time the community composition and functional potential of the microbial mats found in the supratidal, gypsum-rich, and hypersaline region of Blue Holes, Shark Bay. This was achieved via high throughput metagenomic sequencing of total mat community DNA and complementary analyses using hyperspectral confocal microscopy. Mat communities were dominated by Proteobacteria (29%), followed by Bacteroidetes/Chlorobi Group (11%), and Planctomycetes (10%). These mats were found to also harbor a diverse community of potentially novel microorganisms including members from the DPANN, Asgard archaea, and Candidate Phyla Radiation, with highest diversity found in the lower regions (∼14-20 mm depth) of the mat. In addition to pathways for major metabolic cycles, a range of putative rhodopsins with previously uncharacterized motifs and functions were identified along with heliorhodopsins and putative schizorhodopsins. Critical microbial interactions were also inferred, and from 117 medium-to-high quality metagenome-assembled genomes (MAGs), viral defense mechanisms (CRISPR, BREX, and DISARM), elemental transport, osmoprotection, heavy metal and UV resistance were also detected. These analyses have provided a greater understanding of these distinct mat systems in Shark Bay, including key insights into adaptive responses and proposing that photoheterotrophy may be an important lifestyle in Blue Holes.
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Affiliation(s)
- Gareth S Kindler
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Hon Lun Wong
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Anthony W D Larkum
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Michael Johnson
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.,Australian Centre for Astrobiology, University of New South Wales Sydney, Sydney, NSW, Australia
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16
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Saghaï A, Zivanovic Y, Moreira D, Tavera R, López-García P. A Novel Microbialite-Associated Phototrophic Chloroflexi Lineage Exhibiting a Quasi-Clonal Pattern along Depth. Genome Biol Evol 2021; 12:1207-1216. [PMID: 32544224 PMCID: PMC7486959 DOI: 10.1093/gbe/evaa122] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2020] [Indexed: 01/05/2023] Open
Abstract
Chloroflexales (Chloroflexi) are typical members of the anoxygenic photosynthesizing component of microbial mats and have mostly been characterized from communities associated to hot springs. Here, we report the assembly of five metagenome-assembled genomes (MAGs) of a novel lineage of Chloroflexales found in mesophilic lithifying microbial mats (microbialites) in Lake Alchichica (Mexico). Genomic and phylogenetic analyses revealed that the bins shared 92% of their genes, and these genes were nearly identical despite being assembled from samples collected along a depth gradient (1-15 m depth). We tentatively name this lineage Candidatus Lithoflexus mexicanus. Metabolic predictions based on the MAGs suggest that these chlorosome-lacking mixotrophs share features in central carbon metabolism, electron transport, and adaptations to life under oxic and anoxic conditions, with members of two related lineages, Chloroflexineae and Roseiflexineae. Contrasting with the other diverse microbialite community members, which display much lower genomic conservation along the depth gradient, Ca. L. mexicanus MAGs exhibit remarkable similarity. This might reflect a particular flexibility to acclimate to varying light conditions with depth or the capacity to occupy a very specific spatial ecological niche in microbialites from different depths. Alternatively, Ca. L. mexicanus may also have the ability to modulate its gene expression as a function of the local environmental conditions during diel cycles in microbialites along the depth gradient.
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Affiliation(s)
- Aurélien Saghaï
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yvan Zivanovic
- Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Saclay, Orsay, France
| | - David Moreira
- Ecologie Systématique Evolution, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, Mexico City, Mexico
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17
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Reid RP, Oehlert AM, Suosaari EP, Demergasso C, Chong G, Escudero LV, Piggot AM, Lascu I, Palma AT. Electrical conductivity as a driver of biological and geological spatial heterogeneity in the Puquios, Salar de Llamara, Atacama Desert, Chile. Sci Rep 2021; 11:12769. [PMID: 34140571 PMCID: PMC8211675 DOI: 10.1038/s41598-021-92105-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 06/04/2021] [Indexed: 02/05/2023] Open
Abstract
Reputed to be the driest desert in the world, the Atacama Desert in the Central Andes of Northern Chile is an extreme environment with high UV radiation, wide temperature variation, and minimum precipitation. Scarce lagoons associated with salt flats (salars) in this desert are the surface expression of shallow groundwater; these ponds serve as refugia for life and often host microbial communities associated with evaporitic mineral deposition. Results based on multidisciplinary field campaigns and associated laboratory examination of samples collected from the Puquios of the Salar de Llamara in the Atacama Desert during austral summer provide unprecedented detail regarding the spatial heterogeneity of physical, chemical, and biological characteristics of these salar environments. Four main lagoons ('Puquios') and more than 400 smaller ponds occur within an area less than 5 km2, and are characterized by high variability in electrical conductivity, benthic and planktonic biota, microbiota, lagoon bottom type, and style of mineral deposition. Results suggest that electrical conductivity is a driving force of system heterogeneity. Such spatial heterogeneity within the Puquios is likely to be expanded with temporal observations incorporating expected seasonal changes in electrical conductivity. The complexity of these Andean ecosystems may be key to their ability to persist in extreme environments at the edge of habitability.
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Affiliation(s)
- R P Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA.
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA.
| | - A M Oehlert
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA
| | - E P Suosaari
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, 33149, USA
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - C Demergasso
- Centro de Biotecnología , Universidad Católica del Norte, Antofagasta, Chile
| | - G Chong
- Departamento de Ciencias Geológicas , Universidad Católica del Norte, Antofagasta, Chile
| | - L V Escudero
- Centro de Biotecnología , Universidad Católica del Norte, Antofagasta, Chile
| | - A M Piggot
- Bahamas Marine EcoCentre, Miami, FL, 33156, USA
- AP Research Inc., Miami, FL, 33157, USA
| | - I Lascu
- Department of Mineral Sciences, National Museum of Natural History, Smithsonian Institution, Washington DC, 20560, USA
| | - A T Palma
- FisioAqua, Las Condes , 7550024, Santiago, Chile
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18
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Kurth D, Elias D, Rasuk MC, Contreras M, Farías ME. Carbon fixation and rhodopsin systems in microbial mats from hypersaline lakes Brava and Tebenquiche, Salar de Atacama, Chile. PLoS One 2021; 16:e0246656. [PMID: 33561170 PMCID: PMC7872239 DOI: 10.1371/journal.pone.0246656] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 01/25/2021] [Indexed: 01/08/2023] Open
Abstract
In this work, molecular diversity of two hypersaline microbial mats was compared by Whole Genome Shotgun (WGS) sequencing of environmental DNA from the mats. Brava and Tebenquiche are lakes in the Salar de Atacama, Chile, where microbial communities are growing in extreme conditions, including high salinity, high solar irradiance, and high levels of toxic metals and metaloids. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. The mat from Brava was more rich and diverse, with a higher number of different taxa and with species more evenly distributed. At the phylum level, Proteobacteria, Cyanobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the most abundant, including ~75% of total sequences. At the genus level, the most abundant sequences were affilitated to anoxygenic phototropic and cyanobacterial genera. In Tebenquiche mats, Proteobacteria and Bacteroidetes covered ~70% of the sequences, and 13% of the sequences were affiliated to Salinibacter genus, thus addressing the lower diversity. Regardless of the differences at the taxonomic level, functionally the two mats were similar. Thus, similar roles could be fulfilled by different organisms. Carbon fixation through the Wood-Ljungdahl pathway was well represented in these datasets, and also in other mats from Andean lakes. In spite of presenting less taxonomic diversity, Tebenquiche mats showed increased abundance and variety of rhodopsin genes. Comparison with other metagenomes allowed identifying xantorhodopsins as hallmark genes not only from Brava and Tebenquiche mats, but also for other mats developing at high altitudes in similar environmental conditions.
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Affiliation(s)
- Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - Dario Elias
- Facultad de Ingeniería, Universidad Nacional de Entre Ríos, Oro Verde, Entre Ríos, Argentina
| | - María Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | | | - María Eugenia Farías
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
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19
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Bonelli C, Dorador C. Endangered Salares: micro-disasters in Northern Chile. TAPUYA: LATIN AMERICAN SCIENCE, TECHNOLOGY AND SOCIETY 2021; 4:1968634. [PMID: 35252764 PMCID: PMC8887917 DOI: 10.1080/25729861.2021.1968634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
This article emerges from a transdisciplinary collaboration between a micro-biologist and an anthropologist deeply concerned with the protection of endangered salares (saltpans) in northern Chile. Our aim is to establish the concept of “micro-disaster” as a tool for examining how extractivism is disrupting salares and their “deep-time” microbial ecologies. These ecologies are key for understanding early events on Earth, as their evolution enabled the oxygenation of the planet 2.5 billion years ago and caused the biodiversity explosion. By considering how beinghuman involves beingmicroorganismal – and how human time is entangled with microorganismic time –, this article connects neoliberal extractivist history with geo-biological evolutionary history. “Micro-disasters” therefore affect us deeply as complex humans, and oblige us to develop further a planet-centered mode of collaborating, thinking, feeling, and acting. In the context of this special issue on extinction, we insist that concerns over extinction must be considered in continuity with deep-time ecologies. We propose to rethink humans as an “environmentally complex we” simultaneously entangled with historical experiential time and microbial “deep-time.”
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Affiliation(s)
| | - Cristina Dorador
- Department of Biotechnology, Universidad de Antofagasta, Antofagasta, Chile
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Chen Y, Nishihara A, Haruta S. Nitrogen-fixing Ability and Nitrogen Fixation-related Genes of Thermophilic Fermentative Bacteria in the Genus Caldicellulosiruptor. Microbes Environ 2021; 36. [PMID: 34108360 PMCID: PMC8209448 DOI: 10.1264/jsme2.me21018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fermentative nitrogen-fixing bacteria have not yet been examined in detail in thermal environments. In the present study, we isolated the thermophilic fermentative bacterium, strain YA01 from a hot spring. This strain grew at temperatures up to 78°C. A phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain YA01 belonged to the genus Caldicellulosiruptor, which are fermentative bacteria in the phylum Firmicutes, with 97.7–98.0% sequence identity to its closest relatives. Strain YA01 clearly exhibited N2-dependent growth at 70°C. We also confirmed N2-dependent growth in the relatives of strain YA01, Caldicellulosiruptor hydrothermalis 108 and Caldicellulosiruptor kronotskyensis 2002. The nitrogenase activities of these three strains were examined using the acetylene reduction assay. Similar activities were detected for all tested strains, and were slightly suppressed by the addition of ammonium. A genome analysis revealed that strain YA01, as well as other Caldicellulosiruptor, possessed a gene set for nitrogen fixation, but lacked the nifN gene, which encodes a nitrogenase iron-molybdenum cofactor biosynthesis protein that is commonly detected in nitrogen-fixing bacteria. The amino acid sequences of nitrogenase encoded by nifH, nifD, and nifK shared 92–98% similarity in Caldicellulosiruptor. A phylogenetic tree of concatenated NifHDK sequences showed that NifHDK of Caldicellulosiruptor was in the deepest clade. To the best of our knowledge, this is the first study to demonstrate the nitrogen-fixing ability of fermentative bacteria at 70°C. Caldicellulosiruptor may have retained an ancient nitrogen-fixing enzyme system.
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Affiliation(s)
- Yuxin Chen
- Department of Biological Sciences, Tokyo Metropolitan University
| | - Arisa Nishihara
- Department of Biological Sciences, Tokyo Metropolitan University.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University
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Iniesto M, Moreira D, Reboul G, Deschamps P, Benzerara K, Bertolino P, Saghaï A, Tavera R, López-García P. Core microbial communities of lacustrine microbialites sampled along an alkalinity gradient. Environ Microbiol 2020; 23:51-68. [PMID: 32985763 DOI: 10.1111/1462-2920.15252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/26/2020] [Accepted: 09/23/2020] [Indexed: 11/28/2022]
Abstract
Microbialites are usually carbonate-rich sedimentary rocks formed by the interplay of phylogenetically and metabolically complex microbial communities with their physicochemical environment. Yet, the biotic and abiotic determinants of microbialite formation remain poorly constrained. Here, we analysed the structure of prokaryotic and eukaryotic communities associated with microbialites occurring in several crater lakes of the Trans-Mexican volcanic belt along an alkalinity gradient. Microbialite size and community structure correlated with lake physicochemical parameters, notably alkalinity. Although microbial community composition varied across lake microbialites, major taxa-associated functions appeared quite stable with both, oxygenic and anoxygenic photosynthesis and, to less extent, sulphate reduction, as major putative carbonatogenic processes. Despite interlake microbialite community differences, we identified a microbial core of 247 operational taxonomic units conserved across lake microbialites, suggesting a prominent ecological role in microbialite formation. This core mostly encompassed Cyanobacteria and their typical associated taxa (Bacteroidetes, Planctomycetes) and diverse anoxygenic photosynthetic bacteria, notably Chloroflexi, Alphaproteobacteria (Rhodobacteriales, Rhodospirilalles), Gammaproteobacteria (Chromatiaceae) and minor proportions of Chlorobi. The conserved core represented up to 40% (relative abundance) of the total community in lakes Alchichica and Atexcac, displaying the highest alkalinities and the most conspicuous microbialites. Core microbialite communities associated with carbonatogenesis might be relevant for inorganic carbon sequestration purposes.
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Affiliation(s)
- Miguel Iniesto
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Guillaume Reboul
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Philippe Deschamps
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Karim Benzerara
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Muséum National d'Histoire Naturelle, Sorbonne Université, Paris, France
| | - Paola Bertolino
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Aurélien Saghaï
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, DF Mexico, Mexico
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
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22
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López-García P, Moreira D. The Syntrophy hypothesis for the origin of eukaryotes revisited. Nat Microbiol 2020; 5:655-667. [DOI: 10.1038/s41564-020-0710-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/13/2020] [Indexed: 11/10/2022]
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Reinold M, Wong HL, MacLeod FI, Meltzer J, Thompson A, Burns BP. The Vulnerability of Microbial Ecosystems in A Changing Climate: Potential Impact in Shark Bay. Life (Basel) 2019; 9:life9030071. [PMID: 31480795 PMCID: PMC6789446 DOI: 10.3390/life9030071] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/22/2019] [Accepted: 08/28/2019] [Indexed: 12/26/2022] Open
Abstract
The potential impact of climate change on eukaryotes, including humans, has been relatively well described. In contrast, the contribution and susceptibility of microorganisms to a changing climate have, until recently, received relatively less attention. In this review, the importance of microorganisms in the climate change discourse is highlighted. Microorganisms are responsible for approximately half of all primary production on earth, support all forms of macroscopic life whether directly or indirectly, and often persist in “extreme” environments where most other life are excluded. In short, microorganisms are the life support system of the biosphere and therefore must be included in decision making regarding climate change. Any effects climate change will have on microorganisms will inevitably impact higher eukaryotes and the activity of microbial communities in turn can contribute to or alleviate the severity of the changing climate. It is of vital importance that unique, fragile, microbial ecosystems are a focus of research efforts so that their resilience to extreme weather events and climate change are thoroughly understood and that conservation efforts can be implemented as a response. One such ecosystem under threat are the evolutionarily significant microbial mats and stromatolites, such as those present in Shark Bay, Western Australia. Climate change models have suggested the duration and severity of extreme weather events in this region will increase, along with rising temperatures, sea levels, and ocean acidification. These changes could upset the delicate balance that fosters the development of microbial mats and stromatolites in Shark Bay. Thus, the challenges facing Shark Bay microbial communities will be presented here as a specific case study.
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Affiliation(s)
- Max Reinold
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Hon Lun Wong
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Fraser I MacLeod
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Julia Meltzer
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - April Thompson
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney 2052, Australia.
- Australian Centre for Astrobiology; The University of New South Wales Sydney 2052, Australia.
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Ślesak I, Kula M, Ślesak H, Miszalski Z, Strzałka K. How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth. Free Radic Biol Med 2019; 140:61-73. [PMID: 30862543 DOI: 10.1016/j.freeradbiomed.2019.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
One of the former definitions of "obligate anaerobiosis" was based on three main criteria: 1) it occurs in organisms, so-called obligate anaerobes, which live in environments without oxygen (O2), 2) O2-dependent (aerobic) respiration, and 3) antioxidant enzymes are absent in obligate anaerobes. In contrast, aerobes need O2 in order to grow and develop properly. Obligate (or strict) anaerobes belong to prokaryotic microorganisms from two domains, Bacteria and Archaea. A closer look at anaerobiosis covers a wide range of microorganisms that permanently or in a time-dependent manner tolerate different concentrations of O2 in their habitats. On this basis they can be classified as obligate/facultative anaerobes, microaerophiles and nanaerobes. Paradoxically, O2 tolerance in strict anaerobes is usually, as in aerobes, associated with the activity of the antioxidant response system, which involves different antioxidant enzymes responsible for removing excess reactive oxygen species (ROS). In our opinion, the traditional definition of "obligate anaerobiosis" loses its original sense. Strict anaerobiosis should only be restricted to the occurrence of O2-independent pathways involved in energy generation. For that reason, a term better than "obligate anaerobes" would be O2/ROS tolerant anaerobes, where the role of the O2/ROS detoxification system is separated from O2-independent metabolic pathways that supply energy. Ubiquitous key antioxidant enzymes like superoxide dismutase (SOD) and superoxide reductase (SOR) in contemporary obligate anaerobes might suggest that their origin is ancient, maybe even the beginning of the evolution of life on Earth. It cannot be ruled out that c. 3.5 Gyr ago, local microquantities of O2/ROS played a role in the evolution of the last universal common ancestor (LUCA) of all modern organisms. On the basis of data in the literature, the hypothesis that LUCA could be an O2/ROS tolerant anaerobe is discussed together with the question of the abiotic sources of O2/ROS and/or the early evolution of cyanobacteria that perform oxygenic photosynthesis.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Monika Kula
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Halina Ślesak
- Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland.
| | - Zbigniew Miszalski
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Kazimierz Strzałka
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
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