1
|
Vedel G, Triadó-Margarit X, Linares O, Moreno-Rojas JM, la Peña ED, García-Bocanegra I, Jiménez-Martín D, Carranza J, Casamayor EO. Exploring the potential links between gut microbiota composition and natural populations management in wild boar (Sus scrofa). Microbiol Res 2023; 274:127444. [PMID: 37421802 DOI: 10.1016/j.micres.2023.127444] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/10/2023]
Abstract
We surveyed wild boar (Sus scrofa) populations using 16S rRNA gene analysis of the gut microbiota in fresh faeces taken from 88 animals hunted in 16 hunting estates. The wild boar is a very convenient model system to explore how environmental factors including game management, food availability, disease prevalence, and behaviour may affect different biological components of wild individuals with potential implications in management and conservation. We tested the hypotheses that diet (according to stable carbon isotopes analyses), gender (i.e., animal behaviour studying males and females), and both health (analyses of serum samples to detect exposure to several diseases) and form statutes (i.e., thoracic circumference in adults) are reflected in changes in the intestinal microbiota. We focused on a gut functional biomarker index combining Oscillospiraceae and Ruminococcaceae vs. Enterobacteriaceae. We found that gender and the estate (population) were explanatory variables (c.a. 28% of the variance), albeit a high degree of overlapping among individuals was observed. The individuals with higher abundance of Enterobacteriaceae showed a gut microbiota with low diversity, mostly in males. Significant statistical differences for thoracic circumference were not found between males and females. Interestingly, the thoracic circumference was significantly and inversely related to the relative abundance of Enterobacteriaceae in males. Overall, we found that diet, gender, and form status were major factors that could be related to the composition and diversity of the gut microbiota. A high variability was observed in the biomarker index for populations with natural diet (rich in C3 plants). Although, we noticed a marginally significant negative trend between the index (higher abundance of Enterobacteriaceae) and the continuous feeding of C4 plants (i.e., supplementary maize) in the diet of males. This result suggests that continuous artificial feeding in hunting estates could be one of the factors negatively influencing the gut microbiota and the form status of wild boars that deserves further investigations.
Collapse
Affiliation(s)
- Giovanni Vedel
- Wildlife Research Unit, University of Cordoba (UIRCP-UCO), 14071 Córdoba, Spain
| | - Xavier Triadó-Margarit
- Ecology of the Global Microbiome, Centre of Advanced Studies of Blanes-Spanish Council for Research (CEAB-CSIC), Accés Cala St Francesc, 14, E-17300 Blanes, Spain
| | - Olmo Linares
- Wildlife Research Unit, University of Cordoba (UIRCP-UCO), 14071 Córdoba, Spain
| | - José Manuel Moreno-Rojas
- Department of Food Science and Health, Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA), Alameda del Obispo, Avda. Menéndez Pidal, s/n, 14071 Córdoba, Spain
| | - Eva de la Peña
- Wildlife Research Unit, University of Cordoba (UIRCP-UCO), 14071 Córdoba, Spain; IREC National Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Ignacio García-Bocanegra
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonoses and Emreging Diseases ENZOEM, University of Cordoba, Cordoba, Spain; CIBERINFEC, ISCIII - CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Spain
| | - Débora Jiménez-Martín
- Department of Animal Health, Animal Health and Zoonosis Research Group (GISAZ), UIC Zoonoses and Emreging Diseases ENZOEM, University of Cordoba, Cordoba, Spain
| | - Juan Carranza
- Wildlife Research Unit, University of Cordoba (UIRCP-UCO), 14071 Córdoba, Spain
| | - Emilio O Casamayor
- Ecology of the Global Microbiome, Centre of Advanced Studies of Blanes-Spanish Council for Research (CEAB-CSIC), Accés Cala St Francesc, 14, E-17300 Blanes, Spain.
| |
Collapse
|
2
|
Casamayor EO, Cáliz J, Triadó-Margarit X, Pointing SB. Understanding atmospheric intercontinental dispersal of harmful microorganisms. Curr Opin Biotechnol 2023; 81:102945. [PMID: 37087840 DOI: 10.1016/j.copbio.2023.102945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
The atmosphere is a major route for microbial intercontinental dispersal, including harmful microorganisms, antibiotic resistance genes, and allergens, with strong implications in ecosystem functioning and global health. Long-distance dispersal is facilitated by air movement at higher altitudes in the free troposphere and is affected by anthropogenic forcing, climate change, and by the general atmospheric circulation, mainly in the intertropical convergence zone. The survival of microorganisms during atmospheric transport and their remote invasive potential are fundamental questions, but data are scarce. Extreme atmospheric conditions represent a challenge to survival that requires specific adaptive strategies, and recovery of air samples from the high altitudes relevant to study harmful microorganisms can be challenging. In this paper, we highlight the scope of the problem, identify challenges and knowledge gaps, and offer a roadmap for improved understanding of intercontinental microbial dispersal and their outcomes. Greater understanding of long-distance dispersal requires research focus on local factors that affect emissions, coupled with conditions influencing transport and survival at high altitudes, and eventual deposition at sink locations.
Collapse
Affiliation(s)
- Emilio O Casamayor
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain.
| | - Joan Cáliz
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain
| | - Xavier Triadó-Margarit
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain
| | - Stephen B Pointing
- Yale-NUS College & Department of Biological Sciences, National University of Singapore, Singapore
| |
Collapse
|
3
|
Cáliz J, Subirats J, Triadó-Margarit X, Borrego CM, Casamayor EO. Global dispersal and potential sources of antibiotic resistance genes in atmospheric remote depositions. Environ Int 2022; 160:107077. [PMID: 35016024 DOI: 10.1016/j.envint.2022.107077] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 09/26/2021] [Revised: 01/01/2022] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Antibiotic resistance has become a major Global Health concern and a better understanding on the global spread mechanisms of antibiotic resistant bacteria (ARB) and intercontinental ARB exchange is needed. We measured atmospheric depositions of antibiotic resistance genes (ARGs) by quantitative (q)PCR in rain/snow collected fortnightly along 4 y. at a remote high mountain LTER (Long-Term Ecological Research) site located above the atmospheric boundary layer (free troposphere). Bacterial composition was characterized by 16S rRNA gene sequencing, and air mass provenances were determined by modelled back trajectories and rain/snow chemical composition. We hypothesize that the free troposphere may act as permanent reservoir and vector for ARB and ARGs global dispersal. We aimed to i) determine whether ARGs are long-range intercontinental and persistently dispersed through aerosols, ii) assess ARGs long-term atmospheric deposition dynamics in a remote high mountain area, and iii) unveil potential diffuse ARGs pollution sources. We showed that the ARGs sul1 (resistance to sulfonamides), tetO (resistance to tetracyclines), and intI1 (a proxy for horizontal gene transfer and anthropogenic pollution) were long-range and persistently dispersed in free troposphere aerosols. Major depositions of tetracyclines resistance matched with intensification of African dust outbreaks. Potential ARB mostly traced their origin back into agricultural soils. Our study unveils that air masses pathways are shaping ARGs intercontinental dispersal and global spread of antibiotic resistances, with potential predictability for interannual variability and remote deposition rates. Because climate regulates aerosolization and long-range air masses movement patterns, we call for a more careful evaluation of the connections between land use, climate change and ARB long-range intercontinental dispersal.
Collapse
Affiliation(s)
- Joan Cáliz
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain.
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona E-17003, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona E-17003, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona E-17003, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain.
| |
Collapse
|
4
|
Triadó-Margarit X, Cáliz J, Casamayor EO. A long-term atmospheric baseline for intercontinental exchange of airborne pathogens. Environ Int 2022; 158:106916. [PMID: 34627012 DOI: 10.1016/j.envint.2021.106916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 04/12/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The atmosphere is a potential pathway for global-scale and long-range dispersal of viable microorganisms, promoting biological interconnections among the total environment. We aimed to provide relevant baseline information for long-range long-term intercontinental exchange of potentially infectious airborne microorganisms of major interest in environmental and health-related disciplines. We used an interannual survey (7-y) with wet depositions fortnightly collected above the boundary layer (free troposphere) at a remote high-elevation LTER (Long-Term-Ecological-Research) site, analyzed by 16S and 18S rRNA genes, and compared to a database of 475 well-known pathogens. We applied a conservative approach on close relatives of pathogenic species (>98% identity) standing their theoretical upper limit for atmospheric baseline relative abundances. We identified c. 2-3% of the total airborne microbiota as potential pathogens. Their most frequent environmental origins were soil, aquatic, and anthropogenic sources. Phytopathogens (mostly fungi) were the potential infectious agents most widely present. We uncovered consistent interannual dynamics with taxa foreseeable over time (i.e., predictable seasonal behavior) and under recurrent environmental scenarios (e.g., Saharan dust intrusions), respectively, being highly valuable microbial forensic environmental indicators. Up to 8 bacterial and 21 fungal genera consistently showed temporal abundances and recurrences unevenly distributed. Incidence of allergenic fungi was lower in summer, and significantly higher in spring. Close relatives to Coccidioides posadasii consistently showed higher signals (i.e., high specificity and high fidelity) in winter, whereas Cryptococcus neoformans had a significant signal in spring. Along Saharan dust intrusions, the bacterial phytopathogens Acidovorax avenae and Agrobacterium tumefaciens and the fungal phytopathogens Pseudozyma hubeiensis and Peniophora sp. consistently showed higher signals. Potential human pathogens showed low proportion, being mostly fungal allergens. Microorganisms related to obligated human, amphibian and fish pathogens were commonly found in winter. More studies in remote field sites above the boundary layer will unveil whether or not a similar trend is found globally.
Collapse
Affiliation(s)
- Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group & LTER-AT Research Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain
| | - Joan Cáliz
- Integrative Freshwater Ecology Group & LTER-AT Research Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group & LTER-AT Research Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain.
| |
Collapse
|
5
|
Menéndez-Serra M, Triadó-Margarit X, Casamayor EO. Ecological and Metabolic Thresholds in the Bacterial, Protist, and Fungal Microbiome of Ephemeral Saline Lakes (Monegros Desert, Spain). Microb Ecol 2021; 82:885-896. [PMID: 33725151 DOI: 10.1007/s00248-021-01732-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/08/2021] [Indexed: 05/20/2023]
Abstract
We studied the 16S and 18S rRNA genes of the bacterial, protist, and fungal microbiomes of 131 samples collected in 14 ephemeral small inland lakes located in the endorheic area of the Monegros Desert (NE Spain). The sampling covered different temporal flooding/desiccation cycles that created natural salinity gradients between 0.1% (w/v) and salt saturation. We aimed to test the hypothesis of a lack of competitive advantage for microorganisms using the "salt-in" strategy in highly fluctuating hypersaline environments where temperature and salinity transitions widely vary within short time periods, as in ephemeral inland lakes. Overall, 5653 bacterial zOTUs and 2658 eukaryal zOTUs were detected heterogeneously distributed with significant variations on taxonomy and general energy-yielding metabolisms and trophic strategies along the gradient. We observed a more diverse bacterial assembly than initially expected at extreme salinities and a lack of dominance of a few "salt-in" organisms. Microbial thresholds were unveiled for these highly fluctuating hypersaline environments with high selective pressures. We conclude that the extremely high dynamism observed in the ephemeral lakes of Monegros may have given a competitive advantage for more versatile ("salt-out") organisms compared to those better adapted to stable high salinities usually more common in solar salterns. Ephemeral inland saline lakes offered a well-suited natural framework for highly detailed evolutionary and ecological studies.
Collapse
Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, 17300, Blanes, Spain.
| |
Collapse
|
6
|
Funosas G, Triadó-Margarit X, Castro F, Villafuerte R, Delibes-Mateos M, Rouco C, Casamayor EO. Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus). Sci Rep 2021; 11:766. [PMID: 33436896 PMCID: PMC7804928 DOI: 10.1038/s41598-020-80782-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/30/2020] [Indexed: 01/12/2023] Open
Abstract
Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.
Collapse
Affiliation(s)
- Gerard Funosas
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Xavier Triadó-Margarit
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain
| | - Francisca Castro
- Departamento de Didácticas Específicas, Universidad de Córdoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14004, Córdoba, Spain
| | - Rafael Villafuerte
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Miguel Delibes-Mateos
- Institute of Advanced Social Studies-Spanish Council for Research (IESA-CSIC), 14004, Córdoba, Spain
| | - Carlos Rouco
- Ecology Area, Faculty of Science, University of Cordoba, Sociedad, Ecología y Gestión del Medio Ambiente, UCO-IESA, Unidad Asociada al CSIC, 14071, Córdoba, Spain
| | - Emilio O Casamayor
- Microbial Community Ecology, Centre for Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Accés Cala St Francesc, 14, 17300, Blanes, Spain.
| |
Collapse
|
7
|
Menéndez-Serra M, Ontiveros VJ, Triadó-Margarit X, Alonso D, Casamayor EO. Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain). FEMS Microbiol Ecol 2020; 96:5719565. [PMID: 32006018 DOI: 10.1093/femsec/fiaa019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/01/2019] [Accepted: 01/30/2020] [Indexed: 11/15/2022] Open
Abstract
We characterized the rich Archaea microbiome of shallow inland lakes (Monegros Desert, NE Spain) by 16S rRNA gene tag sequencing covering a wide salinity range (0.1%-40% w/v) along 3 years. Up to 990 operational taxonomic units (OTUs; >97% identity) were detected allocated in 14 major archaeal phyla and heterogeneously distributed along the salt gradient. Dynamics and idiosyncratic ecological distributions were uncovered for the different phyla. A high genetic richness was observed for Woesearchaeota and Pacearchaeota (>370 OTUs each), followed by Halobacteria (105), Nanohaloarchaeota (62) and Thermoplasmata (19). Overall, the distribution of genetic richness was strongly correlated with environmental niche amplitude, but not with occurrence. We unveiled high occurrence for a very rich Woesearchaeota assemblage, and an unexpected positive correlation of Pacearchaeota abundance with salinity at >15% dissolved salt content. The estimated dynamic behaviour (temporal 'turnover' rates of presence/absence data) unveiled Thaumarchaeota and Halobacteria as the most dynamic groups, and Aenigmarchaeota and Thermoplasmata as the most stable. The DPANN Pacearchaeota, Woesearchaeota, and Nanohaloarchaeota showed intermediate rates, suggesting higher resilience to environmental perturbations. A rich and dynamic Archaea microbiome was unveiled, including unseen ecological traits for relevant members of the still largely unknown DPANN group, supporting a strong ecological differentiation between Pacearchaeota and Woesearchaeota.
Collapse
Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Vicente J Ontiveros
- Theoretical and Computational Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - David Alonso
- Theoretical and Computational Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| |
Collapse
|
8
|
Triadó-Margarit X, Capitán JA, Menéndez-Serra M, Ortiz-Álvarez R, Ontiveros VJ, Casamayor EO, Alonso D. A Randomized Trait Community Clustering approach to unveil consistent environmental thresholds in community assembly. ISME J 2019; 13:2681-2689. [PMID: 31243330 PMCID: PMC6794281 DOI: 10.1038/s41396-019-0454-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/21/2019] [Accepted: 06/01/2019] [Indexed: 12/30/2022]
Abstract
Similarities and differences of phenotypes within local co-occurring species hold the key to inferring the contribution of stochastic or deterministic processes in community assembly. Developing both phylogenetic-based and trait-based quantitative methods to unravel these processes is a major aim in community ecology. We developed a trait-based approach that: (i) assesses if a community trait clustering pattern is related to increasing environmental constraints along a gradient; and (ii) determines quantitative thresholds for an environmental variable along a gradient to interpret changes in prevailing community assembly drivers. We used a regional set of natural shallow saline ponds covering a wide salinity gradient (0.1-40% w/v). We identify a consistent discrete salinity threshold (ca. 5%) for microbial community assembly drivers. Above 5% salinity a strong environmental filtering prevailed as an assembly force, whereas a combination of biotic and abiotic factors dominated at lower salinities. This method provides a conceptual approach to identify consistent environmental thresholds in community assembly and enables quantitative predictions for the ecological impact of environmental changes.
Collapse
Affiliation(s)
- Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain
| | - José A Capitán
- Departamento de Matemática Aplicada, Universidad Politécnica de Madrid, Av. Juan de Herrera, 6, E-28040, Madrid, Spain
- Theoretical and Computational Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain
| | - Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain
- Theoretical and Computational Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain
| | - Rüdiger Ortiz-Álvarez
- Integrative Freshwater Ecology Group Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain
| | - Vicente J Ontiveros
- Theoretical and Computational Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain.
| | - David Alonso
- Theoretical and Computational Ecology, Centre for Advanced Studies of Blanes (CEAB-CSIC), Spanish Council for Scientific Research, Accés Cala St. Francesc 14, E-17300, Blanes, Spain.
| |
Collapse
|
9
|
Turon M, Cáliz J, Triadó-Margarit X, Casamayor EO, Uriz MJ. Sponges and Their Microbiomes Show Similar Community Metrics Across Impacted and Well-Preserved Reefs. Front Microbiol 2019; 10:1961. [PMID: 31507568 PMCID: PMC6713927 DOI: 10.3389/fmicb.2019.01961] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/09/2019] [Indexed: 11/13/2022] Open
Abstract
Sponge diversity has been reported to decrease from well-preserved to polluted environments, but whether diversity and intra-species variation of their associated microbiomes also change as function of environmental quality remains unknown. Our study aimed to assess whether microbiome composition and structure are related to the proliferation of some sponges and not others under degraded conditions. We characterized the most frequent sponges and their associated bacteria in two close areas (impacted and well-preserved) of Nha Trang Bay (Indo-Pacific). Sponge assemblages were richer and more diverse in the well-preserved reefs, but more abundant (individuals/m. transect) in the impacted environments, where two species (Clathria reinwardti and Amphimedon paraviridis) dominated. Sponge microbiomes from the polluted zones had, in general, lower bacterial diversity and core size and consequently, higher intra-species dispersion than microbiomes of sponges from the well-preserved environments. Microbial communities reflect the reduction of diversity and richness shown by their host sponges. In this sense, sponges with less complex and more variable microbiomes proliferate under degraded environmental conditions, following the ecological paradigm that negatively correlates community diversity and environmental degradation. Thereby, the diversity and structure of sponge microbiomes might indirectly determine the presence and proliferation of sponge species in certain habitats.
Collapse
Affiliation(s)
| | | | | | | | - Maria J. Uriz
- Centre d’Estudis Avançats de Blanes, CEAB-CSIC, Girona, Spain
| |
Collapse
|
10
|
Menéndez-Serra M, Triadó-Margarit X, Castañeda C, Herrero J, Casamayor EO. Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain). Sci Total Environ 2019; 650:343-353. [PMID: 30199680 DOI: 10.1016/j.scitotenv.2018.09.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 07/23/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 06/08/2023]
Abstract
Soil microbial communities (both Bacteria and Archaea) were studied after 16S rRNA genes massive sequencing in two hypersaline and gypsum-rich contrasted sites located in NE Spain. Soil microbial communities were also locally analysed according to environmental variables, including geological, physico-chemical, biogeochemically, and climatic data. Typical soil characteristics, climate data, and plant composition clearly split the two sites and major differences among the microbial communities for the areas were initially expected. Overall, high values of microbial species richness (up to 2300 taxa) and ecological diversity was detected in both sites. High genetic novelty levels were found mostly to environmental sequences, highlighting the high potential for microbiological studies. In contrast to the initial expectations, a substantial overlapping between Monegros and Gallocanta microbes was observed, indicating a high similarity despite of the geographical, botanical and environmental distances between sites, in agreement with both high dispersal and local selection inherent to the microbial world. The potential biogeochemical cycling showed small differences between sites, with presence of photosynthetic green and purple sulfur bacteria, cyanobacteria and aerobic and anaerobic chemolitotrophs. Potential for aerobic methane oxidation and anaerobic methanogenesis was observed in both sites, with predominance of potential nitrification mostly by ammonia-oxidizing archaea, nitrite oxidation and denitrification, and minor contribution for nitrate reduction and nitrate ammonification. The predicted functions based on the taxonomic composition showed high overlapping between the two studied regions, despite their difference in gypsum richness.
Collapse
Affiliation(s)
- Mateu Menéndez-Serra
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain
| | - Carmen Castañeda
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Juan Herrero
- Estación Experimental de Aula Dei (EEAD-CSIC), Av. Montañana 1005, 50059 Zaragoza, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Acces Cala Sant Francesc 14, Blanes 17300, Spain.
| |
Collapse
|
11
|
Ortiz-Álvarez R, Triadó-Margarit X, Camarero L, Casamayor EO, Catalan J. High planktonic diversity in mountain lakes contains similar contributions of autotrophic, heterotrophic and parasitic eukaryotic life forms. Sci Rep 2018. [PMID: 29535368 PMCID: PMC5849755 DOI: 10.1038/s41598-018-22835-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A rich eukaryotic planktonic community exists in high-mountain lakes despite the diluted, oligotrophic and cold, harsh prevailing conditions. Attempts of an overarching appraisal have been traditionally hampered by observational limitations of small, colorless, and soft eukaryotes. We aimed to uncover the regional eukaryotic biodiversity of a mountain lakes district to obtain general conclusions on diversity patterns, dominance, geographic diversification, and food-web players common to oligotrophic worldwide distributed freshwater systems. An unprecedented survey of 227 high-altitude lakes comprising large environmental gradients was carried out using Illumina massive tag sequencing of the 18S rRNA gene. We observed a large Chrysophyceae dominance in richness, abundance and novelty, and unveiled an unexpected richness in heterotrophic phagotrophs and parasites. In particular, Cercozoa and Chytridiomycota showed diversity features similar to the dominant autotrophic groups. The prominent beta-dispersion shown by parasites suggests highly specific interactions and a relevant role in food webs. Interestingly, the freshwater Pyrenean metacommunity contained more diverse specific populations than its closest marine oligotrophic equivalent, with consistently higher beta-diversity. The relevance of unseen groups opens new perspectives for the better understanding of planktonic food webs. Mountain lakes, with remarkable environmental idiosyncrasies, may be suitable environments for the genetic diversification of microscopic eukaryotic life forms.
Collapse
Affiliation(s)
- Rüdiger Ortiz-Álvarez
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Lluís Camarero
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes-CSIC. Acc. Cala St Francesc 14, E-17300, Blanes, Catalonia, Spain.
| | - Jordi Catalan
- CREAF - CSIC, Campus UAB, Edifici C, 08193, Cerdanyola del Vallès, Catalonia, Spain
| |
Collapse
|
12
|
Auguet O, Pijuan M, Borrego CM, Rodriguez-Mozaz S, Triadó-Margarit X, Giustina SVD, Gutierrez O. Sewers as potential reservoirs of antibiotic resistance. Sci Total Environ 2017; 605-606:1047-1054. [PMID: 28709370 DOI: 10.1016/j.scitotenv.2017.06.153] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [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: 06/06/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 05/06/2023]
Abstract
Wastewater transport along sewers favors the colonization of inner pipe surfaces by wastewater-derived microorganisms that grow forming biofilms. These biofilms are composed of rich and diverse microbial communities that are continuously exposed to antibiotic residues and antibiotic resistant bacteria (ARB) from urban wastewater. Sewer biofilms thus appear as an optimal habitat for the dispersal and accumulation of antibiotic resistance genes (ARGs). In this study, the concentration of antibiotics, integron (intI1) and antibiotic resistance genes (qnrS, sul1, sul2, blaTEM, blaKPC, ermB, tetM and tetW), and potential bacterial pathogens were analyzed in wastewater and biofilm samples collected at the inlet and outlet sections of a pressurized sewer pipe. The most abundant ARGs detected in both wastewater and biofilm samples were sul1 and sul2 with roughly 1 resistance gene for each 10 copies of 16s RNA gene. Significant differences in the relative abundance of gene intI1 and genes conferring resistance to fluoroquinolones (qnrS), sulfonamides (sul1 and sul2) and betalactams (blaTEM) were only measured between inlet and outlet biofilm samples. Composition of bacterial communities also showed spatial differences in biofilms and a higher prevalence of Operational Taxonomic Units (OTUs) with high sequence identity (>98%) to well-known human pathogens was observed in biofilms collected at the inlet pipe section. Our study highlights the role of sewer biofilms as source and sink of ARB and ARGs and supports the idea that community composition rather than antibiotic concentration is the main factor driving the diversity of the sewage resistome.
Collapse
Affiliation(s)
- Olga Auguet
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Maite Pijuan
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain; Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Sara Rodriguez-Mozaz
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Xavier Triadó-Margarit
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain; Integrative Freshwater Ecology Group, Centre d'Estudis Avançats de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Saulo Varela Della Giustina
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain
| | - Oriol Gutierrez
- Catalan Institute for Water Research (ICRA), Scientific and Technologic Park of the University of Girona, Emili Grahit 101, 17003 Girona, Spain.
| |
Collapse
|
13
|
Subirats J, Triadó-Margarit X, Mandaric L, Acuña V, Balcázar JL, Sabater S, Borrego CM. Wastewater pollution differently affects the antibiotic resistance gene pool and biofilm bacterial communities across streambed compartments. Mol Ecol 2017; 26:5567-5581. [DOI: 10.1111/mec.14288] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/19/2017] [Accepted: 06/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Jèssica Subirats
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group; Centre d'Estudis Avançats de Blanes; CEAB-CSIC; Blanes Girona Spain
- Group of Molecular Microbial Ecology; Institute of Aquatic Ecology; University of Girona; Girona Spain
| | - Ladislav Mandaric
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - Vicenç Acuña
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
| | - Sergi Sabater
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
- GRECO; Institute of Aquatic Ecology; University of Girona; Girona Spain
| | - Carles M. Borrego
- Catalan Institute for Water Research (ICRA); Scientific and Technological Park of the University of Girona; Girona Spain
- Group of Molecular Microbial Ecology; Institute of Aquatic Ecology; University of Girona; Girona Spain
| |
Collapse
|
14
|
Triadó-Margarit X, Veillette M, Duchaine C, Talbot M, Amato F, Minguillón MC, Martins V, de Miguel E, Casamayor EO, Moreno T. Bioaerosols in the Barcelona subway system. Indoor Air 2017; 27:564-575. [PMID: 27687789 DOI: 10.1111/ina.12343] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/23/2016] [Indexed: 05/22/2023]
Abstract
Subway systems worldwide transport more than 100 million people daily; therefore, air quality on station platforms and inside trains is an important urban air pollution issue. We examined the microbiological composition and abundance in space and time of bioaerosols collected in the Barcelona subway system during a cold period. Quantitative PCR was used to quantify total bacteria, Aspergillus fumigatus, influenza A and B, and rhinoviruses. Multitag 454 pyrosequencing of the 16S rRNA gene was used to assess bacterial community composition and biodiversity. The results showed low bioaerosol concentrations regarding the targeted microorganisms, although the bacterial bioburden was rather high (104 bacteria/m3 ). Airborne bacterial communities presented a high degree of overlap among the different subway environments sampled (inside trains, platforms, and lobbies) and were dominated by a few widespread taxa, with Methylobacterium being the most abundant genus. Human-related microbiota in sequence dataset and ascribed to potentially pathogenic bacteria were found in low proportion (maximum values below 2% of sequence readings) and evenly detected. Hence, no important biological exposure marker was detected in any of the sampled environments. Overall, we found that commuters are not the main source of bioaerosols in the Barcelona subway system.
Collapse
Affiliation(s)
- X Triadó-Margarit
- Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Blanes, Spain
| | - M Veillette
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC, Canada
| | - C Duchaine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC, Canada
| | - M Talbot
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, QC, Canada
| | - F Amato
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - M C Minguillón
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - V Martins
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| | - E de Miguel
- Transports Metropolitans de Barcelona, TMB Santa Eulalia, Barcelona, Spain
| | - E O Casamayor
- Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), Blanes, Spain
| | - T Moreno
- Institute for Environmental Assessment and Water Research (IDAEA-CSIC), Barcelona, Spain
| |
Collapse
|
15
|
Larsen T, Ventura M, Maraldo K, Triadó-Margarit X, Casamayor EO, Wang YV, Andersen N, O'Brien DM. The dominant detritus-feeding invertebrate in Arctic peat soils derives its essential amino acids from gut symbionts. J Anim Ecol 2016; 85:1275-85. [PMID: 27322934 DOI: 10.1111/1365-2656.12563] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 02/13/2016] [Accepted: 06/09/2016] [Indexed: 02/04/2023]
Abstract
Supplementation of nutrients by symbionts enables consumers to thrive on resources that might otherwise be insufficient to meet nutritional demands. Such nutritional subsidies by intracellular symbionts have been well studied; however, supplementation of de novo synthesized nutrients to hosts by extracellular gut symbionts is poorly documented, especially for generalists with relatively undifferentiated intestinal tracts. Although gut symbionts facilitate degradation of resources that would otherwise remain inaccessible to the host, such digestive actions alone cannot make up for dietary insufficiencies of macronutrients such as essential amino acids (EAA). Documenting whether gut symbionts also function as partners for symbiotic EAA supplementation is important because the question of how some detritivores are able to subsist on nutritionally insufficient diets has remained unresolved. To answer this poorly understood nutritional aspect of symbiont-host interactions, we studied the enchytraeid worm, a bulk soil feeder that thrives in Arctic peatlands. In a combined field and laboratory study, we employed stable isotope fingerprinting of amino acids to identify the biosynthetic origins of amino acids to bacteria, fungi and plants in enchytraeids. Enchytraeids collected from Arctic peatlands derived more than 80% of their EAA from bacteria. In a controlled feeding study with the enchytraeid Enchytraeus crypticus, EAA derived almost exclusively from gut bacteria when the worms fed on higher fibre diets, whereas most of the enchytraeids' EAA derived from dietary sources when fed on lower fibre diets. Our gene sequencing results of gut microbiota showed that the worms harbour several taxa in their gut lumen absent from their diets and substrates. Almost all gut taxa are candidates for EAA supplementation because almost all belong to clades capable of biosynthesizing EAA. Our study provides the first evidence of extensive symbiotic supplementation of EAA by microbial gut symbionts and demonstrates that symbiotic bacteria in the gut lumen appear to function as partners both for symbiotic EAA supplementation and for digestion of insoluble plant fibres.
Collapse
Affiliation(s)
- Thomas Larsen
- Department of Agroecology, Faculty of Sciences and Technology, Aarhus University, Blichers Allé, Postbox 50, 8830, Tjele, Denmark.,Leibniz-Laboratory for Radiometric Dating and Stable Isotope Research, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany
| | - Marc Ventura
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Kristine Maraldo
- Department of Agroecology, Faculty of Sciences and Technology, Aarhus University, Blichers Allé, Postbox 50, 8830, Tjele, Denmark
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centre for Advanced Studies of Blanes (CEAB), Spanish Research Council (CSIC), 17300 Blanes, Catalonia, Spain
| | - Yiming V Wang
- Leibniz-Laboratory for Radiometric Dating and Stable Isotope Research, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany
| | - Nils Andersen
- Leibniz-Laboratory for Radiometric Dating and Stable Isotope Research, Christian-Albrechts-Universität zu Kiel, 24118, Kiel, Germany
| | - Diane M O'Brien
- Institute of Arctic Biology and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK, 99775-7000, USA
| |
Collapse
|
16
|
Llorens-Marès T, Triadó-Margarit X, Borrego CM, Dupont CL, Casamayor EO. High Bacterial Diversity and Phylogenetic Novelty in Dark Euxinic Freshwaters Analyzed by 16S Tag Community Profiling. Microb Ecol 2016; 71:566-574. [PMID: 26552395 DOI: 10.1007/s00248-015-0696-2] [Citation(s) in RCA: 4] [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: 08/12/2015] [Accepted: 10/26/2015] [Indexed: 06/05/2023]
Abstract
Microbial communities growing under extreme low redox conditions are present in anoxic and sulfide-rich (euxinic) environments such as karstic lakes and experience limitation of electron acceptors. The fine natural chemical gradients and the large diversity of organic and inorganic compounds accumulated in bottom waters are impossible to mimic under laboratory conditions, and only a few groups have been cultured. We investigated the bacterial composition in the oxic-anoxic interface and in the deep waters of three sulfurous lakes from the Lake Banyoles karstic area (NE Spain) through 16S rRNA gene tag sequencing and identified the closest GenBank counterpart. High diversity indices were found in most of the samples with >15 phyla/classes and >45 bacterial orders. A higher proportion of operational taxonomic units (OTUs) of the "highest novelty" was found in the hypolimnia (38 % of total sequences) than in the metalimnia (17 %), whereas the percentage of OTUs closer to cultured counterparts (i.e., 97 % identity in the 16S rRNA gene) was 6 to 21 %, respectively. Elusimicrobia, Chloroflexi, Fibrobacteres, and Spirochaetes were the taxa with the highest proportion of novel sequences. Interestingly, tag sequencing results comparison with metagenomics data available from the same dataset, showed a systematic underestimation of sulfur-oxidizing Epsilonproteobacteria with the currently available 907R "universal" primer. Overall, despite the limitation of electron acceptors, a highly diverse and novel assemblage was present in dark and euxinic hypolimnetic freshwaters, unveiling a hotspot of microbial diversity with a remarkable gap with cultured counterparts.
Collapse
Affiliation(s)
- Tomàs Llorens-Marès
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain
| | - Carles M Borrego
- Water Quality and Microbial Diversity, Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Spain
| | - Chris L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Accés Cala Sant Francesc, 14, 17300, Blanes, Girona, Spain.
| |
Collapse
|
17
|
Caliz J, Montes-Borrego M, Triadó-Margarit X, Metsis M, Landa BB, Casamayor EO. Influence of edaphic, climatic, and agronomic factors on the composition and abundance of nitrifying microorganisms in the rhizosphere of commercial olive crops. PLoS One 2015; 10:e0125787. [PMID: 25950678 PMCID: PMC4423868 DOI: 10.1371/journal.pone.0125787] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/25/2015] [Indexed: 01/11/2023] Open
Abstract
The microbial ecology of the nitrogen cycle in agricultural soils is an issue of major interest. We hypothesized a major effect by farm management systems (mineral versus organic fertilizers) and a minor influence of soil texture and plant variety on the composition and abundance of microbial nitrifiers. We explored changes in composition (16S rRNA gene) of ammonia-oxidizing archaea (AOA), bacteria (AOB), and nitrite-oxidizing bacteria (NOB), and in abundance of AOA and AOB (qPCR of amoA genes) in the rhizosphere of 96 olive orchards differing in climatic conditions, agricultural practices, soil properties, and olive variety. Majority of archaea were 1.1b thaumarchaeota (soil crenarchaeotic group, SCG) closely related to the AOA genus Nitrososphaera. Most AOB (97%) were identical to Nitrosospira tenuis and most NOB (76%) were closely related to Nitrospira sp. Common factors shaping nitrifiers assemblage composition were pH, soil texture, and olive variety. AOB abundance was positively correlated with altitude, pH, and clay content, whereas AOA abundances showed significant relationships with organic nitrogen content and exchangeable K. The abundances of AOA differed significantly among soil textures and olive varieties, and those of AOB among soil management systems and olive varieties. Overall, we observed minor effects by orchard management system, soil cover crop practices, plantation age, or soil organic matter content, and major influence of soil texture, pH, and olive tree variety.
Collapse
Affiliation(s)
- Joan Caliz
- Biogeodynamics & Biodiversity Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Blanes, Girona
| | - Miguel Montes-Borrego
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario (ceiA3), Córdoba, Spain
| | - Xavier Triadó-Margarit
- Biogeodynamics & Biodiversity Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Blanes, Girona
| | - Madis Metsis
- Tallinn University, Institute of Mathematics and Natural Sciences, Narva mnt 25, Tallinn 10120, Estonia
| | - Blanca B. Landa
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Campus de Excelencia Internacional Agroalimentario (ceiA3), Córdoba, Spain
| | - Emilio O. Casamayor
- Biogeodynamics & Biodiversity Group, Centro de Estudios Avanzados de Blanes, CEAB-CSIC, Blanes, Girona
- * E-mail:
| |
Collapse
|
18
|
Casamayor EO, Triadó-Margarit X, Castañeda C. Microbial biodiversity in saline shallow lakes of the Monegros Desert, Spain. FEMS Microbiol Ecol 2013; 85:503-18. [DOI: 10.1111/1574-6941.12139] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Emilio O. Casamayor
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
| | - Xavier Triadó-Margarit
- Biodiversity and Biogeodynamics Group; Centre d'Estudis Avançats de Blanes; CSIC; Blanes Spain
| | | |
Collapse
|
19
|
Triadó-Margarit X, Casamayor EO. High genetic diversity and novelty in planktonic protists inhabiting inland and coastal high salinity water bodies. FEMS Microbiol Ecol 2013; 85:27-36. [DOI: 10.1111/1574-6941.12095] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/04/2013] [Accepted: 02/07/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Xavier Triadó-Margarit
- Biogeodynamics & Biodiversity Group; Centre d'Estudis Avançats de Blanes; CEAB-CSIC; Blanes; Spain
| | - Emilio O. Casamayor
- Biogeodynamics & Biodiversity Group; Centre d'Estudis Avançats de Blanes; CEAB-CSIC; Blanes; Spain
| |
Collapse
|
20
|
Caliz J, Montserrat G, Martí E, Sierra J, Cruañas R, Garau MA, Triadó-Margarit X, Vila X. The exposition of a calcareous Mediterranean soil to toxic concentrations of Cr, Cd and Pb produces changes in the microbiota mainly related to differential metal bioavailability. Chemosphere 2012; 89:494-504. [PMID: 22658943 DOI: 10.1016/j.chemosphere.2012.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Revised: 04/25/2012] [Accepted: 05/03/2012] [Indexed: 06/01/2023]
Abstract
The involvement of the bacterial community of an agricultural Mediterranean calcareous soil in relation to several heavy metals has been studied in microcosms under controlled laboratory conditions. Soil samples were artificially polluted with Cr(VI), Cd(II) and Pb(II) at concentrations ranging from 0.1 to 5000 mg kg(-1) and incubated along 28 d. The lowest concentrations with significant effects in soil respirometry were 10 mg kg(-1) Cr and 1000 mg kg(-1) Cd and Pb. However, only treatments showing more than 40% inhibition of respirometric activity led to significant changes in bacterial composition, as indicated by PCR-DGGE analyses. Presumable Cr- and Cd-resistant bacteria were detected in polluted microcosms, but development of the microbiota was severely impaired at the highest amendments of both metals. Results also showed that bioavailability is an important factor determining the impact of the heavy metals assayed, and even an inverted potential toxicity ranking could be achieved if their soluble fraction is considered instead of the total concentration. Moreover, multiresistant bacteria were isolated from Cr-polluted soil microcosms, some of them showing the capacity to reduce Cr(VI) concentrations between 26% and 84% of the initial value. Potentially useful strains for bioremediation were related to Arthrobacter crystallopoietes, Stenotrophomonas maltophilia and several species of Bacillus.
Collapse
Affiliation(s)
- Joan Caliz
- Institute of Aquatic Ecology, University of Girona, Avda Montilivi s/n, Girona 17071, Spain
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Triadó-Margarit X, Casamayor EO. Genetic diversity of planktonic eukaryotes in high mountain lakes (Central Pyrenees, Spain). Environ Microbiol 2012; 14:2445-56. [DOI: 10.1111/j.1462-2920.2012.02797.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
22
|
Triadó-Margarit X, Vila X, Galinski EA. Osmoadaptative accumulation of N ɛ-acetyl-β-lysine in green sulfur bacteria and Bacillus cereus CECT 148T. FEMS Microbiol Lett 2011; 318:159-67. [DOI: 10.1111/j.1574-6968.2011.02254.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
23
|
Saccà A, Borrego CM, Renda R, Triadó-Margarit X, Bruni V, Guglielmo L. Predation impact of ciliated and flagellated protozoa during a summer bloom of brown sulfur bacteria in a meromictic coastal lake. FEMS Microbiol Ecol 2009; 70:42-53. [PMID: 19622068 DOI: 10.1111/j.1574-6941.2009.00735.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [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] Open
Abstract
Anaerobic phagotrophic protozoa may play an important role in the carbon flux of chemically stratified environments, especially when phototrophic sulfur bacteria account for a high proportion of the primary production. To test this assumption, we investigated the vertical and temporal distribution of microbial heterotrophs and of autotrophic picoplankton throughout the water column of the meromictic coastal lake Faro (Sicily, Italy), in the summer of 2004, coinciding with a bloom of brown-colored green sulfur bacteria. We also assessed the grazing impact of ciliated and flagellated protozoa within the sulfur bacteria plate using a modification of the fluorescently labeled bacteria uptake approach, attempting to minimize the biases intrinsic to the technique and to preserve the in situ anoxic conditions. Significant correlations were observed between ciliate biomass and bacteriochlorophyll e concentration, and between heterotrophic nanoflagellate biomass and chlorophyll a concentration in the water column. The major predators of anaerobic picoplankton were pleuronematine ciliates and cryptomonad flagellates, with clearances of 26.6 and 9.5 nL per cell h(-1), respectively, and a cumulative impact on the picoplankton gross growth rate ranging between 36% and 72%. We concluded that protozoan grazing channels a large proportion of anaerobic picoplankton production to higher trophic levels without restraining photosynthetic bacteria productivity.
Collapse
Affiliation(s)
- Alessandro Saccà
- Department of Animal Biology and Marine Ecology, University of Messina, Messina, Italy.
| | | | | | | | | | | |
Collapse
|