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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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2
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Guan Y, Hou T, Li X, Feng L, Wang Z. Metagenomic insights into comparative study of nitrogen metabolic potential and microbial community between primitive and urban river sediments. ENVIRONMENTAL RESEARCH 2022; 212:113592. [PMID: 35654160 DOI: 10.1016/j.envres.2022.113592] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/17/2022] [Accepted: 05/29/2022] [Indexed: 05/27/2023]
Abstract
As a result of anthropogenic pollution, the nitrogen nutrients load in urban rivers has increased, potentially raising the risk of river eutrophication. Here, we studied how anthropogenic impacts alter nitrogen metabolism in river sediments by comparing the metagenomic function of microbial communities between relatively primitive and human-disturbed sediments. The contents of organic matter (OM), total nitrogen (TN), NO3--N and NO2--N were higher in primitive site than in polluted sites, which might be due to vegetation density, sediment type, hydrology, etc. Whereas, NH4+-N content was higher in midstream and downstream, indicating that nitrogen loading increased in the anthropogenic regions and subsequently leading higher NH4+-N. Hierarchical cluster analyses revealed significant changes in the community structure and functional potential between the primitive and human-affected sites. Metagenomic analysis demonstrated that Demequina, Streptomyces, Rubrobacter and Dechloromonas were the predominant denitrifiers. Ardenticatena and Dechloromonas species were the most important contributors to dissimilatory nitrate reduction. Furthermore, anthropogenic pollution significantly increased their abundance, and resulting in a decrease in NO3-, NO2--N and an increase in NH4+-N contents. Additionally, the SOX metabolism of Dechloromonas and Sulfuritalea may involve in the sulfur-dependent autotrophic denitrification process by coupling the conversion of thiosulfate to sulfate with the reduction of NO3--N to N2. From pristine to anthropogenic pollution sediments, the major nitrifying bacteria harboring Hao transitioned from Nitrospira to Nitrosomonas. This study sheds light on the consequences of anthropogenic activities on nitrogen metabolism in river sediments, allowing for better management of nitrogen pollution and eutrophication in river.
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Affiliation(s)
- Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Leilei Feng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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3
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Nguyen STT, Vardeh DP, Nelson TM, Pearson LA, Kinsela AS, Neilan BA. Bacterial community structure and metabolic potential in microbialite-forming mats from South Australian saline lakes. GEOBIOLOGY 2022; 20:546-559. [PMID: 35312212 PMCID: PMC9311741 DOI: 10.1111/gbi.12489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/28/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Microbialites are sedimentary rocks created in association with benthic microorganisms. While they harbour complex microbial communities, Cyanobacteria perform critical roles in sediment stabilisation and accretion. Microbialites have been described from permanent and ephemeral saline lakes in South Australia; however, the microbial communities that generate and inhabit these biogeological structures have not been studied in detail. To address this knowledge gap, we investigated the composition, diversity and metabolic potential of bacterial communities from different microbialite-forming mats and surrounding sediments in five South Australian saline coastal lakes using 16S rRNA gene sequencing and predictive metagenome analyses. While Proteobacteria and Bacteroidetes were the dominant phyla recovered from the mats and sediments, Cyanobacteria were significantly more abundant in the mat samples. Interestingly, at lower taxonomic levels, the mat communities were vastly different across the five lakes. Comparative analysis of putative mat and sediment metagenomes via PICRUSt2 revealed important metabolic pathways driving the process of carbonate precipitation, including cyanobacterial oxygenic photosynthesis, ureolysis and nitrogen fixation. These pathways were highly conserved across the five examined lakes, although they appeared to be performed by distinct groups of bacterial taxa found in each lake. Stress response, quorum sensing and circadian clock were other important pathways predicted by the in silico metagenome analysis. The enrichment of CRISPR/Cas and phage shock associated genes in these cyanobacteria-rich communities suggests that they may be under selective pressure from viral infection. Together, these results highlight that a very stable ecosystem function is maintained by distinctly different communities in microbialite-forming mats in the five South Australian lakes and reinforce the concept that 'who' is in the community is not as critical as their net metabolic capacity.
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Affiliation(s)
- Suong T. T. Nguyen
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - David P. Vardeh
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNew South WalesAustralia
| | - Tiffanie M. Nelson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Leanne A. Pearson
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Andrew S. Kinsela
- School of Civil and Environmental EngineeringThe University of New South WalesSydneyNew South WalesAustralia
| | - Brett A. Neilan
- School of Environmental and Life SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNew South WalesAustralia
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4
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Medina Ferrer F, Rosen MR, Feyhl-Buska J, Russell VV, Sønderholm F, Loyd S, Shapiro R, Stamps BW, Petryshyn V, Demirel-Floyd C, Bailey JV, Johnson HA, Spear JR, Corsetti FA. Potential role for microbial ureolysis in the rapid formation of carbonate tufa mounds. GEOBIOLOGY 2022; 20:79-97. [PMID: 34337850 DOI: 10.1111/gbi.12467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/10/2021] [Indexed: 06/13/2023]
Abstract
Modern carbonate tufa towers in the alkaline (~pH 9.5) Big Soda Lake (BSL), Nevada, exhibit rapid precipitation rates (exceeding 3 cm/year) and host diverse microbial communities. Geochemical indicators reveal that carbonate precipitation is, in part, promoted by the mixing of calcium-rich groundwater and carbonate-rich lake water, such that a microbial role for carbonate precipitation is unknown. Here, we characterize the BSL microbial communities and evaluate their potential effects on carbonate precipitation that may influence fast carbonate precipitation rates of the active tufa mounds of BSL. Small subunit rRNA gene surveys indicate a diverse microbial community living endolithically, in interior voids, and on tufa surfaces. Metagenomic DNA sequencing shows that genes associated with metabolisms that are capable of increasing carbonate saturation (e.g., photosynthesis, ureolysis, and bicarbonate transport) are abundant. Enzyme activity assays revealed that urease and carbonic anhydrase, two microbial enzymes that promote carbonate precipitation, are active in situ in BSL tufa biofilms, and urease also increased calcium carbonate precipitation rates in laboratory incubation analyses. We propose that, although BSL tufas form partially as a result of water mixing, tufa-inhabiting microbiota promote rapid carbonate authigenesis via ureolysis, and potentially via bicarbonate dehydration and CO2 outgassing by carbonic anhydrase. Microbially induced calcium carbonate precipitation in BSL tufas may generate signatures preserved in the carbonate microfabric, such as stromatolitic layers, which could serve as models for developing potential biosignatures on Earth and elsewhere.
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Affiliation(s)
- Fernando Medina Ferrer
- Department of Earth & Environmental Sciences, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Michael R Rosen
- US Geological Survey, California Water Science Center, Carson City, Nevada, USA
| | - Jayme Feyhl-Buska
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Virginia V Russell
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Fredrik Sønderholm
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Sean Loyd
- Department of Geological Sciences, California State University Fullerton, Fullerton, California, USA
| | | | - Blake W Stamps
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, Dayton, Ohio, USA
- UES, Inc., Dayton, Ohio, USA
| | - Victoria Petryshyn
- Environmental Studies Program, University of Southern California, Los Angeles, California, USA
| | | | - Jake V Bailey
- Department of Earth & Environmental Sciences, University of Minnesota, Twin Cities, Minneapolis, Minnesota, USA
| | - Hope A Johnson
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - John R Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Frank A Corsetti
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
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Osman JR, Viedma P, Mendoza J, Fernandes G, DuBow MS, Cotoras D. Prokaryotic diversity and biogeochemical characteristics of field living and laboratory cultured stromatolites from the hypersaline Laguna Interna, Salar de Atacama (Chile). Extremophiles 2021; 25:327-342. [PMID: 33993356 DOI: 10.1007/s00792-021-01232-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
Stromatolites are organo-sedimentary structures found principally in seas and saline lakes that contain sheets of sediments and minerals formed by layers of microbial communities, which trap sediments and induce the precipitation of minerals.A living stromatolite from the alkaline Laguna Interna in the Salar de Atacama was collected and one of the fragments was deposited in an experimental aquarium for 18 months. We used Illumina sequencing of PCR-amplified V4 regions of 16S rRNA genes from total extracted DNA to identify the microbial populations. The chemical structure was studied using X-Ray Diffraction (XRD) and bench chemical methods. We found that members belonging to the Proteobacteria, Planctomycetes, Chloroflexi and Bacteroidetes phyla dominated the bacterial communities of the living and aquarium cultured samples. The potential metabolic functionality of the prokaryotic community reveals that sulfur, nitrogen, methane and carbon fixation metabolism functions are present in the samples. This study is the first to provide new insights into the prokaryotic community composition from this unusual aquatic desert site. Further studies will be helpful to obtain a better understanding of the biotic and abiotic mechanisms residing in stromatolites from Laguna Interna, as well as to have better knowledge about the formation of these biosignatures.
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Affiliation(s)
- Jorge R Osman
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile. .,Instituto de Geología Económica Aplicada (GEA), Universidad de Concepción, Concepción, Chile.
| | - Pabla Viedma
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile
| | - Jorge Mendoza
- Laboratorio de Química de Suelos, Departamento de Química Inorgánica y Analítica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
| | - Gustavo Fernandes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Michael S DuBow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay Campus CNRS, Bâtiment 21, Avenue de la Terasse, 91190, Gif-sur-Yvette, France
| | - Davor Cotoras
- Laboratorio de Microbiología y Biotecnología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santos Dumont #964, Independencia, Santiago, Chile
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Waterworth SC, Isemonger EW, Rees ER, Dorrington RA, Kwan JC. Conserved bacterial genomes from two geographically isolated peritidal stromatolite formations shed light on potential functional guilds. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:126-137. [PMID: 33369160 PMCID: PMC8408775 DOI: 10.1111/1758-2229.12916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/17/2020] [Accepted: 12/06/2020] [Indexed: 05/24/2023]
Abstract
Stromatolites are complex microbial mats that form lithified layers. Fossilized stromatolites are the oldest evidence of cellular life on Earth, dating back over 3.4 billion years. Modern stromatolites are relatively rare but may provide clues about the function and evolution of their ancient counterparts. In this study, we focus on peritidal stromatolites occurring at Cape Recife and Schoenmakerskop on the southeastern South African coastline, the former being morphologically and structurally similar to fossilized phosphatic stromatolites formations. Using assembled shotgun metagenomic analysis, we obtained 183 genomic bins, of which the most dominant taxa were from the Cyanobacteria phylum. We identified functional gene sets in genomic bins conserved across two geographically isolated stromatolite formations, which included relatively high copy numbers of genes involved in the reduction of nitrates and phosphatic compounds. Additionally, we found little evidence of Archaeal species in these stromatolites, suggesting that they may not play an important role in peritidal stromatolite formations, as proposed for hypersaline formations.
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Affiliation(s)
- Samantha C. Waterworth
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Eric W. Isemonger
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Evan R. Rees
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin 53705, USA
| | - Rosemary A. Dorrington
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Jason C. Kwan
- Division of Pharmaceutical Sciences, University of Wisconsin, Madison, Wisconsin 53705, USA
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Liu J, Mu W, Shi M, Zhao Q, Kong W, Xie H, Shi L. The Species Identification in Traditional Herbal Patent Medicine, Wuhu San, Based on Shotgun Metabarcoding. Front Pharmacol 2021; 12:607200. [PMID: 33664667 PMCID: PMC7921783 DOI: 10.3389/fphar.2021.607200] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
Traditional herbal patent medicine typically consists of multiple ingredients, making it challenging to supervise contamination by impurities and the improper use of raw materials. This study employed shotgun metabarcoding for the species identification of biological ingredients in traditional herbal patent medicine, Wuhu San. The five prescribed herbal materials found in Wuhu San were collected, and their reference sequences were obtained by traditional DNA barcoding using Sanger sequencing. Two lab-made and three commercial Wuhu San samples were collected, and a total of 37.14 Gb of shotgun sequencing data was obtained for these five samples using the Illumina sequencing platform. A total of 1,421,013 paired-end reads were enriched for the Internal Transcribed Spacer 2 (ITS2), psbA and trnH intergenic spacer region (psbA-trnH), maturase k (matK), and ribulose-1, 5-bisphosphate carboxylase (rbcL) regions. Furthermore, 80, 11, 9, and 8 operational taxonomic units were obtained for the ITS2, psbA-trnH, matK, and rbcL regions, respectively, after metagenomic assembly, annotation, and chimeric detection. In the two lab-made mock samples, all labeled ingredients in the Wuhu San prescription were successfully detected, and the positive control, Panax quinquefolius L., was detected in the HSZY172 mock sample. Three species, namely Angelica sinensis (Oliv.) Diels, Saposhnikovia divaricata (Turcz. ex Ledeb.) Schischk., and Carthamus tinctorius L., belonging to three labeled ingredients, Angelicae Sinensis Radix (Danggui), Saposhnikoviae Radix (Fangfeng), and Carthami Flos (Honghua), were detected in the three commercial samples. Angelica dahurica (Hoffm.) Benth. & Hook. f. ex Franch. & Sav., the original Angelicae Dahuricae Radix (Baizhi) species, was only detected in WHS003. Arisaema erubescens (Wall.) Schott, Arisaema heterophyllum Blume, or Arisaema amurense Maxim., the original Arisaematis Rhizoma (Tiannanxing) species, were not detected in any of the commercial samples, which could be attributed to the fact that this medicinal material underwent extensive processing. In addition, the Saposhnikovia divaricata adulterant was detected in all the commercial samples, while 24 fungal genera, including Aspergillus, were identified in both the lab-made and commercial samples. This study showed that shotgun metabarcoding provided alternative strategy and technical means for identifying prescribed ingredients in traditional herbal patent medicine and displayed the potential to effectively complement traditional methods.
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Affiliation(s)
- Jinxin Liu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China.,Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Weishan Mu
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Mengmeng Shi
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Qing Zhao
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Weijun Kong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hongbo Xie
- Hebei Key Laboratory of Study and Exploitation of Chinese Medicine, Chengde Medical University, Chengde, China
| | - Linchun Shi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Monaco P, Divino F, Naclerio G, Bucci A. Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01604-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Purpose
Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).
Methods
Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.
Result
The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.
Conclusion
The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.
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Medina Ferrer F, Hobart K, Bailey JV. Field detection of urease and carbonic anhydrase activity using rapid and economical tests to assess microbially induced carbonate precipitation. Microb Biotechnol 2020; 13:1877-1888. [PMID: 32720477 PMCID: PMC7533345 DOI: 10.1111/1751-7915.13630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Microbial precipitation of calcium carbonate is a widespread environmental phenomenon that has diverse engineering applications, from building and soil restoration to carbon sequestration. Urease-mediated ureolysis and CO2 (de)hydration by carbonic anhydrase (CA) are known for their potential to precipitate carbonate minerals, yet many environmental microbial community studies rely on marker gene or metagenomic approaches that are unable to determine in situ activity. Here, we developed fast and cost-effective tests for the field detection of urease and CA activity using pH-sensitive strips inside microcentrifuge tubes that change colour in response to the reaction products of urease (NH3 ) and CA (CO2 ). The urease assay proved sensitive and useful in the field to detect in situ activity in biofilms from a saline lake, a series of calcareous fens, and ferrous springs, finding relatively high urease activity in lake samples. Incubations of lake microbes with urea resulted in significantly higher CaCO3 precipitation compared to incubations with a urease inhibitor, showing that the rapid assay indicated an on-site active metabolism potentially mediating carbonate precipitation. The CA assay, however, showed less sensitivity compared to the urease test. While its sensitivity limits its utility, the assay may still be useful as a preliminary indicator given the paucity of other means for detecting CA activity in the field. Field urease, and potentially CA, activity assays complement molecular approaches and facilitate the search for carbonate-precipitating microbes and their in situ activity, which could be applied toward agriculture, engineering and carbon sequestration technologies.
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Affiliation(s)
- Fernando Medina Ferrer
- Department of Earth & Environmental SciencesCollege of Science & EngineeringUniversity of Minnesota, Twin CitiesMinneapolisMNUSA
| | - Kathryn Hobart
- Department of Earth & Environmental SciencesCollege of Science & EngineeringUniversity of Minnesota, Twin CitiesMinneapolisMNUSA
- Institute for Rock MagnetismUniversity of Minnesota, Twin CitiesMinneapolisMNUSA
| | - Jake V. Bailey
- Department of Earth & Environmental SciencesCollege of Science & EngineeringUniversity of Minnesota, Twin CitiesMinneapolisMNUSA
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10
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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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11
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12
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Global distribution of a chlorophyll f cyanobacterial marker. ISME JOURNAL 2020; 14:2275-2287. [PMID: 32457503 PMCID: PMC7608106 DOI: 10.1038/s41396-020-0670-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 04/16/2020] [Accepted: 04/28/2020] [Indexed: 02/04/2023]
Abstract
Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype’s distribution.
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13
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Warden JG, Coshell L, Rosen MR, Breecker DO, Ruthrof KX, Omelon CR. The importance of groundwater flow to the formation of modern thrombolitic microbialites. GEOBIOLOGY 2019; 17:536-550. [PMID: 31119865 DOI: 10.1111/gbi.12344] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 02/11/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
Modern microbialites are often located within groundwater discharge zones, yet the role of groundwater in microbialite accretion has yet to be resolved. To understand relationships between groundwater, microbialites, and associated microbial communities, we quantified and characterized groundwater flow and chemistry in active thrombolitic microbialites in Lake Clifton, Western Australia, and compared these observations to inactive thrombolites and lakebed sediments. Groundwater flows upward through an interconnected network of pores within the microstructure of active thrombolites, discharging directly from thrombolite heads into the lake. This upwelling groundwater is fresher than lake water and is hypothesized to support microbial mat growth by reducing salinity and providing limiting nutrients in an osmotically stressful and oligotrophic habitat. This is in contrast to inactive thrombolites that show no evidence of microbial mat colonization and are infiltrated by hypersaline lake water. Groundwater discharge through active thrombolites contrasts with the surrounding lakebed, where hypersaline lake water flows downward through sandy sediments at very low rates. Based on an appreciation for the role of microorganisms in thrombolite accretion, our findings suggest conditions favorable to thrombolite formation still exist in certain locations of Lake Clifton despite increasing lake water salinity. This study is the first to characterize groundwater flow rates, paths, and chemistry within a microbialite-forming environment and provides new insight into how groundwater can support microbial mats believed to contribute to microbialite formation in modern and ancient environments.
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Affiliation(s)
- John G Warden
- Jackson School of Geosciences, University of Texas at Austin, Austin, Texas
| | - Lee Coshell
- Coshell and Associates, South Perth, Western Australia, Australia
| | | | - Daniel O Breecker
- Jackson School of Geosciences, University of Texas at Austin, Austin, Texas
| | - Katinka X Ruthrof
- Murdoch University, Murdoch, Western Australia, Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Christopher R Omelon
- Department of Mining and Materials Engineering, McGill University, Montréal, Québec, Canada
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14
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De Anda V, Zapata-Peñasco I, Blaz J, Poot-Hernández AC, Contreras-Moreira B, González-Laffitte M, Gámez-Tamariz N, Hernández-Rosales M, Eguiarte LE, Souza V. Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach. Front Microbiol 2018; 9:2606. [PMID: 30555424 PMCID: PMC6280815 DOI: 10.3389/fmicb.2018.02606] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.
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Affiliation(s)
- Valerie De Anda
- 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, Eje Central Lázaro Cárdenas, Ciudad de México, Mexico
| | - Jazmín Blaz
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Augusto Cesar Poot-Hernández
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Ciudad Universitaria, Ciudad de México, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | | | - Niza Gámez-Tamariz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 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
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15
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Babilonia J, Conesa A, Casaburi G, Pereira C, Louyakis AS, Reid RP, Foster JS. Comparative Metagenomics Provides Insight Into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia. Front Microbiol 2018; 9:1359. [PMID: 29988640 PMCID: PMC6027182 DOI: 10.3389/fmicb.2018.01359] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
Stromatolites are organosedimentary build-ups that have formed as a result of the sediment trapping, binding and precipitating activities of microbes. Today, extant systems provide an ideal platform for understanding the structure, composition, and interactions between stromatolite-forming microbial communities and their respective environments. In this study, we compared the metagenomes of three prevalent stromatolite-forming microbial mat types in the Spaven Province of Hamelin Pool, Shark Bay located in Western Australia. These stromatolite-forming mat types included an intertidal pustular mat as well as a smooth and colloform mat types located in the subtidal zone. Additionally, the metagenomes of an adjacent, non-lithifying mat located in the upper intertidal zone were also sequenced for comparative purposes. Taxonomic and functional gene analyses revealed distinctive differences between the lithifying and non-lithifying mat types, which strongly correlated with water depth. Three distinct populations emerged including the upper intertidal non-lithifying mats, the intertidal pustular mats associated with unlaminated carbonate build-ups, and the subtidal colloform and smooth mat types associated with laminated structures. Functional analysis of metagenomes revealed that amongst stromatolite-forming mats there was an enrichment of photosynthesis pathways in the pustular stromatolite-forming mats. In the colloform and smooth stromatolite-forming mats, however, there was an increase in the abundance of genes associated with those heterotrophic metabolisms typically associated with carbonate mineralization, such as sulfate reduction. The comparative metagenomic analyses suggest that stromatolites of Hamelin Pool may form by two distinctive processes that are highly dependent on water depth. These results provide key insight into the potential adaptive strategies and synergistic interactions between microbes and their environments that may lead to stromatolite formation and accretion.
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Affiliation(s)
- Joany Babilonia
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Ana Conesa
- Department of Microbiology and Cell Science, Genetics Institute, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.,Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Giorgio Casaburi
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Cecile Pereira
- Department of Microbiology and Cell Science, Genetics Institute, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States.,EURA NOVA, Marseille, France
| | - Artemis S Louyakis
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - R Pamela Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Jamie S Foster
- Space Life Science Lab, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
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16
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Valdespino-Castillo PM, Hu P, Merino-Ibarra M, López-Gómez LM, Cerqueda-García D, González-De Zayas R, Pi-Puig T, Lestayo JA, Holman HY, Falcón LI. Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba. Front Microbiol 2018; 9:510. [PMID: 29666607 PMCID: PMC5891642 DOI: 10.3389/fmicb.2018.00510] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/06/2018] [Indexed: 01/23/2023] Open
Abstract
Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.
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Affiliation(s)
- Patricia M Valdespino-Castillo
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Ping Hu
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Martín Merino-Ibarra
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luz M López-Gómez
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Cerqueda-García
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Teresa Pi-Puig
- Instituto de Geología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Laboratorio Nacional de Geoquímica y Mineralogía, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Julio A Lestayo
- Centro de Investigaciones de Ecosistemas Costeros, Cayo Coco, Cuba
| | - Hoi-Ying Holman
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, Berkeley, CA, United States
| | - Luisa I Falcón
- Laboratorio de Ecología Bacteriana, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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17
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Louyakis AS, Gourlé H, Casaburi G, Bonjawo RME, Duscher AA, Foster JS. A year in the life of a thrombolite: comparative metatranscriptomics reveals dynamic metabolic changes over diel and seasonal cycles. Environ Microbiol 2017; 20:842-861. [DOI: 10.1111/1462-2920.14029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 12/01/2022]
Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Hadrien Gourlé
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
- Department of Animal Breeding and Genetics; Global Bioinformatics Centre, Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Rachelle M. E. Bonjawo
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Alexandrea A. Duscher
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
| | - Jamie S. Foster
- Department of Microbiology and Cell Science; University of Florida, Space Life Sciences Lab; Merritt Island FL USA
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18
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Berlanga M, Palau M, Guerrero R. Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats. Front Microbiol 2017; 8:2619. [PMID: 29312277 PMCID: PMC5744480 DOI: 10.3389/fmicb.2017.02619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 12/15/2017] [Indexed: 01/11/2023] Open
Abstract
Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France) were analyzed over 3 years during two different seasons (spring and autumn) and at different layers of the mat (0–2, 2–4, and 4–6 mm). To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i) inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii) a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%), followed by Archaea (∼4%) and Eukarya (∼1%). The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology) were significantly more abundant in the top layer (0–2 mm) than in the lower layers (2–4 and 4–6 mm). In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox reactions required for anaerobic respiration. Sulfatase genes had the highest relative abundance below 2 mm. Finally, chemotaxis signature genes peaked sharply at the oxic/photic and transitional oxic-anoxic boundary. This functional differentiation reflected the taxonomic diversity of the different layers of the mat.
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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 - Institut d'Investigació Biomédica de Bellvitge, Barcelona, Spain.,Academia Europaea-Barcelona Knowledge Hub, Barcelona, Spain
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19
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Bradley JA, Daille LK, Trivedi CB, Bojanowski CL, Stamps BW, Stevenson BS, Nunn HS, Johnson HA, Loyd SJ, Berelson WM, Corsetti FA, Spear JR. Carbonate-rich dendrolitic cones: insights into a modern analog for incipient microbialite formation, Little Hot Creek, Long Valley Caldera, California. NPJ Biofilms Microbiomes 2017; 3:32. [PMID: 29177068 PMCID: PMC5698408 DOI: 10.1038/s41522-017-0041-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/24/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
Ancient putative microbial structures that appear in the rock record commonly serve as evidence of early life on Earth, but the details of their formation remain unclear. The study of modern microbial mat structures can help inform the properties of their ancient counterparts, but modern mineralizing mat systems with morphological similarity to ancient structures are rare. Here, we characterize partially lithified microbial mats containing cm-scale dendrolitic coniform structures from a geothermal pool ("Cone Pool") at Little Hot Creek, California, that if fully lithified, would resemble ancient dendrolitic structures known from the rock record. Light and electron microscopy revealed that the cm-scale 'dendrolitic cones' were comprised of intertwined microbial filaments and grains of calcium carbonate. The degree of mineralization (carbonate content) increased with depth in the dendrolitic cones. Sequencing of 16S rRNA gene libraries revealed that the dendrolitic cone tips were enriched in OTUs most closely related to the genera Phormidium, Leptolyngbya, and Leptospira, whereas mats at the base and adjacent to the dendrolitic cones were enriched in Synechococcus. We hypothesize that the consumption of nutrients during autotrophic and heterotrophic growth may promote movement of microbes along diffusive nutrient gradients, and thus microbialite growth. Hour-glass shaped filamentous structures present in the dendrolitic cones may have formed around photosynthetically-produced oxygen bubbles-suggesting that mineralization occurs rapidly and on timescales of the lifetime of a bubble. The dendrolitic-conical structures in Cone Pool constitute a modern analog of incipient microbialite formation by filamentous microbiota that are morphologically distinct from any structure described previously. Thus, we provide a new model system to address how microbial mats may be preserved over geological timescales.
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Affiliation(s)
- James A. Bradley
- Department of Earth Sciences, University of Southern California, Los Angeles, CA USA
| | - Leslie K. Daille
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christopher B. Trivedi
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO USA
| | - Caitlin L. Bojanowski
- Soft Matter Materials Branch, Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright-Patterson AFB, OH 45433 USA
| | - Blake W. Stamps
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO USA
| | - Bradley S. Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
| | - Heather S. Nunn
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
| | - Hope A. Johnson
- Department of Biological Science, California State University, Fullerton, Fullerton, CA USA
| | - Sean J. Loyd
- Department of Geological Sciences, California State University, Fullerton, Fullerton, CA USA
| | - William M. Berelson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA USA
| | - Frank A. Corsetti
- Department of Earth Sciences, University of Southern California, Los Angeles, CA USA
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO USA
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20
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Mobberley JM, Lindemann SR, Bernstein HC, Moran JJ, Renslow RS, Babauta J, Hu D, Beyenal H, Nelson WC. Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat. FEMS Microbiol Ecol 2017; 93:3071443. [PMID: 28334407 PMCID: PMC5812542 DOI: 10.1093/femsec/fix028] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/13/2017] [Indexed: 02/06/2023] Open
Abstract
Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms; however, little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity and metabolic gradient measurements. Draft reconstructed genomes of 34 abundant organisms revealed three dominant cyanobacterial populations differentially distributed across the top layers of the mat suggesting niche separation along light and oxygen gradients. Many organisms contained diverse functional profiles, allowing for metabolic response to changing conditions within the mat. Organisms with partial nitrogen and sulfur metabolisms were widespread indicating dependence on metabolite exchange. In addition, changes in community spatial structure were observed over the diel. These results indicate that organisms within the mat community have adapted to the temporally dynamic environmental gradients in this hypersaline mat through metabolic flexibility and fluid syntrophic interactions, including shifts in spatial arrangements.
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Affiliation(s)
- Jennifer M Mobberley
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA.,Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
| | - Hans C Bernstein
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - James J Moran
- Chemical and Biological Signature Sciences, National Security Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Ryan S Renslow
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Jerome Babauta
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - Dehong Hu
- Environmental Molecular Sciences Laboratory, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Haluk Beyenal
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA 99164, USA
| | - William C Nelson
- Biological Science Division, Earth and Environmental Science Directorate, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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21
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Louyakis AS, Mobberley JM, Vitek BE, Visscher PT, Hagan PD, Reid RP, Kozdon R, Orland IJ, Valley JW, Planavsky NJ, Casaburi G, Foster JS. A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses. ASTROBIOLOGY 2017; 17:413-430. [PMID: 28520472 PMCID: PMC5767104 DOI: 10.1089/ast.2016.1563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems. Key Words: Thrombolites-Microbial diversity-Metagenome-Stable isotopes-Microbialites. Astrobiology 17, 413-430.
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Affiliation(s)
- Artemis S. Louyakis
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jennifer M. Mobberley
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Brooke E. Vitek
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut
| | - Paul D. Hagan
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - R. Pamela Reid
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, Florida
| | - Reinhard Kozdon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, New York
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Ian J. Orland
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - John W. Valley
- Department of Geoscience, University of Wisconsin, Madison, Wisconsin
| | - Noah J. Planavsky
- Department of Geology and Geophysics, Yale University, New Haven, Connecticut
| | - Giorgio Casaburi
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
| | - Jamie S. Foster
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Lab, Merritt Island, Florida
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