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Duperron S, Halary S, Bouly JP, Roussel T, Hugoni M, Bruto M, Oger PM, Duval C, Woo A, Jézéquel D, Ader M, Leboulanger C, Agogué H, Grossi V, Troussellier M, Bernard C. Transcriptomic insights into the dominance of two phototrophs throughout the water column of a tropical hypersaline-alkaline crater lake (Dziani Dzaha, Mayotte). Front Microbiol 2024; 15:1368523. [PMID: 38741748 PMCID: PMC11089139 DOI: 10.3389/fmicb.2024.1368523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Saline-alkaline lakes often shelter high biomasses despite challenging conditions, owing to the occurrence of highly adapted phototrophs. Dziani Dzaha (Mayotte) is one such lake characterized by the stable co-dominance of the cyanobacterium Limnospira platensis and the picoeukaryote Picocystis salinarum throughout its water column. Despite light penetrating only into the uppermost meter, the prevailing co-dominance of these species persists even in light- and oxygen-deprived zones. Here, a depth profile of phototrophs metatranscriptomes, annotated using genomic data from isolated strains, is employed to identify expression patterns of genes related to carbon processing pathways including photosynthesis, transporters and fermentation. The findings indicate a prominence of gene expression associated with photosynthesis, with a peak of expression around 1 m below the surface, although the light intensity is very low and only red and dark red wavelengths can reach it, given the very high turbidity linked to the high biomass of L. platensis. Experiments on strains confirmed that both species do grow under these wavelengths, at rates comparable to those obtained under white light. A decrease in the expression of photosynthesis-related genes was observed in L. platensis with increasing depth, whereas P. salinarum maintained a very high pool of psbA transcripts down to the deepest point as a possible adaptation against photodamage, in the absence and/or very low levels of expression of genes involved in protection. In the aphotic/anoxic zone, expression of genes involved in fermentation pathways suggests active metabolism of reserve or available dissolved carbon compounds. Overall, L. platensis seems to be adapted to the uppermost water layer, where it is probably maintained thanks to gas vesicles, as evidenced by high expression of the gvpA gene. In contrast, P. salinarum occurs at similar densities throughout the water column, with a peak in abundance and gene expression levels which suggests a better adaptation to lower light intensities. These slight differences may contribute to limited inter-specific competition, favoring stable co-dominance of these two phototrophs.
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Affiliation(s)
- Sébastien Duperron
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Sébastien Halary
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Jean-Pierre Bouly
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Théotime Roussel
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Myléne Hugoni
- Université Claude Bernard Lyon 1, CNRS, INSA de Lyon, UMR 5240 Microbiologie Adaptation et Pathogénie, University of Lyon, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Maxime Bruto
- Anses, UMR Mycoplasmoses Animales, VetAgro Sup, Université de Lyon, Marcy-l’Étoile, France
| | - Philippe M. Oger
- Université Claude Bernard Lyon 1, CNRS, INSA de Lyon, UMR 5240 Microbiologie Adaptation et Pathogénie, University of Lyon, Villeurbanne, France
| | - Charlotte Duval
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Anthony Woo
- Pôle Analyse de Données UAR 2700 2AD, Muséum National d’Histoire Naturelle, Paris, France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris, Université de Paris Cité, CNRS, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon-les-Bains, France
| | - Magali Ader
- Institut de Physique du Globe de Paris, Université de Paris Cité, CNRS, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon-les-Bains, France
| | | | - Hélène Agogué
- Littoral Environnement et Sociétés, UMR 7266, CNRS La Rochelle Université, La Rochelle, France
| | - Vincent Grossi
- LGL-TPE, UMR 5276, CNRS, ENSL, Université Claude Bernard Lyon 1, Villeurbanne, France
| | | | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
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Jung J, Loschko T, Reich S, Rassoul-Agha M, Werner MS. Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions. Proc Biol Sci 2024; 291:20232653. [PMID: 38471558 PMCID: PMC10932707 DOI: 10.1098/rspb.2023.2653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.
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Affiliation(s)
- Julie Jung
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tobias Loschko
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
- Max Planck Institute for Biology, Tübingen, Germany
| | - Shelley Reich
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Maxim Rassoul-Agha
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Michael S. Werner
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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3
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Bruto M, Oger PM, Got P, Bernard C, Melayah D, Cloarec LA, Duval C, Escalas A, Duperron S, Guigard L, Leboulanger C, Ader M, Sarazin G, Jézéquel D, Agogué H, Troussellier M, Hugoni M. Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome. Mol Ecol 2023; 32:6824-6838. [PMID: 37901963 DOI: 10.1111/mec.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023]
Abstract
Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co-dominate: a cyanobacterium, Arthrospira fusiformis, and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell-sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non-negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free-living microbiome (i.e. present in the 3-0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free-living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.
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Affiliation(s)
- Maxime Bruto
- VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | - Philippe M Oger
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Patrice Got
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Delphine Melayah
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Lilian A Cloarec
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Charlotte Duval
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Arthur Escalas
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Ludivine Guigard
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | | | - Magali Ader
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon, France
| | - Hélène Agogué
- LIENSs, UMR7266, La Rochelle Université - CNRS, La Rochelle, France
| | | | - Mylène Hugoni
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
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4
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Şahin Doğan S, Kocabaş A. Seasonal dynamics of eukaryotic microbial diversity in hypersaline Tuz Lake characterized by 18S rDNA sequencing. J Eukaryot Microbiol 2023; 70:e12993. [PMID: 37528557 DOI: 10.1111/jeu.12993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/23/2023] [Accepted: 07/18/2023] [Indexed: 08/03/2023]
Abstract
Microbial diversity found in hypersaline ecosystems is structurally unique and essential in many microbiological and ecological processes. Tuz Lake, the second biggest lake in Türkiye, is a talassohaline (over 32% [w/v]) lake with near-neutral pH. The aim of study was to investigate the composition of the eukaryotic microbial community in Tuz Lake by 18S rDNA amplicon sequencing, as well as its relationship and change with environmental factors during 1-year period. Next-generation sequencing and bioinformatic analysis were applied to describe the eukaryotic microbial community in Tuz Lake. As a result of bioinformatics analysis, Archaeplastida (39%) and Stramenopiles, Alveolata, Rhizaria (SAR) (51%) were the most abundant taxa represented in the dataset. The Archaeplastida phylum showed a significant difference between winter and summer and higher abundance in summer in contrast to the SAR group, which represented higher abundance in winter. Genus level assessment showed that the most abundant genera were Navicula, Chlorophyta;unclassified_taxa, Dunaliella, Cladosporium, Paraphelidium, Scuticociliates;unclassified_taxa, and Chlamydomonadales;unclassified_taxa. Navicula abundance was significantly different and overwhelmingly dominant in winter. On the other hand, Cladosporium and Chlorophyta; unclassified_taxa represented a significant difference between seasons and high abundance in summer. Furthermore, Dunaliella populations were not detected in midsummer and early fall when the temperature increased and water volume in the lake decreased.
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Affiliation(s)
- Suzan Şahin Doğan
- Biology Department, KO Science Faculty of Karamanoglu Mehmetbey University, Karaman, Turkey
| | - Aytaç Kocabaş
- Biology Department, KO Science Faculty of Karamanoglu Mehmetbey University, Karaman, Turkey
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Maucourt F, Cébron A, Budzinski H, Le Menach K, Peluhet L, Czarnes S, Melayah D, Chapulliot D, Vallon L, Plassart G, Hugoni M, Fraissinet-Tachet L. Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield. MICROBIAL ECOLOGY 2023; 86:1696-1708. [PMID: 36646913 DOI: 10.1007/s00248-022-02161-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.
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Affiliation(s)
- Flavien Maucourt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
- ENVISOL, 2-4 Rue Hector Berlioz, 38110, La Tour du Pin, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | | | | | | | - Sonia Czarnes
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
| | - Delphine Melayah
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
- Univ Lyon, INSA Lyon, CNRS, UMR 5240 Microbiologie Adaptation Et Pathogénie, 69621, Villeurbanne, France
| | - David Chapulliot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
| | - Laurent Vallon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
| | - Gaël Plassart
- ENVISOL, 2-4 Rue Hector Berlioz, 38110, La Tour du Pin, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
- Univ Lyon, INSA Lyon, CNRS, UMR 5240 Microbiologie Adaptation Et Pathogénie, 69621, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
| | - Laurence Fraissinet-Tachet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France.
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6
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Melayah D, Bontemps Z, Bruto M, Nguyen A, Oger P, Hugoni M. Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems. Methods Mol Biol 2022; 2605:17-35. [PMID: 36520387 DOI: 10.1007/978-1-0716-2871-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.
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Affiliation(s)
- Delphine Melayah
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Zélia Bontemps
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | | | - Philippe Oger
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Mylène Hugoni
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France.
- Institut Universitaire de France (IUF), Paris, France.
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Bacteria Associated with Benthic Invertebrates from Extreme Marine Environments: Promising but Underexplored Sources of Biotechnologically Relevant Molecules. Mar Drugs 2022; 20:md20100617. [DOI: 10.3390/md20100617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Microbe–invertebrate associations, commonly occurring in nature, play a fundamental role in the life of symbionts, even in hostile habitats, assuming a key importance for both ecological and evolutionary studies and relevance in biotechnology. Extreme environments have emerged as a new frontier in natural product chemistry in the search for novel chemotypes of microbial origin with significant biological activities. However, to date, the main focus has been microbes from sediment and seawater, whereas those associated with biota have received significantly less attention. This review has been therefore conceived to summarize the main information on invertebrate–bacteria associations that are established in extreme marine environments. After a brief overview of currently known extreme marine environments and their main characteristics, a report on the associations between extremophilic microorganisms and macrobenthic organisms in such hostile habitats is provided. The second part of the review deals with biotechnologically relevant bioactive molecules involved in establishing and maintaining symbiotic associations.
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Cadeau P, Cartigny P, Thomazo C, Jézéquel D, Leboulanger C, Sarazin G, Ader M. The Dziani Dzaha Lake: A long-awaited modern analogue for superheavy pyrites. GEOBIOLOGY 2022; 20:444-461. [PMID: 35064739 DOI: 10.1111/gbi.12486] [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: 03/04/2021] [Revised: 10/22/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Sedimentary records of superheavy pyrites in Phanerozoic and Proterozoic successions (i.e., extremely positive δ34 Spyrite values together with higher δ34 Spyrite than coeval δ34 SCAS ) are mostly interpreted as resulting either from secondary postdepositional processes or from multiple redox reactions between sulfate and sulfide in stratified sulfate-poor environments. We report here the first observation of strongly positive δ34 S values for both dissolved sulfate and sulfide (average δ34 Sdiss.sulfate value of 34.6‰ and δ34 Sdiss.sulfide values of 36.7‰) compared to the present-day seawater δ34 Sdiss .sulfate (~21‰), with a negative apparent fractionation between sulfate and sulfide (∆34 Sdiss.sulfate-diss.sulfide ~ -2.1 ± 1.4‰), in the sulfate-poor (<3 mm) modern thalassohaline lacustrine system Dziani Dzaha (Mayotte, Indian Ocean). Overall, surface sediments faithfully record the water column isotopic signatures including a mainly negative ∆34 Ssed.sulfate-sed.sulfide (-4.98 ± 4.5‰), corresponding to the definition of superheavy pyrite documented in the rock record. We propose that in the Dziani Dzaha this superheavy pyrite signature results from a two-stage evolution of the sulfur biogeochemical cycle. In a first stage, the sulfur cycle would have been dominated by sulfate from initially sulfate-rich marine waters. Overtime, Raleigh distillation by microbial sulfate reduction coupled with sulfide burial in the sediment would have progressively enriched in 34 S the water column residual sulfate. In a second still active stage, quantitative sulfate reduction not only occurs below the halocline during stratified periods but also in the whole water column during fully anoxic episodes. Sulfates are then regenerated by partial oxidation of sulfides as the oxic-anoxic interface moves downward. These results demonstrate that the atypical superheavy pyrite isotope signature does not necessarily require postdepositional or secondary oxidative processes and can result from primary processes in restricted sulfate-poor and highly productive environments analogous to the Dziani Dzaha.
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Affiliation(s)
- Pierre Cadeau
- Université de Paris, Institut de physique du globe de Paris, CNRS, Paris, France
| | - Pierre Cartigny
- Université de Paris, Institut de physique du globe de Paris, CNRS, Paris, France
| | - Christophe Thomazo
- Biogéosciences, UMR CNRS 6282, Université de Bourgogne Franche-Comté, Dijon, France
- Institut Universitaire de France, Paris, France
| | - Didier Jézéquel
- Université de Paris, Institut de physique du globe de Paris, CNRS, Paris, France
- UMR CARRTEL, INRAE &, Université Savoie Mont Blanc, Thonon-les-Bains, France
| | | | - Gérard Sarazin
- Université de Paris, Institut de physique du globe de Paris, CNRS, Paris, France
| | - Magali Ader
- Université de Paris, Institut de physique du globe de Paris, CNRS, Paris, France
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9
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Sala D, Grossi V, Agogué H, Leboulanger C, Jézéquel D, Sarazin G, Antheaume I, Bernard C, Ader M, Hugoni M. Influence of aphotic haloclines and euxinia on organic biomarkers and microbial communities in a thalassohaline and alkaline volcanic crater lake. GEOBIOLOGY 2022; 20:292-309. [PMID: 34687126 DOI: 10.1111/gbi.12477] [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: 12/23/2020] [Revised: 09/29/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Studies on microbial communities, and their associated organic biomarkers, that are found thriving in the aphotic euxinic waters in modern stratified ecosystems are scarce compared to those undertaken in euxinic photic zones. The Dziani Dzaha (Mayotte, Indian Ocean) is a tropical, saline, alkaline crater lake that has recently been presented as a modern analog of Proterozoic Oceans due to its thalassohaline classification (having water of marine origin) and specific biogeochemical characteristics. Continuous intense photosynthetic production and microbial mineralization keep most of the water column permanently aphotic and anoxic preventing the development of a euxinic (sulfidic and anoxic) photic zone despite a high sulfide/sulfate ratio and the presence of permanent or seasonal haloclines. In this study, the molecular composition of the organic matter in Lake Dziani Dzaha was investigated and compared to the microbial diversity evaluated through 16S rRNA gene amplicon sequencing, over two contrasting seasons (rainy vs. dry) that influence water column stratification. Depth profiles of organic biomarker concentrations (chlorophyll-a and lipid biomarkers) and bacterial and archaeal OTU abundances appeared to be strongly dependent on the presence of aphotic haloclines and euxinia. OTU abundances revealed the importance of specific haloalkaliphilic bacterial and archaeal assemblages in phytoplanktonic biomass recycling and the biogeochemical functioning of the lake, suggesting new haloalkaline non-phototrophic anaerobic microbial precursors for some of the lipid biomarkers. Uncultured Firmicutes from the family Syntrophomonadaceae (Clostridiales), and Bacteroidetes from the ML635J-40 aquatic group, emerged as abundant chemotrophic bacterial members in the anoxic or euxinic waters and were probably responsible for the production of short-chain n-alkenes, wax esters, diplopterol, and tetrahymanol. Halocline-dependent euxinia also had a strong impact on the archaeal community which was dominated by Woesearchaeota in the sulfide-free waters. In the euxinic waters, methanogenic Euryarchaeota from the Methanomicrobia, Thermoplasmata, and WSA2 classes dominated and were likely at the origin of common hydrocarbon biomarkers of methanogens (phytane, pentamethyl-eicosenes, and partially hydrogenated squalene).
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Affiliation(s)
- David Sala
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENSL, UJM, LGL-TPE, Villeurbanne, France
| | - Vincent Grossi
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENSL, UJM, LGL-TPE, Villeurbanne, France
| | - Hélène Agogué
- LIENSs, UMR 7266, La Rochelle Université - CNRS, La Rochelle, France
| | | | - Didier Jézéquel
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
- INRAE & Université Savoie Mont Blanc, UMR CARRTEL, Thonon-les-Bains, France
| | - Gérard Sarazin
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
| | - Ingrid Antheaume
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENSL, UJM, LGL-TPE, Villeurbanne, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris, France
| | - Magali Ader
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, Villeurbanne, France
- Univ Lyon, INSA Lyon, CNRS, UMR 5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
- Institut Universitaire de France, Paris, France
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10
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Korbel KL, Greenfield P, Hose GC. Agricultural practices linked to shifts in groundwater microbial structure and denitrifying bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150870. [PMID: 34627912 DOI: 10.1016/j.scitotenv.2021.150870] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/21/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Irrigation enhances the connectivity between the surface and groundwater by facilitating the transport of energy sources and oxygen. When combined with fertilisers, the impact on groundwater microbial communities and their interactions with nitrogen cycling in aquifers is poorly understood. This study examines the impact of different landuses (irrigated and non-irrigated) on groundwater microbial communities. A total of 38 wells accessing shallow aquifers in three sub-catchments of the Murray Darling Basin, Australia, were sampled for water chemistry and microbial community structure using environmental DNA (eDNA) techniques. All sub-catchments showed evidence of intense irrigation and groundwater contamination with total nitrogen, nitrates and phosphorus concentrations often well above background, with total nitrogen concentrations up to 70 mg/L and nitrate concentration up to 18 mg/L. Across sub-catchments there was high microbial diversity, with differences in community structure and function between catchments and landuses. Of the 1100 operational taxonomic units (OTUs) recorded, 47 OTUs were common across catchments with species from Woesearchaeota, Nitrospirales, Nitrosopumilales and Acidobacter taxonomic groups contributing greatly to groundwater microbial communities. Within non-irrigated sites, groundwaters contained similar proportions of nitrifying and denitrifying capable taxa, whereas irrigated sites had significantly higher abundances of microbes with nitrifying rather than denitrifying capabilities. Microbial diversity was lower in irrigated sites in the Macquarie catchment. These results indicate that irrigated landuses impact microbial community structure and diversity within groundwaters and suggest that the ratios of denitrifying to nitrifying capable microbes as well as specific orders (e.g., Nitrososphaerales) may be useful to indicate long-term nitrogen contamination of groundwaters. Such research is important for understanding the biogeochemical processes that are key predictors of redox state and contamination of groundwater by N species and other compounds. This will help to predict human impacts on groundwater microbial structure, diversity, and ecosystem functions, aiding the long-term management groundwater resources.
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Affiliation(s)
- K L Korbel
- Department of Biological Sciences, Macquarie University, Australia.
| | | | - G C Hose
- Department of Biological Sciences, Macquarie University, Australia
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11
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Escalas A, Troussellier M, Melayah D, Bruto M, Nicolas S, Bernard C, Ader M, Leboulanger C, Agogué H, Hugoni M. Strong reorganization of multi-domain microbial networks associated with primary producers sedimentation from oxic to anoxic conditions in an hypersaline lake. FEMS Microbiol Ecol 2021; 97:6464137. [PMID: 34918080 DOI: 10.1093/femsec/fiab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/14/2021] [Indexed: 11/14/2022] Open
Abstract
Understanding the role of microbial interactions in the functioning of natural systems is often impaired by the levels of complexity they encompass. In this study, we used the relative simplicity of an hypersaline crater lake hosting only microbial organisms (Dziani Dzaha) to provide a detailed analysis of the microbial networks including the three domains of life. We identified two main ecological zones, one euphotic and oxic zone in surface, where two phytoplanktonic organisms produce a very high biomass, and one aphotic and anoxic deeper zone, where this biomass slowly sinks and undergoes anaerobic degradation. We highlighted strong differences in the structure of microbial communities from the two zones and between the microbial consortia associated with the two primary producers. Primary producers sedimentation was associated with a major reorganization of the microbial network at several levels: global properties, modules composition, nodes and links characteristics. We evidenced the potential dependency of Woesearchaeota to the primary producers' exudates in the surface zone, and their disappearance in the deeper anoxic zone, along with the restructuration of the networks in the anoxic zone toward the decomposition of the organic matter. Altogether, we provided an in-depth analysis of microbial association network and highlighted putative changes in microbial interactions supporting the functioning of the two ecological zones in this unique ecosystem.
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Affiliation(s)
- Arthur Escalas
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Marc Troussellier
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Delphine Melayah
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, 43 bd du 11 novembre 1918, 69622 Villeurbanne, France
| | - Sébastien Nicolas
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, CP 39, 75005 Paris, France
| | - Magali Ader
- Université de Paris, Institut de physique du globe de Paris, CNRS, 75005 Paris, France
| | - Christophe Leboulanger
- MARBEC, Université de Montpellier, CNRS, IRD, IFREMER, Place Eugène Bataillon, Case 093, 34 095 Montpellier Cedex 5, France
| | - Hélène Agogué
- Littoral Environnement et Sociétés (LIENSs) UMR 7266 CNRS -La Rochelle Université, 17000 La Rochelle, France
| | - Mylène Hugoni
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.,Institut Universitaire de France (IUF)
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12
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Azpiazu-Muniozguren M, Perez A, Rementeria A, Martinez-Malaxetxebarria I, Alonso R, Laorden L, Gamboa J, Bikandi J, Garaizar J, Martinez-Ballesteros I. Fungal Diversity and Composition of the Continental Solar Saltern in Añana Salt Valley (Spain). J Fungi (Basel) 2021; 7:1074. [PMID: 34947056 PMCID: PMC8703443 DOI: 10.3390/jof7121074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 12/19/2022] Open
Abstract
The Añana Salt Valley in Spain is an active continental solar saltern formed 220 million years ago. To date, no fungal genomic studies of continental salterns have been published, although DNA metabarcoding has recently expanded researchers' ability to study microbial community structures. Accordingly, the aim of this present study was to evaluate fungal diversity using the internal transcribed spacer (ITS) metabarcoding at different locations along the saltern (springs, ponds, and groundwater) to describe the fungal community of this saline environment. A total of 380 fungal genera were detected. The ubiquity of Saccharomyces was observed in the saltern, although other halotolerant and halophilic fungi like Wallemia, Cladosporium, and Trimmatostroma were also detected. Most of the fungi observed in the saltern were saprotrophs. The fungal distribution appeared to be influenced by surrounding conditions, such as the plant and soil contact, cereal fields, and vineyards of this agricultural region.
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Affiliation(s)
- Maia Azpiazu-Muniozguren
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Alba Perez
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Aitor Rementeria
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Spain;
| | - Irati Martinez-Malaxetxebarria
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Rodrigo Alonso
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Lorena Laorden
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Javier Gamboa
- Biogenetics, Portal de Zurbano 3, 6-B, 01013 Vitoria-Gasteiz, Spain;
| | - Joseba Bikandi
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Javier Garaizar
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
| | - Ilargi Martinez-Ballesteros
- MikroIker Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy, University of the Basque Country UPV/EHU, Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain; (M.A.-M.); (A.P.); (I.M.-M.); (R.A.); (L.L.); (J.B.); (J.G.)
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13
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Zhu J, Li T, Liao C, Li N, Wang X. A promising destiny for Feammox: From biogeochemical ammonium oxidation to wastewater treatment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 790:148038. [PMID: 34090165 DOI: 10.1016/j.scitotenv.2021.148038] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
Ammonium is one of the most common forms of nitrogen that exists in wastewater, and it can cause severe pollution when it is discharged without treatment. New technologies must be developed to effectively remove ammonium because conventional nitrification-denitrification methods are limited by the lack of organic carbon. Anaerobic ammonium oxidation coupled to Fe(III) reduction is known as Feammox, and is a recently discovered nitrogen cycling process. Feammox can proceed under autotrophic or anaerobic conditions and effectively transforms ammonium to stable, innocuous dinitrogen gas, using the ferric iron as an electron acceptor. This method is cost-effective, environmentally friendly, and conducive to joint application with other nitrogen removal reactions in low-C/N municipal wastewater treatments. This review provides a comprehensive survey of Feammox mechanistic investigations and presents studies regarding the functional microorganism colonies. The potential for Feammox to be applied for the removal of nitrogen from various polluted water sources and the combination of the Feammox process with other frontier environmental technologies are also discussed. In addition, future perspectives for removing ammonium using Feammox are presented.
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Affiliation(s)
- Jiaxuan Zhu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Tian Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Chengmei Liao
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
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14
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Hugoni M, Nunan N, Thioulouse J, Dubost A, Abrouk D, Martins JMF, Goffner D, Prigent-Combaret C, Grundmann G. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. MICROBIAL ECOLOGY 2021; 82:470-483. [PMID: 33443587 DOI: 10.1007/s00248-020-01660-0] [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: 07/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.
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Affiliation(s)
- Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France.
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences - Paris, CNRS - Sorbonne Université, 4 place Jussieu, 75005, Paris, France
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Jean Thioulouse
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Jean M F Martins
- Université Grenoble Alpes, CNRS, IRD, IGE UMR 5001, 38000, Grenoble, France
| | - Deborah Goffner
- Unité Mixte Internationale CNRS 3189 « Environment, Health and Societies », Faculté de Médecine, 51 Bd Pierre Dramard, 13344, Marseille, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Geneviève Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
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15
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Morphology and Ecology of Two New Amoebae, Isolated From a Thalassohaline Lake, Dziani Dzaha. Protist 2020; 171:125770. [PMID: 33166717 DOI: 10.1016/j.protis.2020.125770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 09/08/2020] [Accepted: 09/29/2020] [Indexed: 12/28/2022]
Abstract
Dziani Dzaha is a hypersaline lake (Mayotte island), whose microbial community is dominated by photosynthetic microorganisms. Here, we describe two new free-living heteroloboseans. One belonging to the Pharyngomonas genus and the other, whose 18S rRNA gene sequence shares only 85% homology to its closest relatives Euplaesiobystra hypersalinica, was proposed as a new species of this genus being called Euplaesiobystra dzianiensis. Both strains were salt tolerant to 75‰ and grew between 25 and 37°C. Their distribution patterns varied seasonally and depended also on depth. Noticeably, both free-living amoebae isolates were able to graze on Arthrospira filaments, which are found within the same water layer. In conclusion, we document for the first time the presence and ecology of free-living amoebae in the thalassohaline lake Dziani Dzaha, and describe a new species of the Euplaesiobystra genus.
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16
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Carbon isotope evidence for large methane emissions to the Proterozoic atmosphere. Sci Rep 2020; 10:18186. [PMID: 33097795 PMCID: PMC7585424 DOI: 10.1038/s41598-020-75100-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/08/2020] [Indexed: 11/08/2022] Open
Abstract
The Proterozoic Era records two periods of abundant positive carbon isotope excursions (CIEs), conventionally interpreted as resulting from increased organic carbon burial and leading to Earth’s surface oxygenation. As strong spatial variations in the amplitude and duration of these excursions are uncovered, this interpretation is challenged. Here, by studying the carbon cycle in the Dziani Dzaha Lake, we propose that they could be due to regionally variable methane emissions to the atmosphere. This lake presents carbon isotope signatures deviated by ~ + 12‰ compared to the modern ocean and shares a unique combination of analogies with putative Proterozoic lakes, interior seas or restricted epireic seas. A simple box model of its Carbon cycle demonstrates that its current isotopic signatures are due to high primary productivity, efficiently mineralized by methanogenesis, and to subsequent methane emissions to the atmosphere. By analogy, these results might allow the reinterpretation of some positive CIEs as at least partly due to regionally large methane emissions. This supports the view that methane may have been a major greenhouse gas during the Proterozoic Era, keeping the Earth from major glaciations, especially during periods of positive CIEs, when increased organic carbon burial would have drowned down atmospheric CO2.
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17
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Ding B, Qin Y, Luo W, Li Z. Spatial and seasonal distributions of Feammox from ecosystem habitats in the Wanshan region of the Taihu watershed, China. CHEMOSPHERE 2020; 239:124742. [PMID: 31514005 DOI: 10.1016/j.chemosphere.2019.124742] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/21/2019] [Accepted: 08/31/2019] [Indexed: 06/10/2023]
Abstract
Anaerobic ammonium oxidation coupled to Fe(III) reduction, termed Feammox, is a newly identified microbial process that occurs in nitrogen and iron cycles. As the seasonal distribution of Feammox in different ecosystem habitats has not been fully explored, this study investigated the potential Feammox rates and the diversity and abundance of iron reducing bacteria (IRB) in three habitats during two seasons by using isotope tracing technique and molecular analysis, respectively. Results showed that potential Feammox rates vary both seasonally and spatially, having relatively higher rates in summer (0.05-0.19 mg N kg-1 d-1) and lower rates in winter (0.02-0.09 mg N kg-1 d-1). In addition, relatively higher and lower rates were observed in farmland soils (0.09-0.19 mg N kg-1 d-1) and river sediments (0.02-0.05 mg N kg-1 d-1), respectively. The abundance and diversity of IRB were also found to vary both spatially and seasonally. Furthermore, the results show that Feammox may transform nitrogen at a rate of approximately 2.4-22.5 kg N ha-1 yr-1 within the investigated area. It is considered that the soil moisture, the Fe(III) content, and the total organic carbon are important factors controlling Feammox and IRB. Overall, these results extend current scientific knowledge about nitrogen and iron cycles in ecosystem habitats.
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Affiliation(s)
- Bangjing Ding
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Yunbin Qin
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Wenqi Luo
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China
| | - Zhengkui Li
- State Key Laboratory of Pollution Control and Resource Reuse, Nanjing University, Nanjing, 210023, China; School of the Environment, Nanjing University, Nanjing, 210023, China.
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18
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Bernard C, Escalas A, Villeriot N, Agogué H, Hugoni M, Duval C, Carré C, Got P, Sarazin G, Jézéquel D, Leboulanger C, Grossi V, Ader M, Troussellier M. Very Low Phytoplankton Diversity in a Tropical Saline-Alkaline Lake, with Co-dominance of Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). MICROBIAL ECOLOGY 2019; 78:603-617. [PMID: 30729265 PMCID: PMC6744573 DOI: 10.1007/s00248-019-01332-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/16/2019] [Indexed: 05/03/2023]
Abstract
Lake Dziani Dzaha (Mayotte Island, Indian Ocean) is a tropical thalassohaline lake which geochemical and biological conditions make it a unique aquatic ecosystem considered as a modern analogue of Precambrian environments. In the present study, we focused on the diversity of phytoplanktonic communities, which produce very high and stable biomass (mean2014-2015 = 652 ± 179 μg chlorophyll a L-1). As predicted by classical community ecology paradigms, and as observed in similar environments, a single species is expected to dominate the phytoplanktonic communities. To test this hypothesis, we sampled water column in the deepest part of the lake (18 m) during rainy and dry seasons for two consecutive years. Phytoplanktonic communities were characterized using a combination of metagenomic, microscopy-based and flow cytometry approaches, and we used statistical modeling to identify the environmental factors determining the abundance of dominant organisms. As hypothesized, the overall diversity of the phytoplanktonic communities was very low (15 OTUs), but we observed a co-dominance of two, and not only one, OTUs, viz., Arthrospira fusiformis (Cyanobacteria) and Picocystis salinarum (Chlorophyta). We observed a decrease in the abundance of these co-dominant taxa along the depth profile and identified the adverse environmental factors driving this decline. The functional traits measured on isolated strains of these two taxa (i.e., size, pigment composition, and concentration) are then compared and discussed to explain their capacity to cope with the extreme environmental conditions encountered in the aphotic, anoxic, and sulfidic layers of the water column of Lake Dziani Dzaha.
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Affiliation(s)
- C Bernard
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France.
| | - A Escalas
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - N Villeriot
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - H Agogué
- UMR 7266 LIENSs, Université de La Rochelle - CNRS, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - M Hugoni
- UMR 5557 Ecologie Microbienne, Université Lyon 1 - CNRS - INRA, 69220, Villeurbanne Cedex, France
| | - C Duval
- UMR 7245 MCAM, Muséum National d'Histoire Naturelle - CNRS, 57 Rue Cuvier, CP 39, 75231, Paris Cedex 05, France
| | - C Carré
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - P Got
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - G Sarazin
- UMR 7154 Institut de Physique du Globe de Paris - Sorbonne Paris Cité, Université Paris Diderot, 1 rue de Jussieu, 75005, Paris, France
| | - D Jézéquel
- UMR 7154 Institut de Physique du Globe de Paris - Sorbonne Paris Cité, Université Paris Diderot, 1 rue de Jussieu, 75005, Paris, France
| | - C Leboulanger
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
| | - V Grossi
- Laboratoire de Géologie de Lyon, Université de Lyon - CNRS - UCBL - ENSL, 69220 Villeurbanne, France
| | - M Ader
- UMR 7154 Institut de Physique du Globe de Paris - Sorbonne Paris Cité, Université Paris Diderot, 1 rue de Jussieu, 75005, Paris, France
| | - M Troussellier
- UMR 9190 MARBEC, CNRS - Université de Montpellier - IRD - IFREMER, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France
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Singer GAC, Fahner NA, Barnes JG, McCarthy A, Hajibabaei M. Comprehensive biodiversity analysis via ultra-deep patterned flow cell technology: a case study of eDNA metabarcoding seawater. Sci Rep 2019; 9:5991. [PMID: 30979963 PMCID: PMC6461652 DOI: 10.1038/s41598-019-42455-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/01/2019] [Indexed: 11/09/2022] Open
Abstract
The characterization of biodiversity is a crucial element of ecological investigations as well as environmental assessment and monitoring activities. Increasingly, amplicon-based environmental DNA metabarcoding (alternatively, marker gene metagenomics) is used for such studies given its ability to provide biodiversity data from various groups of organisms simply from analysis of bulk environmental samples such as water, soil or sediments. The Illumina MiSeq is currently the most popular tool for carrying out this work, but we set out to determine whether typical studies were reading enough DNA to detect rare organisms (i.e., those that may be of greatest interest such as endangered or invasive species) present in the environment. We collected sea water samples along two transects in Conception Bay, Newfoundland and analyzed them on the MiSeq with a sequencing depth of 100,000 reads per sample (exceeding the 60,000 per sample that is typical of similar studies). We then analyzed these same samples on Illumina's newest high-capacity platform, the NovaSeq, at a depth of 7 million reads per sample. Not surprisingly, the NovaSeq detected many more taxa than the MiSeq thanks to its much greater sequencing depth. However, contrary to our expectations this pattern was true even in depth-for-depth comparisons. In other words, the NovaSeq can detect more DNA sequence diversity within samples than the MiSeq, even at the exact same sequencing depth. Even when samples were reanalyzed on the MiSeq with a sequencing depth of 1 million reads each, the MiSeq's ability to detect new sequences plateaued while the NovaSeq continued to detect new sequence variants. These results have important biological implications. The NovaSeq found 40% more metazoan families in this environment than the MiSeq, including some of interest such as marine mammals and bony fish so the real-world implications of these findings are significant. These results are most likely associated to the advances incorporated in the NovaSeq, especially a patterned flow cell, which prevents similar sequences that are neighbours on the flow cell (common in metabarcoding studies) from being erroneously merged into single spots by the sequencing instrument. This study sets the stage for incorporating eDNA metabarcoding in comprehensive analysis of oceanic samples in a wide range of ecological and environmental investigations.
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Affiliation(s)
- G A C Singer
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - N A Fahner
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - J G Barnes
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - A McCarthy
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada
| | - M Hajibabaei
- Centre for Environmental Genomics Applications, eDNAtec Inc., St. John's, NL, Canada.
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada.
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