Estelle Couradeau

Estelle Couradeau
Pennsylvania State University | Penn State · Department of Ecosystem Science and Management

Ph.D.

About

62
Publications
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1,218
Citations

Publications

Publications (62)
Article
Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active g...
Chapter
Since the 1980s, the quantity of sequence data has boomed by seven orders of magnitude. These successive technical revolutions, among others, have allowed us to begin shedding light on complex microbial communities. Here, we consolidate literature on the most recent and innovative methods that could be applied to the study of microbial consortia fr...
Article
Full-text available
Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes...
Chapter
Soil is Nature’s support medium for plant growth, but soils on only 12% of Earth’s land area possess the inherent physical requirements to function for long periods as cropland. One-fourth of this land is now moderately to severely degraded, and efforts are now underway to determine the best means to increase their productivity by improving soil he...
Article
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Letter to the Editor of the European Journal of Soil Science as a reaction to the Russell Review by Phillipe Baveye “Bypass and hyperbole in soil research: worrisome practices critically reviewed through examples” and to his follow‐up Invited Opinion paper “Bypass and hyperbole in soil research: a personal view on plausible causes and possible reme...
Article
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Cueva de la Mora (CM) is an acidic, meromictic pit lake in the Iberian Pyrite Belt characterized by extremely high metal(loid) concentrations and strong gradients in oxygen, metal, and nutrient concentrations. We hypothesized that geochemical variations with depth would result in differences in community composition and in metal resistance strategi...
Article
Stable isotope signatures of elements related to life such as carbon and nitrogen can be powerful biomarkers that provide key information on the biological origin of organic remains and their paleoenvironments. Marked advances have been achieved in the last decade in our understanding of the coupled evolution of biological carbon and nitrogen cycli...
Chapter
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En el presente libro, se describe en detalle el axalapazco Alchichica, un cráter volcánico de casi dos kilómetros de diámetro que alberga un Iago de hasta sesenta metros de profundidad con aguas de color azul turquesa. En esta isla acuática se ha desarrollado una comunidad de organismos únicos en el mundo (microendémicos), protagonistas de la ecolo...
Article
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The ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. Here, we use BONCAT (bioorthogonal non-canonical amino acid tagging) to measure translationally active cells in soils. We compare the active population of two soil depths from Oak Ridge (T...
Article
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Plant roots and bacteria are capable of buffering erratic fluctuations of water content in their local soil environment by releasing a diverse, highly polymeric blend of substances (e.g. extracellular polymeric substances [EPS] and mucilage). Although this concept is well accepted, the physical mechanisms by which EPS and mucilage interact with the...
Article
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Background: Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenome...
Article
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Background Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentous, non-nitrogen-fixing cyanobacterium Microcoleus vaginatus is a pioneer primary producer, often the dominant member of the biocru...
Preprint
Full-text available
Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes...
Preprint
Full-text available
Background. Metagenomics has transformed our understanding of microbial diversity across ecosystems, with recent advances enabling de novo assembly of genomes from metagenomes. These metagenome-assembled genomes are critical to provide ecological, evolutionary, and metabolic context for all the microbes and viruses yet to be cultivated. Metagenomes...
Preprint
Full-text available
The ability to link soil microbial diversity to soil processes requires technologies that differentiate active subpopulations of microbes from so-called relic DNA and dormant cells. Measures of microbial activity based on various techniques including DNA labelling has suggested that most cells in soils are inactive, a fact that has been difficult t...
Article
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Aims Biological soil crusts (biocrusts) are microbial communities commonly found in the upper layer of arid soils. These microorganisms release exopolysaccharides (EPS), which form the exopolymeric matrix (EPM), allowing them to bond soil particles together and survive long periods of dryness. The aim of this work is to develop methods for measurin...
Article
Full-text available
Biological soil crusts (biocrusts) are millimeter-sized microbial communities developing on the topsoils of arid lands that cover some 12% of Earth's continental area. Biocrusts consist of an assemblage of mineral soil particles consolidated into a crust by microbial organic polymeric substances that are mainly produced by filamentous bundle-formin...
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While significant efforts have been invested in reconstructing the early evolution of the Earth's atmosphere-ocean-biosphere biogeochemical nitrogen cycle, the potential role of an early continental contribution by a terrestrial, microbial phototrophic biosphere has been largely overlooked. By transposing to the Archean nitrogen fluxes of modern to...
Article
Full-text available
Biological soil crusts (biocrusts) account for a substantial portion of primary production in dryland ecosystems. They successionally mature to deliver a suite of ecosystem services, such as carbon sequestration, water retention and nutrient cycling, and climate regulation. Biocrust assemblages are extremely well adapted to survive desiccation and...
Article
Anoxygenic phototrophic bacteria (APBs) occur in a wide range of aquatic habitats, from hot springs to freshwater lakes and intertidal microbial mats. Here, we report the discovery of a novel niche for APBs: endoliths within marine littoral carbonates. In a study of 40 locations around Isla de Mona, Puerto Rico, and Menorca, Spain, 16S rRNA high-th...
Article
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Endolithic microbial communities are prominent features of intertidal marine habitats, where they colonize a variety of substrates, contributing to their erosion. Almost 2 centuries worth of naturalistic studies focused on a few true-boring (euendolithic) phototrophs, but substrate preference has received little attention. The Isla de Mona (Puerto...
Article
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A unicellular cyanobacterium, strain Alchichica-D10, was isolated from microbialites of the alkaline Lake Alchichica, Mexico. The cells were short rods (3.9 ± 0.6 μm in length and 1.1 ± 0.1 μm in width) forming biofilms of intense emerald green color. They exhibited red autofluorescence under UV light excitation. UV-visible absorption spectra revea...
Article
Full-text available
Endolithic microbial communities are prominent features of intertidal marine habitats, where they colonize a variety of substrates, contributing to their erosion. Almost two centuries worth of naturalistic studies focused on a few true-boring (euendolithic) phototrophs, but substrate preference has received little attention. The Isla de Mona (Puert...
Article
Full-text available
Soil surface temperature, an important driver of terrestrial biogeochemical processes, depends strongly on soil albedo, which can be significantly modified by factors such as plant cover. In sparsely vegetated lands, the soil surface can be colonized by photosynthetic microbes that build biocrust communities. Here we use concurrent physical, bioche...
Data
Parameter file used for the treatment of Illumina 16S rDNA libraries data in the qiime pipeline.
Chapter
Full-text available
Microbialites are organo-sedimentary structures formed by the direct or indirect action of microorganisms. Fossil stromatolites (laminated microbialites) constitute the oldest reliable traces of life, a fact that generates considerable interest in how these structures are formed and what biogenic traces can be preserved. Although found extensively...
Article
Full-text available
Cyanobacteria have played a significant role in theformation of past and modern carbonate deposits at the surface of the Earth using a biomineralization process that has been almost systematically considered induced and extracellular. Recently, a deep-branching cyanobacterial species, Candidatus Gloeomargarita lithophora, was reported to form intra...
Article
Cyanobacteria have played a significant role in the formation of past and modern carbonate deposits at the surface of the Earth using a biomineralization process that has been almost systematically considered induced and extracellular. Recently, a deep-branching cyanobacterial species, Candidatus Gloeomargarita lithophora, was reported to form intr...
Data
Full-text available
et al. 10.1073/pnas.1403510111 Table S1. List of cyanobacterial strains analyzed in this study Strain Strain ID Culture medium Inclusions Subsection I Chamaesiphon minutus PCC 6605 BG11 PolyP Cyanobacterium aponinum PCC 10605 T BG11 Numerous PolyP Cyanobacterium stanieri PCC 7202 T BG11 + 10%ASN-III PolyP Cyanobium gracile PCC 6307 T BG11 o -NaHCO...
Article
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Microbialites are sedimentary formations that are found throughout the geological record and are usually considered as one of the oldest traces of life on Earth. Although they have been known for more than a century and hold as an emblematic object in Earth Sciences, we yet do not understand in details how they form and how microbial processes impa...
Article
Microbialites are sedimentary formations that are found throughout the geological record and are usually considered as one of the oldest traces of life on Earth. Although they have been known for more than a century and hold as an emblematic object in Earth Sciences, we yet do not understand in details how they form and how microbial processes impa...
Data
Full-text available
The search for microfossils in the geological record has been a long-term challenge. Part of the prob-lem comes from the difficulty of identifying such micro-fossils unambiguously, since they can be morphologically confused with abiotic biomorphs. One route to improve our ability to correctly identify microfossils involves studying fossilization pr...
Article
Full-text available
The search for microfossils in the geological record has been a long-term challenge. Part of the prob-lem comes from the difficulty of identifying such micro-fossils unambiguously, since they can be morphologically confused with abiotic biomorphs. One route to improve our ability to correctly identify microfossils involves studying fossilization pr...
Article
Full-text available
The role of microorganisms in microbialite formation remains unresolved: do they induce mineral precipitation (microbes first) or do they colonize and/or entrap abiotic mineral precipitates (minerals first)? Does this role vary from one species to another? And what is the impact of mineral precipitation on microbial ecology? To explore potential bi...
Article
Full-text available
Cyanobacteria have affected major geochemical cycles (carbon, nitrogen, and oxygen) on Earth for billions of years. In particular, they have played a major role in the formation of calcium carbonates (i.e., calcification), which has been considered to be an extracellular process. We identified a cyanobacterium in modern microbialites in Lake Alchic...
Article
Full-text available
Stromatolites are organosedimentary structures resulting from the activity of microbes. Fossil stromatolites are considered to be among the oldest traces of life on Earth, their oldest occurrence being at 3.5Ga. Although stromatolites dominate the Precambrian geological record, the abiotic and biological processes leading to their formation and thu...
Data
Alchichica microbialites maintained in laboratory aquaria. A. Initial setting of microbialites fragments in aquaria with different photoperiods. B. Microbialites after one year of cultivation in aquaria. C. Measurements of pH and temperature over time. Orange symbols (aquarium 1); blue symbols, aquarium 2. Red bars indicate points at which aquaria...
Data
Cluster analysis of DGGE fingerprints of bacteria associated to Alchichica microbialites. The name and depth of each sample are given on the right. AQ1 and AQ2 correspond to samples from laboratory aquaria. The scale bar above the dendrogram shows distances (%) between samples based on presence/absence of bands. Grey bars at nodes indicate the stan...
Data
Maximum likelihood (ML) phylogenetic tree of alphaproteobacterial SSU rDNAs from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Relative proportions of the different OTUs in each sample are indicated by circles of proportional size on the right. The number (n) indicates the number total...
Data
Maximum likelihood phylogenetic tree of SSU rDNA sequences of Chloroflexi and Chlorobi from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given on the right. Asterisks indicate OTUs also identified in DGGE patterns. The scale...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Bacteroidetes from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given on the right. Asterisks indicate OTUs also identified in DGGE patterns. The scale bar i...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Deltaproteobacteria and Gammaproteobacteria from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given on the right. The scale bar indicates the number of subst...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Gemmatimonadetes and Acidobacteria from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given on the right. The scale bar indicates the number of substitutions...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Actinobacteria and Firmicutes from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given on the right. Asterisks indicate OTUs also identified in DGGE patterns....
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Archaea from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given in brackets. The scale bar indicates the number of substitutions per site for a unit branch l...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Betaproteobacteria from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given on the right. The scale bar indicates the number of substitutions per site for a u...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Planctomycetales and Verrucomicrobia from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU are given on the right. The scale bar indicates the number of substitution...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of CD OP11, CD WS6, Deinoccocus-Thermus, CD SBR1, CD BRC1, CD NKB19, Nitrospira, CD TM6, CD OP3 and Spirochaeta from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Sequences from this study are in bold. Numbers of clones retrieved from each sample for each OTU ar...
Data
Maximum likelihood (ML) phylogenetic tree of SSU rDNA sequences of Unikonts (Amoebozoa plus Opisthokonta) from Alchichica microbialites. Numbers at nodes indicate bootstrap values. Numbers of clones retrieved from each sample for each OTU are given on the right. The scale bar indicates the number of substitutions per site for a unit branch length....
Data
Hypothetical model of carbonate formation dynamics based on known metabolisms of microbial lineages detected in Alchichica microbialites. The panels represent the activities that would occur during day (left) and; night (right) in areas where oxygenic (upper panels) or anoxygenic (lower panels) photosynthesis predominates. (TIF)
Article
Full-text available
The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both...

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This is Goldschmidt 2017 session 15i. Get ready for the conference by checking here relevant articles, and start a discussion (use "Questions" below). Session summary: Microorganisms have been shaping the geochemical environments of the Earth for the past 3.8 Ga. Their ability to precipitate solid phases from aqueous species in a variety of environments has led to the deposition of mineral deposits of various sizes in the rock record and in modern environments. The breadth of this session encompasses the formation, geochemical impact, preservation and potential applications of all microbial biominerals. We therefore invite contributions from field, experimental and theoretical studies pinpointing the mechanisms of induced and controlled biomineralization by prokaryotic and unicellular eukaryotic organisms themselves as well as the role of the organic compounds they produce especially the extracellular polymeric substances (EPS). We highly encourage interdisciplinary studies addressing the impact of biominerals – carbonates, phosphates, silicates, sulfides and oxides – on biogeochemical cycles (e.g. Fe, Mn, Ca, P, S, Si, C), the interactions between minerals and cellular or extracellular organic compounds, the role of biominerals in the preservation of organic matter, and the potential industrial and bioremediation applications of biominerals.