title: Comparative metagenomics unveils functions and genome features of microbialite-associated communities along a depth gradient.
abstract: Modern microbialites are often used as analogs of Precambrian stromatolites; therefore, studying the metabolic interplay within their associated microbial communities can help formulating hypotheses on their formation and long-term preservation within the fossil record. We performed a comparative metagenomic analysis of microbialite samples collected at two sites and along a depth gradient in Lake Alchichica (Mexico). The community structure inferred from single-copy gene family identification and long-contig (>10 kb) assignation, consistently with previous rRNA gene surveys, showed a wide prokaryotic diversity dominated by Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria, and Bacteroidetes, while eukaryotes were largely dominated by green algae or diatoms. Functional analyses based on RefSeq, COG and SEED assignations revealed the importance of housekeeping functions, with an overrepresentation of genes involved in carbohydrate metabolism, as compared with other metabolic capacities. The search for genes diagnostic of specific metabolic functions revealed the important involvement of Alphaproteobacteria in anoxygenic photosynthesis and sulfide oxidation, and Cyanobacteria in oxygenic photosynthesis and nitrogen fixation. Surprisingly, sulfate reduction appeared negligible. Comparative analyses suggested functional similarities among various microbial mat and microbialite metagenomes as compared with soil or oceans, but showed differences in microbial processes among microbialite types linked to local environmental conditions.
authors.affiliation: Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Saghaï
authors.affiliation: Institut de Biologie Intégrative de la Cellule, CNRS, Université Paris-Sud Orsay, Université Paris-Saclay, Orsay, France.
authors.forename: Yvan
authors.initials: Y
authors.lastname: Zivanovic
authors.affiliation: Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France.
authors.forename: David
authors.initials: D
authors.lastname: Moreira
authors.affiliation: Institut de Minéralogie et de Physique des Matériaux et de Cosmochimie, CNRS, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Sorbonne Universités, Paris, France.
authors.forename: Karim
authors.initials: K
authors.lastname: Benzerara
authors.affiliation: Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France.
authors.forename: Paola
authors.initials: P
authors.lastname: Bertolino
authors.affiliation: Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Ragon
authors.affiliation: Departamento de Ecología y Recursos Naturales, Universidad Nacional Autónoma de México, DF Mexico, Mexico.
authors.forename: Rosaluz
authors.initials: R
authors.lastname: Tavera
authors.affiliation: Departamento de Ecología, Universidad Autónoma de Madrid, Madrid, Spain.
authors.forename: Ana Isabel
authors.initials: AI
authors.lastname: López-Archilla
authors.affiliation: Ecologie Systématique Evolution, CNRS, Université Paris-Sud, Université Paris-Saclay, AgroParisTech, Orsay, France.
authors.forename: Purificación
authors.initials: P
authors.lastname: López-García
mesh_terms: D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D050260:Carbohydrate Metabolism / Q000235:genetics; D000460:Chlorophyta / Q000235:genetics; D000458:Cyanobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D017377:Diatoms / Q000302:isolation & purification*; D005580:Fossils; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D019015:Geologic Sediments / Q000382:microbiology*; D060106:Lakes / Q000382:microbiology*; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics / Q000379:methods; D008800:Mexico; D010788:Photosynthesis