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Narum, S. R., Di Genova, A., Micheletti, S. J., & Maass, A. (2018). Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon. Proc. R. Soc. B-Biol. Sci., 285(1883), 9 pp.
Abstract: A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon (Oncorhynchus tshawytscha; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.
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Plominsky, A. M., Henriquez-Castillo, C., Delherbe, N., Podell, S., Ramirez-Flandes, S., Ugalde, J. A., et al. (2018). Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation. Front. Microbiol., 9, 13 pp.
Abstract: Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cahuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cahuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cahuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.
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Puig-Castellvi, F., Midoux, C., Guenne, A., Conteau, D., Franchi, O., Bureau, C., et al. (2022). A longitudinal study of the effect of temperature modification in full-scale anaerobic digesters – dataset combining 16S rDNA gene sequencing, metagenomics, and metabolomics data. Data Br., 41, 107960.
Abstract: Data in this article provides detailed information on the microbial dynamics and degradation performances in two fullscale anaerobic digesters operated in parallel for 476 days. One of them was kept at 35 degrees C for the whole experiment, while the other was submitted to sub-mesophilic (25 degrees C) conditions between days 123 and 373. Sludge samples were collected from both digesters at days 0, 80, 177, 218, 281, 353, and 462. The provided data include the operational conditions of the digesters and the characterization of the sludge samples at the physicochemical level, indicative of the digesters' degradation performance. It also includes the characterization of the sludge samples at the multiomics level (16S rRNA gene sequencing, metagenomics, and metabolomics profiling), to decipher the changes in the microbial structure and molecular activity. The 16S rDNA gene sequencing, metagenomics, and metabolomics data were generated using an IonTorrent PGM sequencer, an Illumina NextSeq 500 sequencer, and LTQ-Orbitrap XL mass spectrometer respectively. The 16S rDNA gene raw data and the metagenomics data have been deposited in the BioProject PRJEB49115, in the ENA database (https://www.ebi.ac.uk/ena/browser/view/PRJEB49115). The metabolomics data has been deposited at the Metabolomics Workbench, with study id ST002004 (DOI: 10.21228/M8JM6B). The data can be used as a source for comparisons with other studies working with data from full-scale anaerobic digesters, especially for those investigating the effect of the temperature modification. The data is associated with the research article “Metataxonomics, metagenomics, and metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters” (Puig-Castellvi et al [1]). (c) 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)
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Puig-Castellvi, F., Midoux, C., Guenne, A., Conteau, D., Franchi, O., Bureau, C., et al. (2022). Metataxonomics, metagenomics and metabolomics analysis of the influence of temperature modification in full-scale anaerobic digesters. Bioresour. Technol., 346, 126612.
Abstract: Full-scale anaerobic digesters' performance is regulated by modifying their operational conditions, but little is known about how these modifications affect their microbiome. In this work, we monitored two originally mesophilic (35 degrees C) full-scale anaerobic digesters during 476 days. One digester was submitted to sub-mesophilic (25 degrees C) conditions between days 123 and 373. We characterized the effect of temperature modification using a multi-omics (metataxonomics, metagenomics, and metabolomics) approach. The metataxonomics and metagenomics results revealed that the lower temperature allowed a substantial increase of the sub-dominant bacterial population, destabilizing the microbial community equilibrium and reducing the biogas production. After restoring the initial mesophilic temperature, the bacterial community manifested resilience in terms of microbial structure and functional activity. The metabolomic signature of the sub-mesophilic acclimation was characterized by a rise of amino acids and short peptides, suggesting a protein degradation activity not directed towards biogas production.
Keywords: Metagenomics; Sub-mesophilic; Metabolomics; Full-scale; Chemometrics
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Ramirez-Flandes, S., Gonzalez, B., & Ulloa, O. (2019). Redox traits characterize the organization of global microbial communities. Proc. Natl. Acad. Sci. U. S. A., 116(9), 3630–3635.
Abstract: The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e. g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.
Keywords: microbial ecology; functional traits; oxidoreductases; biomes; metagenomics
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