Biology subjects

Alvarez-Cohen, L.

Publications and source records attributed to Alvarez-Cohen, L..

3 recordsLinked to original sources

bioRxiv2024

De novo assembled databases enable species-specific protein-based stable isotope probing of microbiomes without prior knowledge of the community composition

BackgroundProtein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbial communities. In Protein-SIP, peptides and corresponding taxa are identified by database matching, making database quality crucial for accurate analyses. For samples with unknown community composition, Protein-SIP typically employs either unrestricted reference databases or metagenome-derived databases. While (meta)genome-derived databases represent the gold standard, they may be incomplete and are typically resource-intensive to generate. In contrast, unrestricted reference databases can inflate the search space and require complex post-processing. ResultsHere, we explore the feasibility of using de novo peptide sequencing to construct peptide databases directly from mass spectrometry raw data. We then use the mass spectrometric data from labeled cultures to quantify isotope incorporation into specific peptides. We benchmark our approach against the canonical approach in which a sample-matching (meta)genome-derived protein sequence database is used on three different datasets: 1) a proteome analysis from a defined microbial community containing 13C-labeled E. coli cells, 2) time-course data of an anammox-dominated continuous reactor after feeding with 13C-labeled bicarbonate, and 3) a model of the human distal gut simulating a high-protein and high-fiber diet cultivated in either 2H2O or H218O. Our results show that de novo peptide databases are applicable to different isotopes, detecting similar amounts of labeled peptides compared to sample-matching (meta)genome-derived databases, and also identify labeled peptides missed by this canonical approach. Furthermore, we show that peptide-centric Protein-SIP allows up to species-specific resolution and enables the assessment of activity related to individual biological processes. Finally, we provide access to our modular Python pipeline to assist the construction of de novo peptide databases and subsequent peptide-centric Protein-SIP data analysis (https://git.ufz.de/meb/denovo-sip). ConclusionsDe novo peptide databases enable Protein-SIP of microbial communities without prior knowledge of the composition and can be used complementarily to (meta)genome-derived databases or as a standalone alternative in exploratory or resource-limited settings.

bioinformatics↗

bioRxiv2020

Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

1.Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented. 2. ImportanceIn this study, TNT and DNT removal has been observed in field-scale experiments following periodic tilling of historically contaminated soils. The microbial community structures of uncontaminated pristine soils, untilled contaminated soils, and tilled contaminated soils were investigated using high-throughput sequencing platforms. In addition, shotgun metagenome libraries of samples from tilled contaminated soils were generated. The results indicated that a significant shift of the bacterial community at the family level between tilled and untilled contaminated soils, with tilled soils being dominated by Alcaligenaceae and untilled soils by Burkholderiacea. In-depth metagenomic analysis of samples from tilled contaminated soils, indicate the presence of genes that encode for enzymes that potentially could lead to mineralization of TNT and DNT under mixed aerobic and anaerobic periods.

genomics↗

bioRxiv2019

Increased Replication Rates of Dissimilatory Nitrogen-Reducing Bacteria Leads to Decreased Anammox Reactor Performance

BackgroundAnaerobic ammonium oxidation (anammox) is a biological process employed to remove reactive nitrogen from wastewater. While a substantial body of literature describes the performance of anammox bioreactors under various operational conditions and perturbations, few studies have resolved the metabolic roles of their core microbial community members. ResultsHere, we used metagenomics to study the microbial community of a laboratory-scale anammox bioreactor from inoculation, through a performance destabilization event, to robust steady-state performance. Metabolic analyses revealed that nutrient acquisition from the environment is selected for in the anammox community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen removal pathway that competed with anammox. Increased replication of bacteria capable of DNRA led to the out-competition of annamox bacteria, and the loss of the bioreactors nitrogen removal capacity. These bacteria were highly associated with the anammox bacterium and considered part of the core microbial community. ConclusionsOur findings highlight the importance of metabolic interdependencies related to nitrogen- and carbon-cycling within anammox bioreactors and the potentially detrimental effects of bacteria that are otherwise considered core microbial community members.

microbiology↗