Current-day metagenomics analyses increasingly involve de novo taxonomic classification of long DNA sequences and metagenome-assembled genomes. Here, we show that the conventional best-hit approach often leads to classifications are too specific, especially when represent novel deep lineages. We present a method integrates multiple signals classify (Contig Annotation Tool, CAT) genomes (Bin BAT). Classifications automatically made at low ranks if closely related organisms in reference...

Abstract Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although classical concept ecology, niche breadth has remained challenging quantify for microorganisms because it depends on an objective definition of the Here, by defining environment microorganism as community resides in, we integrated information from over 22,000 environmental sequencing samples derive quantitative measure niche, which call social breadth. At level genera,...

Heterocytes, specialized cells for nitrogen fixation in cyanobacteria, are surrounded by heterocyte glycolipids (HGs), which contribute to protection of the nitrogenase enzyme from oxygen. Diverse HGs preserve sediment and have been widely used as evidence past fixation, structural variation has suggested taxonomic information reflect paleoenvironmental conditions. Here, comprehensive HG identification screening biosynthetic gene clusters throughout we reconstruct convergent evolutionary...

Abstract Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol-1-phosphate (G1P), while Bacteria/Eukarya produce consisting fatty acids ester-bound glycerol-3-phosphate (G3P). This dichotomy in membrane lipid composition (i.e., the ‘lipid divide’) is believed have arisen after Last Universal Common Ancestor (LUCA). A leading hypothesis LUCA possessed a heterochiral ‘mixed archaeal/bacterial membrane’. However, no natural microbial representatives supporting this...

Abstract Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust signals from MAGs contigs to enhance read annotation. RAT reconstructs profiles with high precision sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, annotates a large fraction the metagenomic reads, calling novel taxa at...

Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation poly-contaminants pipeline for heavily contaminated groundwater. Groundwater moves from polluted park treatment plant, where an aerated bioreactor effectively removes the contaminants. While biomass does not settle reactor, sediment collected afterwards used seed new via backwash cycle. The has successfully operated since...

Bacterial membranes are composed of fatty acids (FAs) ester-linked to glycerol-3-phosphate, while archaea have made isoprenoid chains ether-linked glycerol-1-phosphate. Many archaeal species organize their membrane as a monolayer membrane-spanning lipids (MSLs). Exceptions this “lipid divide” the production by some bacterial (ether-bound) MSLs, formed tail-to-tail condensation FAs resulting in formation (iso) diabolic (DAs), which likely precursors paleoclimatological relevant branched...

Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural (SC) widespread in the tree of life, underlying genetics and genomics are not well understood. Here, we collected sequenced a set 87 structurally colored bacterial isolates 30 related strains lacking SC. Optical analysis colonies indicated that diverse bacteria at least two different phyla (

The sedimentary lipid pool is comprised of a myriad individual components. Due to their importance for organic carbon sequestration and application in paleoclimatic geobiological reconstructions, its composition has been studied many decades with targeted approaches but an overall view on still lacking. In part this uncertainty relates the different sources lipids, they can be both delivered from overlying water column by sedimentation, also produced in-situ sediment dwelling organisms....

ABSTRACT Bacterial membrane lipids are typically characterised by fatty acid bilayers linked through ester bonds, whereas those of Archaea ether‐linked isoprenoids forming or monolayers membrane‐spanning known as isoprenoidal glycerol dialkyl tetraethers (isoGDGTs). However, this understanding has been reconsidered with the identification branched GDGTs (brGDGTs), which ether‐bound alkyl acids bacterial origin, though their producers often unidentified. The limited availability microbial...

The human intestinal microbiota is a homeostatic ecosystem with remarkable impact on health and the disruption of this equilibrium leads to an increased susceptibility infection by numerous pathogens. In study, we used shotgun metagenomic sequencing two different bioinformatics approaches, based mapping reads onto databases reconstruction putative draft genomes, investigate possible changes in composition samples from patients Shiga Toxin-producing E. coli (STEC) compared healthy healed...

An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method measure phages that are preferentially adsorbed specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages added envelopes, isolated through gel electrophoresis, after which phage DNA sequenced and compared with full virome. Here, show allows for separation of based on receptor-adsorbing...

Abstract Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures environmental microbes, thereby restricting insights into diversity lipids their ecological roles. Addressing limitation, here we apply metalipidomics combined with metagenomics in Black Sea, classifying tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200...

ABSTRACT Current-day metagenomics increasingly requires taxonomic classification of long DNA sequences and metagenome-assembled genomes (MAGs) unknown microorganisms. We show that the standard best-hit approach often leads to classifications are too specific. present tools classify high-quality metagenomic contigs (Contig Annotation Tool, CAT) MAGs (Bin BAT) thoroughly benchmark them with simulated classified against a reference database where related removed, thereby simulating queries....

The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, first phage be discovered, a protein encoding Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because repeats hotspots evolution, BACON domains may provide insight into evolution phages. Here, we studied biodiversity and in bacteriophages by analysing over 2 million viral...

Teredinidae are a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution is linked to the acquisition cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within gills. In present work we applied metagenomics characterize microbiomes gills digestive tract Neoteredo reynei, mangrove-adapted shipworm species found over large range Brazilian coast. Comparative grouped gill symbiont community different N. reynei specimens,...

ABSTRACT Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures environmental microbes, thereby restricting insights into diversity lipids their ecological roles. Addressing limitation, here we apply for first time metalipidomics combined with metagenomics in Black Sea, classifying tentatively identifying 1,623 lipid-like species across 18 lipid classes. We...

Archaea synthesize membranes of isoprenoid lipids that are ether-linked to glycerol, while Bacteria/Eukarya produce consisting ester-bound fatty acids. This dichotomy in membrane lipid composition or ‘lipid divide’ is believed have arisen after the Last Universal Common Ancestor (LUCA). A leading hypothesis LUCA possessed a ‘mixed heterochiral archaeal/bacterial membrane’, however no natural microbial representatives supporting this scenario been shown exist today. Here, we demonstrate...

Paleontological and phylogenomic observations have shed light on the evolution of cyanobacteria. Nevertheless, emergence heterocytes, specialized cells for nitrogen fixation, remains unclear. Heterocytes are surrounded by heterocyte glycolipids (HGs), which contribute to protection nitrogenase enzyme from oxygen. Here, comprehensive HG identification screening biosynthesis genes throughout cyanobacteria, we identify analogs produced specific distantly related non-heterocytous These...

In the past few decades, population genetics and phylogeographic studies have improved our knowledge of connectivity demography in marine environments. Studies deep-sea hydrothermal vent populations identified barriers to gene flow, hybrid zones, demographic events, such as historical expansions contractions. These studies, however, used loci, which limit amount information they provided for coalescent analysis thus ability confidently test complex dynamics scenarios. this study, we...

In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations pollutants, such as mercury, become more likely. Being largest anoxic basin worldwide, with high concentrations potent neurotoxic methylmercury (MeHg), Black Sea is an ideal natural laboratory to provide new insights about link between dissolved oxygen concentration hgcAB gene-carrying (hgc+) microorganisms involved...

Abstract Teredinidae is a family of highly adapted wood-feeding and wood-boring bivalves, commonly known as shipworms, whose evolution linked to the acquisition cellulolytic gammaproteobacterial symbionts harbored in bacteriocytes within gills. In present work we applied metagenomics characterize microbiomes gills digestive tract Neoteredo reynei , mangrove-adapted shipworm species found over large range Brazilian coast. Comparative grouped symbiotic community different N. specimens,...

Summary Bacterial membrane lipids have been traditionally defined as fatty acids (FAs) bilayers linked through ester bonds, while those of Archaea ether-linked isoprenoids forming or monolayers spanning (MSLs) known isoprenoidal glycerol dialkyl tetraethers (isoGDGTs). This paradigm has challenged with the discovery branched GDGTs (brGDGTs), ether-bound alkyl FAs, that are bacterial origin but whose specific producers in environment often unknown. The limited number available microbial...