Inside the Paper

Abstract. Although extensive work has characterized high-affinity atmospheric methane oxidation in upland soils and sustained oxidation in chronically meth

Abstract. Increased human impacts on Earth systems are radically altering biogeochemical cycles. While long-term environmental observatories and Earth System Models (ESMs) provide valuable insights in...

Microbial Evolution

Mathematical models of horizontal gene transfer reveal the determinants underlying multistability of microbial communities, offering key insights for the predictive control and engineering of complex ...

Octocorals are the major source of marine-derived bioactive terpenoids. However, the vast majority of explored chemistry is known from shallow-wate...

All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...

Climate-driven variation in traits is crucial for predicting ecological responses to environmental change, yet global patterns and drivers of micro...

Gene cluster comparison figure generator. Contribute to gamcil/clinker development by creating an account on GitHub.

Halogenated indole natural products have been isolated from a variety of organisms, including plants, marine algae, marine invertebrates, and bacteria. Aquatic cyanobacteria, in particular, are rich producers of brominated indoles, but their cognate biosynthetic enzymes have only been successfully linked in a limited number of natural products, such as the eagle-killing toxin aetokthonotoxin (AETX). The biosynthetic pathway for AETX involves five enzymes, two of which were previously undescribed due to incomplete annotations as hypothetical proteins. Our recent elucidation of AETX biosynthesis established functions of the two previously unknown proteins as enzymes responsible for tryptophan halogenation (AetF) and nitrile synthesis (AetD). Given their sequence novelty, we queried metagenomic data sets for these two enzymes and identified two new cyanobacterial haloindole biosynthetic gene clusters (BGCs) from marine sediment in Moorea, French Polynesia, and soil-derived samples in Maunawili Falls, Hawaii. We characterized the recovered BGCs by biochemically validating a new AetF homologue that exclusively halogenates free indole, rather than tryptophan as observed in AETX biosynthesis, and a new AetD homologue that harbors distinct substrate preferences, expanding the scope of nitrile biosynthesis. Additional characterization of core and accessory enzymes within these AETX-like BGCs highlights the breadth and diversity of haloindole biosynthetic machinery in cyanobacteria.

Vertical stratification in thermokarst lake sediments drives archaeal community assembly, with declining diversity, deterministic selection, and modular networks at depth. Taxa shifts (e.g., rising T....

Cross-feeding, a phenomenon in which organisms share metabolites, is frequently observed in microbial communities across the natural world. One of the most common forms is waste-product cross-feeding,...

Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have inv...

Genomes from metagenomes have revolutionised our understanding of microbial diversity, ecology, and evolution, propelling advances in basic science, biomedicine, and biotechnology. Assembly algorithms...

“Paradox of the sub-plankton: Plausible mechanisms and open problems underlying strain-level diversity in microbial communities” by Akshit Goyal* and Griffin Chure*. This work highlights the limitati...

See current wind, weather, ocean, and pollution conditions, as forecast by supercomputers, on an interactive animated map. Updated every three hours.

Here, by analyzing 306481 microbial genomes from human-associated microbiomes, the authors reveal a largely unexplored biosynthetic landscape of ribosomal peptides (RiPPs), identifying protective pept...

A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common resistanc...

Mandimycin, a polyene macrolide, exhibits strong antifungal activity and possesses a mode of action that is distinct from other compounds of this class.

Understanding the capacity of forests to adapt to climate change is of pivotal importance for conservation science, yet this is still widely unknown. This knowledge gap is particularly acute in high-b...

Microbes drive the Earth’s biogeochemical cycles. Here, Li et al. present a framework for integrating genome-inferred microbial kinetic traits into ecosystem mechanistic models, and use it to benchmar...

Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often ...

In the context of an organism's ecology, physiology, and macroevolutionary history, inheritance and gene loss can yield emergent patterns of trait variability that give the appearance of gene acquisit...

Defining bacterial populations by examining recent horizontal gene transfer events illuminates ecologically meaningful interspecies relationships in the environment and in the human microbiome.

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

The ISME Journal - Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow

AbstractMultiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different prediction