Recent sio_cmbc items

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

Wed, 6 May 2026 00:00:00 +0000

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate...

Correction: A microbial survey of the International Space Station (ISS)

Tue, 21 Apr 2026 00:00:00 +0000

[This corrects the article DOI: 10.7717/peerj.4029.].

Green genes from blue greens: challenges and solutions to unlocking the potential of cyanobacteria in drug discovery

Tue, 9 Dec 2025 00:00:00 +0000

Cyanobacteria are prolific producers of biologically active compounds that are important in influencing ecology, behavior of interacting organisms, and as leads in drug discovery efforts. Here we discuss the challenges faced by all natural product researchers, especially those that focus on cyanobacteria, and then describe progress that has been made in these areas. We also propose some solutions, paths forward, and thoughts for consideration on these challenges.

Osmolyte chemical diversity in Lingulaulax polyedra red tides: a critical overlooked factor to respiratory irritations?

Thu, 4 Dec 2025 00:00:00 +0000

The detrimental effects on human health sometimes observed during blooms of Lingulaulax polyedra have been formerly attributed to the yessotoxin analogs this species produces. In this paper we show that natural concentrations of yessotoxin analogs present in seawater and sea spray aerosols during an unprecedented L. polyedra bloom in 2020 in Southern California did not induce inflammation in mammal macrophage cells, questioning the role played by yessotoxin in causing respiratory irritations. This bloom was associated with unprecedented levels of particulate dimethylsulfoniopropionate (2.74 ± 1.63 to 10.11 ± 1.39 µM), gonyol and several new structural analogs ofgonyol . We profiled the metabolic content of dinoflagellate cells and recorded increasing amounts of quaternary amines of the betaine family (carnitine, actinin, ectoine) as the bloom progressed. Being precursors of sulfur and nitrogenous small volatile compounds, we hypothesize that, in addition to their recognized role...

Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin

Thu, 20 Nov 2025 00:00:00 +0000

Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered...

Population Genomics Reveals Panmixia in Pacific Sardine (Sardinops sagax) of the North Pacific

Fri, 12 Sep 2025 00:00:00 +0000

The spatial structure and dynamics of populations are important considerations when defining management units in organisms that are harvested as natural resources. In the Eastern Pacific, Pacific Sardine range from Chile to Alaska, the northernmost state of the United States (U.S.), and once supported an expansive and productive fishery. Along its North American range, it is hypothesized to comprise three subpopulations: a northern and southern subpopulation, which primarily occur off the coast of the U.S. and Baja California, Mexico (M.X.), respectively, and a third in the Gulf of California, M.X. We used low coverage whole genome sequencing to generate genotype likelihoods for millions of SNPs in 317 individuals collected from the Gulf of California, M.X., to Oregon, U.S., to assess population structure in Pacific Sardine. Differentiation across the genome was driven by variation at several putative chromosomal inversions ranging in size from ~21 MB to 0.89 MB, although none...

Cyanobacteria Join the Kahalalide Conversation: Genome and Metabolite Evidence for Structurally Related Peptides

Thu, 28 Aug 2025 00:00:00 +0000

Kahalalide F is a cyclic depsipeptide with notable anticancer properties, initially discovered from the green alga Bryopsis sp. and its molluscan predator Elysia rufescens. Recent studies have pinpointed a bacterial endosymbiont of the green alga, Candidatus Endobryopsis kahalalidefaciens, as the true producer of kahalalide F. In the present work, we characterize a closely related kahalalide F analog, kahalalide Z₅, from the marine cyanobacterium Limnoraphis sp. collected in the Las Perlas Islands, Panama, and propose the structures of several related compounds by detailed MS analysis. To uncover novel metabolites and prioritize them for targeted isolation from this organism, we employed a robust metabolomics strategy combining LC-MS/MS with SMART NMR and DeepSAT, artificial intelligence platforms trained to infer chemical structures from ¹H-¹³C HSQC NMR data. This integrated approach annotated a compound with structural...

Assessing Ecological Outcomes of Blue Carbon Restoration in Australia: A focus on Tasmanian Salt Marshes

Mon, 14 Jul 2025 00:00:00 +0000

Tidal salt marshes are among Australia’s most important blue carbon ecosystems, offering essential services such as carbon sequestration, coastal protection, and critical habitat for fish and wildlife. Yet many remain degraded, and restoration efforts are constrained by limited guidance on how to effectively monitor ecological outcomes. This capstone project evaluates the utility of imaging sonar as a non-invasive tool to assess fish abundance, behavior, and habitat use in restored tidal wetlands across Tasmania.

The study contributes to the development of a standardized methodology for applying imaging sonar in salt marsh environments—habitats where turbidity and shallow water limit the effectiveness of optical or diver-based surveys. Results show that while imaging sonar is well-suited for detecting fish in these challenging conditions, it must be used alongside traditional gear-based methods, such as pop, fyke, and seine nets, to ensure representative sampling across...

Metagenomic Identification of Brominated Indole Biosynthetic Machinery from Cyanobacteria

Mon, 14 Jul 2025 00:00:00 +0000

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...

Promiscuity in Nature Extends to Central Protein Biosynthetic Machinery

Mon, 14 Jul 2025 00:00:00 +0000

Thioesters, rather than oxo-esters, can be tolerated and processed during translation to incorporate unnatural monomers.

Storytelling for a Species - The White Abalone Story

Thu, 10 Jul 2025 00:00:00 +0000

The White Abalone (Haliotis sorenseni) is functionally extinct in the wild. The only thing standing between this species and complete extinction is a dedicated group of individuals working tirelessly to save it. In a time of uncertain funding for many disciplines, particularly in science, it is crucial to effectively communicate the efforts of scientists, volunteers, and everyday citizens who are striving to protect a species on the brink of extinction due to human-caused impacts. Storytelling for a Species – The White Abalone Story aims to tell the story of the White Abalone and its recovery efforts, helping to illuminate, illustrate, and educate others about the importance of saving this humble creature.

Please see media created for this project here:

https://youtu.be/bC0xbSREATg?si=...

Stakeholder Valuation of CalCOFI Data usage for Improved Decision Making