The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome

Harmful Algae, Год журнала: 2023, Номер 126, С. 102440 - 102440

Опубликована: Апрель 30, 2023

Язык: Английский

---

Trait biases in microbial reference genomes

Scientific Data, Год журнала: 2023, Номер 10(1)

Опубликована: Фев. 9, 2023

Abstract Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample bacterial archaeal diversity, compare MAGs to the popular RefSeq genome database, which heavily relies on cultures. We distribution 12,454 KEGG gene orthologs (used trait proxies) genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, other animals). Using statistical modeling, then determine conditional probabilities species is represented depending its genetic repertoire. find majority examined genes are significantly biased or against RefSeq. Our systematic estimates prevalences across bacteria archaea nature gene-specific reference constitutes resource addressing issues future.

Язык: Английский

---

Role of benthic overwintering cyanobacteria seed stock on estuarine bloom dynamics

Harmful Algae, Год журнала: 2025, Номер 143, С. 102807 - 102807

Опубликована: Фев. 6, 2025

Cyanobacteria blooms (cHABs) comprised of the potentially toxic cyanobacterium Microcystis, are increasing in waterbodies worldwide. CHABs estuaries often originate from upstream locations with longer hydraulic residence times (e.g., reservoirs, static channels). These also accumulate higher concentrations benthic overwintering cells that serve as inoculum for subsequent year's blooms. We investigated Microcystis seed stock hydrologically complex upper San Francisco Estuary known Sacramento-San Joaquin Delta (Delta). Quantitative polymerase chain reaction (qPCR) was used to quantify total sediments available inoculate summertime To study bloom origin and succession, DNA discrete water sediment samples PCR amplified using cyanobacteria-specific 16S-23S ITS rDNA primers. Results confirmed hypothesis peripheral areas have highest generally surface water. high genetic diversity population 36 unique genotypes detected column. This demonstrates should be considered when investigating dynamics across large estuarine systems.

Язык: Английский

---

An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov

Microbial Ecology, Год журнала: 2025, Номер 88(1)

Опубликована: Март 14, 2025

Abstract The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales Chlamydiae ). Here, we provide detailed comprehensive account on the current knowledge . First, acknowledging up-to-date phylogenetic reconstructions recent nomenclatural proposals, reevaluate their taxonomy, thus re-ranking them as suborder, i.e. Holosporineae , within Rhodospirillales Then, examine diversity presenting 20 described genera many yet undescribed sub-lineages, well variety respective environments provenance which belong several different supergroups. Noteworthy representatives are infectious intranuclear Holospora host manipulator ‘ Caedimonas ’, farmed shrimp pathogen Candidatus Hepatobacter’. Next, put these in context whole by comparing available data least studied representatives, including genome sequences. Accordingly, reason most probable trajectories for interactions, specificity, emergence potential pathogens aquaculture possibly humans, future research directions investigate those open points

Язык: Английский

---

Polyploid cyanobacterial genomes provide a reservoir of mutations, allowing rapid evolution of herbicide resistance

Current Biology, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Adaptive mechanisms in bacteria, which are widely assumed to be haploid or partially diploid, thought rely on the emergence of spontaneous mutations lateral gene transfer from a reservoir pre-existing variants within surrounding environment. These then become fixed population upon exposure selective pressures. Here, we show that multiple distinct wild-type (WT) substrains highly polyploid cyanobacterium Synechocystis sp. PCC 6803 can adapt rapidly potent herbicide methyl viologen (MV). Genome sequencing revealed responsible for adaptation MV were already present prior selection genomes unadapted parental strains at low allelic frequencies. This indicates chromosomal polyploidy bacteria provide cells with conditionally beneficial enriched and selection. MV-resistant performed oxygenic photosynthesis less efficiently than WTs when was absent, suggesting trade-offs cellular fitness associated evolution resistance possible role balancing maintenance these alleles under ecologically relevant growth conditions. Resistance reduced intracellular accumulation MV. Our results indicate genome plays rapid some stressful conditions, may include xenobiotics, nutrient limitation, environmental stresses, seasonal changes.

Язык: Английский

---

Insilico Mining of Metagenomic Datasets for Novel PET Hydrolase Homologs: Enhancing Enzyme Discovery for Circular Bioeconomy

Sustainable Chemistry for the Environment, Год журнала: 2025, Номер unknown, С. 100253 - 100253

Опубликована: Май 1, 2025

Язык: Английский

---

Toward a Predictive Understanding of Cyanobacterial Harmful Algal Blooms through AI Integration of Physical, Chemical, and Biological Data

ACS ES&T Water, Год журнала: 2023, Номер 4(3), С. 844 - 858

Опубликована: Ноя. 30, 2023

Freshwater cyanobacterial harmful algal blooms (cyanoHABs) are a worldwide problem resulting in substantial economic losses, due to harm drinking water supplies, commercial fishing, wildlife, property values, recreation, and tourism. Moreover, toxins produced from some cyanoHABs threaten human animal health. Climate warming can affect the distribution of cyanoHABs, where rising temperatures facilitate more intense greater inland freshwater. Nutrient runoff adjacent watersheds is also major driver cyanoHAB formation. While physicochemical factors behind dynamics known, there still gaps our understanding conditions that trigger sustain over time. In this perspective, we suggest sufficient data sets, as well machine learning (ML) artificial intelligence (AI) tools, available build comprehensive model based on integrated environmental/climate, nutrient/water chemistry, microbiome 'omics identify key contributing HAB formation, intensity, toxicity. By taking holistic approach analysis all data, including rapidly growing number biological provide foundational knowledge needed address increasing threat security resources.

Язык: Английский

---

Metagenomic insights into cyanotoxin dynamics in a Mexican subtropical lake

Chemosphere, Год журнала: 2025, Номер 376, С. 144285 - 144285

Опубликована: Март 9, 2025

Valle de Bravo is a vital water supply for part of the metropolitan area Mexico megacity, providing 30% City's demand. This body has experienced an acceleration in its trophic status, going from oligotrophic to eutrophic just few years. temperate lake (at tropical latitude) persistent bloom dominated by variety co-occurring cyanobacteria, many which have toxigenic potential based on microscopic identification, that makes it difficult or even impractical identify cyanotoxin producers. To unravel this complexity and directly genera, we showed integrating classical approaches with metagenomic required. We first characterized, genes metagenomes assembled genomes, Cyanobacteria. found Microcystis was most dominant cyanobacterial genus sole carrier mcy operon, making only microcystin producer. then quantified twenty-one different cyanopeptides, including twelve congeners using high-performance liquid chromatography-high-resolution. Nine microcystins (MCs) emerging anabaenopeptin-A -B were at varying concentrations throughout year, MC-LA being common abundant. Our findings, constrained our sampling strategy, indicate conventional biomarkers (e.g., toxin genes) not consistently reliable indicators freshwater system. In study, followed dynamics community associated cyanopeptides unprecedented resolution. results implications better management toxic blooms system, supplies drinking more than 7 million people megalopolis México.

Язык: Английский

---

Ten‐Year Hindcast Assessment of an Improved Probabilistic Forecast System for Cyanotoxin (Microcystins) Risk Level in Lake Erie

Water Resources Research, Год журнала: 2025, Номер 61(4)

Опубликована: Апрель 1, 2025

Abstract Toxic harmful algal blooms produce public health hazards in freshwater systems around the world. There is a need for forecast that can mitigate risk of exposure to toxins. We improved an approach predict spatially and temporally resolved probability microcystins (MCs) exceeding threshold level (6 μg L −1 ) western Lake Erie. This combines 5‐day chlorophyll‐a model, weekly updated regression model predicting MCs from chlorophyll‐a, empirical relationship between predicted observed calibrated over hindcast period. included additional years database calibration assessment, applied bias adjustment Moderate Resolution Imaging Spectroradiometer consistency with Sentinel‐3 satellite imagery, robust Siegel method. Cross‐validation showed reasonable skill regions including surface water, water system plant intake sites, bottom waters. The also presented useful when assessed against two intensive sampling events Microcystis Erie 2018 2019. Our results provide comprehensive assessment novel method MC risk, which may be recalibrated other affected by toxic cyanobacterial blooms, where similar exists chlorophyll toxin concentrations at levels relevant advisory levels.

Язык: Английский

---

Genomic Identification and Characterization of Saxitoxin Producing Cyanobacteria in Western Lake Erie Harmful Algal Blooms

Environmental Science & Technology, Год журнала: 2025, Номер unknown

Опубликована: Апрель 10, 2025

Saxitoxins (STXs), a group of closely related neurotoxins, are among the most potent natural toxins known. While genes encoding STX biosynthesis have been observed in Lake Erie, organism(s) responsible for producing STXs Laurentian Great Lakes not identified. We identified full suite Dolichospermum metagenome-assembled genome (MAG). The content sxt suggest that this organism can produce STX, decarbamoyl and deoxy-decarbamoyl saxitoxins, other congeners. absence sxtX indicates is unable to neosaxitoxin, congener. However, distinct, lower abundance operon from an unidentified did contain sxtX, indicating neosaxitoxin potential. Metatranscriptomic data confirmed gene expression. also recovered highly similar MAGs lacking genes, implying loss or horizontal transfer. sxtA was detected by quantitative polymerase chain reaction during 47 76 sampling dates between 2015 2019, demonstrating higher sensitivity than metagenomic approaches. positively correlated with temperature particulate nitrogen:phosphorus ratio negatively ammonium concentration. All had required nitrogen fixation. Collectively, study provides foundation understanding potential new threats Erie water quality.

Язык: Английский

---