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At least 19 recordsLinked to original sources
USGS2024

Microbial diversity, genomics, and phage–host interactions of cyanobacterial harmful algal blooms

The occurrence of cyanobacterial harmful algal blooms (cyanoHABs) is related to their physical and chemical environment. However, less is known about their associated microbial interactions and processes. In this study, cyanoHABs were analyzed as a microbial ecosystem, using 1 year of 16S rRNA sequencing and 70 metagenomes collected during the bloom season from Lake Okeechobee (Florida, USA). Biogeographical patterns observed in microbial community composition and function reflected ecological zones distinct in their physical and chemical parameters that resulted in bloom “hotspots” near major lake inflows. Changes in relative abundances of taxa within multiple phyla followed increasing bloom severity. Functional pathways that correlated with increasing bloom severity encoded organic nitrogen and phosphorus utilization, storage of nutrients, exchange of genetic material, phage defense, and protection against oxidative stress, suggesting that microbial interactions may promote cyanoHAB resilience. Cyanobacterial communities were highly diverse, with picocyanobacteria ubiquitous and oftentimes most abundant, especially in the absence of blooms. The identification of novel bloom-forming cyanobacteria and genomic comparisons indicated a functionally diverse cyanobacterial community with differences in its capability to store nitrogen using cyanophycin and to defend against phage using CRISPR and restriction-modification systems. Considering blooms in the context of a microbial ecosystem and their interactions in nature, physiologies and interactions supporting the proliferation and stability of cyanoHABs are proposed, including a role for phage infection of picocyanobacteria. This study displayed the power of “-omics” to reveal important biological processes that could support the effective management and prediction of cyanoHABs.

Florida↗
USGS2025

CaDAVEr: A metagenome-assembled genome catalog of microbial decomposers across vertebrate environments

Microbial degradation of organic matter is a fundamental Earth process, yet a mechanistic understanding of microbial metabolisms and successional ecology involved in decomposition remains poorly understood. Here, we announce the recovery of 277 cadaver-associated soil metagenome-assembled genomes to enhance our understanding of vertebrate decomposition microbial processes.

Microbiology Resource Announcements↗
USGS2011

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

Gulf Of Mexico↗
USGS2011

A survey of alterations in microbial community diversity in marine sediments in response to oil from the Deepwater Horizon spill: Northern Gulf of Mexico shoreline, Texas to Florida

Microbial community genomic DNA was extracted from sediment samples collected from the northern Gulf of Mexico (NGOM) coast. These samples had a high probability of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon (DWH) drilling site. The hypothesis for this project was that presence of M-1 oil in coastal sediments would significantly alter the diversity within the microbial communities associated with the impacted sediments. To determine if community-level changes did or did not occur following exposure to M-1 oil, microbial community-diversity fingerprints were generated and compared. Specific sequences within the community's genomic DNA were first amplified using the polymerase chain reaction (PCR) using a primer set that provides possible resolution to the species level. A second nested PCR that was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. These nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Sediment samples with similar fingerprints were grouped and compared to oil-fingerprint data from Rosenbauer and others (2010). The microbial community fingerprints grouped closely when identifying those sites that had been impacted by M-1 oil (N=12) and/or some mixture of M-1 and other oil (N=4), based upon the oil fingerprints. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the NGOM coast. These communities contain microbes capable of degrading oil and related hydrocarbons, making this information relevant to response and recovery of the NGOM from the DWH incident.

Gulf Of Mexico↗
USGS2024

Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)

With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer ( Odocoileus virginianus ) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants ( Mycoplasma ovipneumoniae , Trueperella pyogenes , Pasteurella multocida , Anaplasma phagocytophilum , Fusobacterium necrophorum ); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.

Microbial Genomics↗
USGS2021

The roles of antimicrobial resistance, phage diversity, isolation source, and selection in shaping the genomic architecture of Bacillus anthracis

Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. While analyses of genetic data from across the globe have increased our understanding of this bacterium’s population genomic structure, the influence of selective pressures on this successful pathogen is not well understood. In this study, we investigate the effects of antimicrobial resistance, phage diversity, geography and isolation source in shaping population genomic structure. We also identify a suite of candidate genes potentially under selection, driving patterns of diversity across 356 globally extant B. anthracis genomes. We report ten antimicrobial resistance genes and 11 different prophage sequences, resulting in the first large-scale documentation of these genetic anomalies for this pathogen. Results of random forest classification suggest genomic structure may be driven by a combination of antimicrobial resistance, geography and isolation source, specific to the population cluster examined. We found strong evidence that a recombination event linked to a gene involved in protein synthesis may be responsible for phenotypic differences between comparatively disparate populations. We also offer a list of genes for further examination of B. anthracis evolution, based on high-impact single nucleotide polymorphisms (SNPs) and clustered mutations. The information presented here sheds new light on the factors driving genomic structure in this notorious pathogen and may act as a road map for future studies aimed at understanding functional differences in terms of B. anthracis biogeography, virulence and evolution.

Microbial Genomics↗
USGS2025

Diversity of polyomaviruses and papillomaviruses in penguins from eastern and western Antarctica

Polyomaviruses and papillomaviruses are icosahedral viruses with small circular dsDNA genomes. Limited information on their diversity and evolution in avian hosts is available, with even less known regarding Antarctic penguins. Prior to this study, only one polyomavirus and two papillomaviruses had been identified in Adélie penguins ( Pygoscelis adeliae ). To expand our knowledge of these viruses in Antarctic penguins, we collected faecal and cloacal swab samples from 246 Adélie penguins over 3 breeding seasons (2021–2024) and 10 emperor penguins ( Aptenodytes forsteri ) during the 2023–2024 season on Ross Island (Ross Sea). Additionally, we sampled 66 Adélie, 40 chinstrap ( Pygoscelis antarcticus ) and 71 gentoo ( Pygoscelis papua ) penguins during the 2022–2023 season across various sites on the Antarctic Peninsula. All samples were screened for papillomaviruses and polyomaviruses. We identified 31 polyomaviruses in Adélie, gentoo and chinstrap penguins and 4 papillomaviruses in Adélie penguins sampled in both eastern and western Antarctica. The 31 penguin polyomaviruses belong to a single species but form four distinct variants that are host species specific with strong geographic clustering. The four papillomaviruses represent three different types, of which two are new types from Adélie penguins sampled on Yalour Island in the West Antarctic Peninsula. Co-occurrence of two polyomavirus variants was identified in two individual gentoo penguins. Both of these variants appear to be circulating in gentoo penguins at Cierva Cove, Hope Bay in Trinity Peninsula along the Antarctic Peninsula, and at Hannah Point on Livingstone Island and Stranger Point on King George Island in the South Shetland Islands. Here, we expand the known diversity, host and geographical ranges of penguin polyomaviruses and, together with a previously identified polyomavirus on Ross Island from 2012 to 2013, show that they form five distinct lineages. The four papillomaviruses identified in this study, together with two previously identified from Ross Island in 2012 and 2013 breeding seasons, show substantial diversity reflecting four papillomavirus types across three viral species and two distinct genera. Continued surveillance and viral genomic analysis across a larger geographical framework will help understand the evolution, transmission and incidence rates of these viruses.

Microbial Genomics↗
USGS2024

Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats

Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19–65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces -bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.

Microbial Genomics↗
USGS2026

The global proliferation of aquatic, benthic Microcoleus : Taxonomy, distribution, toxin production, ecology, and future directions

There have been sporadic reports of aquatic, benthic Microcoleus proliferations in freshwater rivers, lakes, and reservoirs for four decades, with reports increasing in frequency over the last twenty years, suggesting a possible rise in their global distribution, frequency, and intensity. Microcoleus can produce anatoxins which are neurotoxic, and ingestion of toxic mats has caused hundreds of dog fatalities and raised serious human and ecological health concerns. This review synthesizes and evaluates current knowledge on Microcoleus distribution, taxonomy, toxin production, toxicity, ecology, environmental drivers, and biotic interactions. Toxin-producing Microcoleus have been reported in at least 18 countries, though many regions have not conducted toxin testing, suggesting a broader but under-reported distribution. Proliferations occur across diverse habitats, including cobble-bedded streams, large sandy rivers, reservoirs, and lakes. Microcoleus proliferations also occur on macrophytes, both in lakes and rivers. Genomic analyses currently classify anatoxin-producing Microcoleus into distinct species, with all known anatoxin-producers isolated from freshwater ecosystems. Anatoxin concentrations vary widely over space and time, within and among waterbodies. While studies on environmental drivers remain limited, research in cobble-bedded rivers suggests that moderate enrichment of dissolved inorganic nitrogen and low dissolved reactive phosphorus concentrations in the water column promote proliferation. Metagenomic approaches have revealed unique nutrient acquisition and storage strategies used by Microcoleus . Key knowledge gaps remain around the environmental and ecological triggers of proliferation, toxin production, genomic diversity and microbial interactions. Addressing these gaps through coordinated, global studies using robust datasets and consistent methods is critical to improve prediction, monitoring, and mitigation of this increasingly widespread public and ecological health threat.

Water Research↗
USGS2021

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

Background Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). Results We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H 2 18 O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO 2 ) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18 O in soil and respired CO 2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Conclusions Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.

Microbiome↗
USGS2019

Is there convergence of gut microbes in blood-feeding vertebrates?

Animal microbiomes play an important role in dietary adaptation, yet the extent to which microbiome changes exhibit parallel evolution is unclear. Of particular interest is an adaptation to extreme diets, such as blood, which poses special challenges in its content of proteins and lack of essential nutrients. In this study, we assessed taxonomic signatures (by 16S rRNA amplicon profiling) and potential functional signatures (inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt)) of haematophagy in birds and bats. Our goal was to test three alternative hypotheses: no convergence of microbiomes, convergence in taxonomy and convergence in function. We find a statistically significant effect of haematophagy in terms of microbial taxonomic convergence across the blood-feeding bats and birds, although this effect is small compared to the differences found between haematophagous and non-haematophagous species within the two host clades. We also find some evidence of convergence at the predicted functional level, although it is possible that the lack of metagenomic data and the poor representation of microbial lineages adapted to haematophagy in genome databases limit the power of this approach. The results provide a paradigm for exploring convergent microbiome evolution replicated with independent contrasts in different host lineages.

Philosophical Transactions of the Royal Society B:↗
USGS2021

Influence of filter pore size on composition and relative abundance of bacterial communities and select host-specific MST markers in coastal waters of southern Lake Michigan

Water clarity is often the primary guiding factor in determining whether a prefiltration step is needed to increase volumes processed for a range of microbial endpoints. In this study, we evaluate the effect of filter pore size on the bacterial communities detected by 16S rRNA gene sequencing and incidence of two host-specific microbial source tracking (MST) markers in a range of coastal waters from southern Lake Michigan, using two independent data sets collected in 2015 (bacterial communities) and 2016–2017 (MST markers). Water samples were collected from river, shoreline, and offshore areas. For bacterial communities, each sample was filtered through a 5.0-μm filter, followed by filtration through a 0.22-μm filter, resulting in 70 and 143 filter pairs for bacterial communities and MST markers, respectively. Following DNA extraction, the bacterial communities were compared using 16S rRNA gene amplicons of the V3–V4 region sequenced on a MiSeq Illumina platform. Presence of human ( Bacteroides HF183) and gull (Gull2, Catellicoccus marimammalium ) host-specific MST markers were detected by qPCR. Actinobacteriota, Bacteroidota, and Proteobacteria, collectively represented 96.9% and 93.9% of the relative proportion of all phyla in the 0.22- and 5.0-μm pore size filters, respectively. There were more families detected in the 5.0-μm pore size filter (368) than the 0.22-μm (228). There were significant differences in the number of taxa between the two filter sizes at all levels of taxonomic classification according to linear discriminant analysis (LDA) effect size (LEfSe) with as many as 986 taxa from both filter sizes at LDA effect sizes greater than 2.0. Overall, the Gull2 marker was found in higher abundance on the 5.0-μm filter than 0.22 μm with the reverse pattern for the HF183 marker. This discrepancy could lead to problems with identifying microbial sources of contamination. Collectively, these results highlight the importance of analyzing pre- and final filters for a wide range of microbial endpoints, including host-specific MST markers routinely used in water quality monitoring programs. Analysis of both filters may increase costs but provides more complete genomic data via increased sample volume for characterizing microbial communities in coastal waters.

Illinois, Indiana, Wisconsin↗
USGS2021

Activity-based, genome-resolved metagenomics uncovers key populations and pathways involved in subsurface conversions of coal to methane

Microbial metabolisms and interactions that facilitate subsurface conversions of recalcitrant carbon to methane are poorly understood. We deployed an in situ enrichment device in a subsurface coal seam in the Powder River Basin (PRB), USA, and used BONCAT-FACS-Metagenomics to identify translationally active populations involved in methane generation from a variety of coal-derived aromatic hydrocarbons. From the active fraction, high-quality metagenome-assembled genomes (MAGs) were recovered for the acetoclastic methanogen, Methanothrix paradoxum , and a novel member of the Chlorobi with the potential to generate acetate via the Pta-Ack pathway. Members of the Bacteroides and Geobacter also encoded Pta-Ack and together, all four populations had the putative ability to degrade ethylbenzene, phenylphosphate, phenylethanol, toluene, xylene, and phenol. Metabolic reconstructions, gene analyses, and environmental parameters also indicated that redox fluctuations likely promote facultative energy metabolisms in the coal seam. The active “ Chlorobi PRB” MAG encoded enzymes for fermentation, nitrate reduction, and multiple oxygenases with varying binding affinities for oxygen. “ M. paradoxum PRB” encoded an extradiol dioxygenase for aerobic phenylacetate degradation, which was also present in previously published Methanothrix genomes. These observations outline underlying processes for bio-methane from subbituminous coal by translationally active populations and demonstrate activity-based metagenomics as a powerful strategy in next generation physiology to understand ecologically relevant microbial populations.

Montana, Wyoming↗
USGS2022

Millennia-old coral holobiont DNA provides insight into future adaptive trajectories

Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.

Molecular Ecology↗
USGS2022

Microbial source tracking and evaluation of best management practices for restoring degraded beaches of Lake Michigan

Attempts to mitigate shoreline microbial contamination require a thorough understanding of pollutant sources, which often requires multiple years of data collection (e.g., point/nonpoint) and the interacting factors that influence water quality. Because restoration efforts can alter shoreline or beach morphology, revisiting source inputs is often necessary. Microbial source tracking (MST) using source-specific molecular markers, genomic community analyses, and physical modeling was used to identify contamination sources along three Lake Michigan beaches of the Laurentian Great Lakes with historically high fecal indicator bacteria (FIB, E. coli ) concentrations. Genetic markers for human (Bacteroides HF183) and mixed gull species ( Catellicoccus marimammalium ) fecal sources were tested from water and sediment. Gene sequencing (16S rRNA) was used to identify similarities in bacterial communities in nearshore water, river inputs, sand, sediment, and groundwater. Synoptic surveys of water exchange were conducted to determine nearshore-offshore interactions of FIB. In addition to these MST studies, best management practices to mitigate FIB, including gull deterrence, slope grading, wetland establishment, and shoreline plantings, were reviewed for their effectiveness at reducing FIB concentrations over time. Using multiple tools for MST helped identify primary and secondary sources of FIB (gulls, stormwater inputs) and the physical processes that exacerbate FIB concentrations (onshore currents, limited circulation). Management actions were successful in the short-term at reducing FIB, but scope of success was temporally limited, with FIB concentrations often rebounding. Results highlight the usefulness of MST to inform best management practices and the need for a sustained adaptive approach that adjusts for changes in the coastal system.

Illinois, Wisconsin↗
USGS2015

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River

Knowledge of the diversity and ecological function of the microbial consortia of James River in Virginia, USA, is essential to developing a more complete understanding of the ecology of this model river system. Metagenomic analysis of James River's planktonic microbial community was performed for the first time using an unamplified genomic library and a 16S rDNA amplicon library prepared and sequenced by Ion PGM and MiSeq, respectively. From the 0.46-Gb WGS library (GenBank:SRR1146621; MG-RAST:4532156.3), 4 × 10 6 reads revealed >3 × 10 6 genes, 240 families of prokaryotes, and 155 families of eukaryotes. From the 0.68-Gb 16S library (GenBank:SRR2124995; MG-RAST:4631271.3; EMB:2184), 4 × 10 6 reads revealed 259 families of eubacteria. Results of the WGS and 16S analyses were highly consistent and indicated that more than half of the bacterial sequences were Proteobacteria , predominantly Comamonadaceae . The most numerous genera in this group were Acidovorax (including iron oxidizers, nitrotolulene degraders, and plant pathogens), which accounted for 10 % of assigned bacterial reads. Polaromonas were another 6 % of all bacterial reads, with many assignments to groups capable of degrading polycyclic aromatic hydrocarbons. Albidiferax (iron reducers) and Variovorax (biodegraders of a variety of natural biogenic compounds as well as anthropogenic contaminants such as polycyclic aromatic hydrocarbons and endocrine disruptors) each accounted for an additional 3 % of bacterial reads. Comparison of these data to other publically-available aquatic metagenomes revealed that this stretch of James River is highly similar to the upper Mississippi River, and that these river systems are more similar to aquaculture and sludge ecosystems than they are to lakes or to a pristine section of the upper Amazon River. Taken together, these analyses exposed previously unknown aspects of microbial biodiversity, documented the ecological responses of microbes to urban effects, and revealed the noteworthy presence of 22 human-pathogenic bacterial genera (e.g., Enterobacteriaceae , pathogenic Pseudomonadaceae , and ‘ Vibrionales' ) and 6 pathogenic eukaryotic genera (e.g., Trypanosomatidae and Vahlkampfiidae). This information about pathogen diversity may be used to promote human epidemiological studies, enhance existing water quality monitoring efforts, and increase awareness of the possible health risks associated with recreational use of James River.

Virginia↗
USGS2024

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables

Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.

Nature Microbiology↗
USGS2025

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

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 the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of “anthropogenic” carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.

California↗