Geology topics

Diana E. Northup

Publications and source records attributed to Diana E. Northup.

7 recordsLinked to original sources

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↗

USGS2022

Great diversity of KSα sequences from bat-associated microbiota suggests novel sources of uncharacterized natural products

Polyketide synthases (PKSs) are multidomain enzymes in microorganisms that synthesize complex, bioactive molecules. PKS II systems are iterative, containing only a single representative of each domain: ketosynthase alpha (KS α "> α � ⁠ ), ketosynthase beta and the acyl carrier protein. Any gene encoding for one of these domains is representative of an entire PKS II biosynthetic gene cluster (BGC). Bat skin surfaces represent an extreme environment prolific in Actinobacteria that may constitute a source for bioactive molecule discovery. KS α "> α � sequences were obtained from culturable bacteria from bats in the southwestern United States. From 467 bat bacterial isolates, we detected 215 (46%) had KS α "> α � sequences. Sequencing yielded 210 operational taxonomic units, and phylogenetic placement found 45 (21%) shared <85% homology to characterized metabolites. Additionally, 16 Actinobacteria genomes from the bat microbiome were analyzed for biosynthetic capacity. A range of 69–93% of the BGCs were novel suggesting the bat microbiome may contain valuable uncharacterized natural products. Documenting and characterizing these are important in understanding the susceptibility of bats to emerging infectious diseases, such as white-nose syndrome. Also noteworthy was the relationship between KS α "> α � homology and total BGC novelty within each fully sequenced strain. We propose amplification and detection of KS α "> α � could predict a strain's global biosynthetic capacity.

FEMS Microbiology Ecology↗

USGS2021

Southwestern bats and their external bacteria

Bat species diversity within the United States is greatest in the Southwest, with approximately 30 species present. At least 16 of these bat species hibernate and are susceptible to white-nose syndrome (WNS), which is caused by the fungus Pseudogymnoascus destructans . Since 2006, millions of bats from 35 U.S. states and 7 Canadian provinces have died from WNS. In previous studies of external surfaces of bats sampled from southwestern states, Actinobacteria were detected that were shown to have antifungal properties against P. destructans in laboratory testing. These studies motivated us to expand our research to sites that represent possible gateways for P. destructans to enter the Southwest so that we could establish a baseline of bat microbiota before the arrival of WNS. We surveyed for the presence of bats and their external microbiota at 3 national parks and monuments located in southeastern Colorado and northeastern New Mexico. Our results document new occurrence records of bat species and their external bacteria at each sampling location. Additionally, we provide insight on the composition of bat external microbiota in the absence of P. destructans , while revealing information about the Streptomyces and other possible native defenses of bats against P. destructans at a gateway into the Southwest.

Western North American Naturalist↗

USGS2019

Streptomyces corynorhini sp. nov., isolated from Townsend’s big-eared bats (Corynorhinus townsendii)

Four bacterial strains, with the capability of inhibiting Pseudogymnoascus destructans , the causative agent of white-nose syndrome, were isolated from male Townsend’s big-eared bats ( Corynorhinus townsendii , Family: Vespertilionidae) in New Mexico. Isolates AC161, AC162, AC208, and AC230 T were characterised as a novel clade using morphological, phenotypic and phylogenetic analysis. A draft genome of the type strain was completed to determine its taxonomy and secondary metabolite biosynthetic potential. Multi-locus sequence analysis nests AC230 T with neighbours Streptomyces scopuliridis (NRRL B-24574 T ), Streptomyces lushanensis (NRRL B-24994 T ), Streptomyces odonnellii (NRRL B-24891 T ) and Streptomyces niveus (NRRL 2466 T ). Further phylogenetic analysis showed the MLSA distances between AC230 T and its near neighbours are much greater than the generally accepted threshold (> 0.007) for bacterial species delineation. DNA–DNA relatedness between AC230 T and its near neighbours ranged between 25.7 ± 2.1 and 29.9 ± 2.4%. The DNA G+C content of the genomic DNA of the type strain is 71.7 mol%. Isolate AC230 T presents a white to ivory hue on most ISP media and its micromorphology exhibits ovoid spores with smooth surfaces in flexuous chains. Based on our study of AC230 T , the strain warrants the assignment to a novel species, for which the name Streptomyces corynorhini sp. nov. is proposed. The type strain is AC230 T (= JCM 33171 T , = ATCC TSD155 T ).

Antonie van Leeuwenhoek↗

USGS2017

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

PeerJ↗

USGS2017

Western bats as a reservoir of novel Streptomyces species with antifungal activity

At least two-thirds of commercial antibiotics today are derived from Actinobacteria , more specifically from the genus Streptomyces . Antibiotic resistance and new emerging diseases pose great challenges in the field of microbiology. Cave systems, in which actinobacteria are ubiquitous and abundant, represent new opportunities for the discovery of novel bacterial species and the study of their interactions with emergent pathogens. White-nose syndrome is an invasive bat disease caused by the fungus Pseudogymnoascus destructans , which has killed more than six million bats in the last 7 years. In this study, we isolated naturally occurring actinobacteria from white-nose syndrome (WNS)-free bats from five cave systems and surface locations in the vicinity in New Mexico and Arizona, USA. We sequenced the 16S rRNA region and tested 632 isolates from 12 different bat species using a bilayer plate method to evaluate antifungal activity. Thirty-six actinobacteria inhibited or stopped the growth of P. destructans , with 32 (88.9%) actinobacteria belonging to the genus Streptomyces . Isolates in the genera Rhodococcus , Streptosporangium , Luteipulveratus , and Nocardiopsis also showed inhibition. Twenty-five of the isolates with antifungal activity against P. destructans represent 15 novel Streptomyces spp. based on multilocus sequence analysis. Our results suggest that bats in western North America caves possess novel bacterial microbiota with the potential to inhibit P. destructans .

Applied and Environmental Microbiology↗

USGS2014

The transport of nonindigenous microorganisms into caves by human visitation: a case study at Carlsbad Caverns National Park

A series of atmospheric investigations was conducted in Carlsbad Cavern to determine if human visitation is a possible cause for the contamination of the cave system with non-indigenous microorganisms. In 2004, site-specific culture-based data demonstrated that Staphylococcus spp. colony-forming units (CFUs) were the most prevalent members of the atmospheric community along the paved visitor trail (avg. 18.8% of CFU), while Knoellia spp. CFUs dominated off-trail locations (40.1% of CFU). Fungal culture data revealed that Penicillium and Aspergillus were prevalent in the Lunch Room where food is stored, sold, and consumed. Ubiquitous genera such as Cladosporium and Alternaria were prevalent near the Natural Entrance of the cave, and the general trend was a decrease in fungal CFUs with progression into the cave system, except for the area near the Lunch Room. Management practices such as prohibition of crumb-generating types of foods could be considered to protect cave health. In 2009, nonculture-based analyses demonstrated that Enterobacteriaceae were the dominant microbiota at sites along the descent trail and within the Lunch Room. Dominance of Enterobacteriaceae has not been previously demonstrated in caves. Either they are naturally occurring indigenous members, or their presence is a marker of anthropogenic contamination.

New Mexico↗