Alexander B. ChaseSouthern Methodist University | SMU · Department of Earth Sciences
Alexander B. Chase
Professor
Starting my own lab at SMU this Fall. Let me know if you are interested in joining, openings at multiple levels.
About
26
Publications
11,919
Reads
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357
Citations
Citations since 2017
Introduction
Alexander Chase currently works at the Department of Earth Sciences at Southern Methodist University (SMU). Alexander does research in Ecology, Bioinformatics, Natural Product Research, and Microbiology. His most recent publication is 'Adaptive differentiation and rapid evolution of a soil bacterium across a climate gradient' that was published in PNAS.
Additional affiliations
January 2019 - July 2022
September 2014 - June 2018
September 2014 - December 2018
Education
September 2014 - December 2018
September 2014 - December 2017
September 2008 - June 2012
Publications
Publications (26)
Much genetic diversity within a bacterial community is likely obscured by microdiversity within operational taxonomic units (OTUs) defined by 16S rRNA gene sequences. However, it is unclear how variation within this microdiversity influences ecologically relevant traits. Here, we employ a multifaceted approach to investigate microdiversity within t...
The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely‐related soil bacteria and relating these traits to bacterial abundances and geo...
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 compare divergent strains from disparate environments under varied selective pressures. Here, w...
Significance
Increasing evidence suggests that evolutionary processes frequently shape ecological patterns; however, most microbiome studies thus far have focused on only the ecological responses of these communities. By using parallel field experiments and focusing in on a model soil bacterium, we showed that bacterial “species” are differentially...
Microbial natural products are traditionally exploited for their pharmaceutical potential, yet our understanding of the evolutionary processes driving BGC evolution and compound diversification remains poorly developed. While HGT is recognized as an integral driver of BGC distributions, we find that the effects of vertical inheritance on BGC divers...
Microbial natural products remain a crucial source of lead compounds for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, a narrow taxonomic focus on the relatively few microbes that can be cultured, and laboratory growth conditions that do not support biosynthetic gene expression. Here...
Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically important natural products, yet only a small fraction of nature’s polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be delineated into different classes and subclasses based on domain organ...
Earth system models disagree on the future of global soil carbon
A new manumycin-type natural product named pacificamide (1) and its candidate biosynthetic gene cluster (pac) were discovered from the marine actinobacterium Salinispora pacifica CNT-855. The structure of the compound was determined using NMR, electronic circular dichroism, and bioinformatic predictions. The pac gene cluster is unique to S. pacific...
![FIG 3 (a and b) Percent difference (mean 6 standard error [SE]) in...](publication/358308146/figure/fig2/AS:1137764707905537@1648275653525/a-and-b-Percent-difference-mean-6-standard-error-SE-in-relative-abundance-of_Q320.jpg)
Global change experiments often observe shifts in bacterial community composition based on 16S rRNA gene sequences. However, this genetic region can mask a large amount of genetic and phenotypic variation among bacterial strains sharing even identical 16S regions. As such, it remains largely unknown whether variation at the sub-16S level, sometimes...
While marine natural products have been investigated for anticancer drug discovery, they are barely screened against rare cancers. Thus, in our effort to discover potential drug leads against the rare cancer pseudomyxoma peritonei (PMP), which currently lacks effective drug treatments, we screened extracts of marine actinomycete bacteria against th...
Dietary shifts can have a direct impact on the gut microbiome by preferentially selecting for microbes capable of utilizing the various dietary nutrients. The intake of dietary fiber has decreased precipitously in the last century, while consumption of processed foods has increased. Fiber, or microbiota-accessible carbohydrates (MACs), persist in t...
While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving their diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) using 118 strains wi...
Genomics and metabolomics are widely used to explore specialized metabolite diversity. The Paired Omics Data Platform is a community initiative to systematically document links between metabolome and (meta)genome data, aiding the identification of natural product biosynthetic origins and metabolite structures.
Dietary shifts can have a direct impact on the gut microbiome by preferentially selecting for microbes capable of utilizing the various dietary nutrients. Intake of dietary fiber has decreased precipitously in the last century, while consumption of processed foods has increased. Fiber, or microbiota-accessible carbohydrates (MACs), persist in the d...
While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving their distributions, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the diversity and distribution of biosynthetic gene clusters (BGCs) in 118 strains across ni...
Ten representative actinobacterial strains isolated from marine sediments collected worldwide were studied to determine their taxonomic status. The strains were previously identified as members of the genus Salinispora and shared >99 % 16S rRNA gene sequence similarity to the three currently recognized Salinispora species. Comparative genomic analy...
Course-based undergraduate research experiences (CUREs) are an effective way to introduce students to contemporary scientific research. Research experiences have been shown to promote critical thinking, improve understanding and proper use of the scientific method, and help students learn practical skills including writing and oral communication. W...
In microorganisms, specifically free-living bacteria and archaea, the equivalent of the biological species concept does not exist, creating several barriers to the study of the fine-scale genetic structure of microbial populations and thus, the processes contributing to microbial diversification. More often than not, studies attempting to delineate...
Randomness can alter the diversity and composition of ecological communities. Such stochasticity may therefore obscure the relationship between the environment and community composition and hinder our ability to predict the relationship between biodiversity and ecosystem functioning. This study investigated the role of stochastic processes, environ...
Understanding bacterial responses to physiological conditions is an important priority for combating opportunistic infections. The majority of CF patients succumb to inflammation and necrosis in the airways, arising from chronic infection due to ineffective mucociliary clearance. Steep pH gradients characterize the CF airways but are not often inco...
For centuries, ecologists have used biogeographic patterns to test the processes governing the assembly and maintenance of plant and animal communities. Similarly, evolutionary biologists have used historical biogeography (e.g. phylogeography) to understand the importance of geological events as barriers to dispersal that shape species distribution...
Assigning ecological roles to bacterial taxa remains imperative to understanding how microbial communities will respond to changing environmental conditions. Here we analyze the genus Curtobacterium, as it was found to be the most abundant taxon in a leaf litter community in southern California. Traditional characterization of this taxon predominan...
Following the success of the inaugural games, the Microbial Olympics return with a new series of events and microbial competitors. The games may have moved to a new hosting venue, but the dedication to training, fitness, competition (and yes, education and humour) lives on.
Projects
Projects (4)
It is increasingly clear that there is extensive genetic diversity within 16S-based OTUs, so-called microdiversity, in environmental habitats. However, a key question is whether this genetic variation is phenotypically relevant and has consequences for microbial diversity and distribution.
In natural microbial communities, the detection of traits responsible for adaptive responses to environmental conditions is incredibly difficult. While local adaptation may be ongoing, the adaptive changes within a species are small compared to the interspecific differences contributing to community level shifts. We will investigate the types of genetic changes potentially influencing the evolutionary response of Curtobacterium along a climate gradient. The field experiment offers a unique examination on the direct effects of natural environmental variation on a bacterium's capacity for evolutionary change.
Using a course-based undergraduate research experience (CURE) course, we sought to understand the impact of fiber consumption on the gut microbiome. The students drastically shifted their diets to consume 40-50 grams/day of fiber for two weeks. Through the course, students were educated on dietary nutrition and high fiber foods, including lentils, beans, berries, avocados and nuts as effective sources of fiber.
