About

Michael J. Clark is an Assistant Professor of Practice at the University of Arizona, affiliated with the School of Nutritional Sciences and Wellness. He is based on the Yuma Campus and holds the credentials SNS, BS, and MPA. His role involves teaching and practice within the field of nutritional sciences, contributing to the university's educational mission in this area. His contact information includes an email address (mjclark2@arizona.edu) and a phone number (520-621-1186), with office hours from 9AM to 3PM, Monday through Friday. The university recognizes his position as part of its broader efforts in education, community service, and engagement with Indigenous communities.

Research topics

• Biology
• Botany
• Genetics
• Microbiology
• Chemistry

Selected publications

• Rhizosphere controls over subsurface nitrous oxide production during and after severe drought in an experimental tropical rain forest

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• Luteibacter mycovicinus sp. nov., a yellow-pigmented gammaproteobacterium found as an endohyphal symbiont of endophytic Ascomycota

  INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · 2024-05-02 · 2 citations

  articleOpen access

  We isolated and described a yellow-pigmented strain of bacteria (strain 9143 T ), originally characterized as an endohyphal inhabitant of an endophytic fungus in the Ascomycota. Although the full-length sequence of its 16S rRNA gene displays 99 % similarity to Luteibacter pinisoli , genomic hybridization demonstrated <30 % genomic similarity between 9143 T and its closest named relatives, further supported by average nucleotide identity results. This and related endohyphal strains form a well-supported clade separate from L. pinisoli and other validly named species including the most closely related Luteibacter rhizovicinus . The name Luteibacter mycovicinus sp. nov. is proposed, with type strain 9143 T (isolate DBL433), for which a genome has been sequenced and is publicly available from the American Type Culture Collection (ATCC TSD-257 T ) and from the Leibniz Institute DSMZ (DSM 112764 T ). The type strain reliably forms yellow colonies across diverse media and growth conditions (lysogeny broth agar, King’s Medium B, potato dextrose agar, trypticase soy agar and Reasoner's 2A (R2A) agar). It forms colonies readily at 27 °C on agar with a pH of 6–8, and on salt (NaCl) concentrations up to 2 %. It lacks the ability to utilize sulphate as a sulphur source and thus only forms colonies on minimal media if supplemented with alternative sulphur sources. It is catalase-positive and oxidase-negative. Although it exhibits a single polar flagellum, motility was only clearly visible on R2A agar. Its host range and close relatives, which share the endohyphal lifestyle, are discussed.

  PublisherDOI

• Interspecies killing activity of Pseudomonas syringae tailocins

  Microbiology · 2022 · 22 citations

  • Biology
  • Microbiology
  • Genetics

  tailocins and establish a platform for further investigations into the evolution of tailocin host range and strain specificity.

  PublisherDOI

• Interspecies Killing Activity of <i>Pseudomonas syringae</i> Tailocins

  bioRxiv (Cold Spring Harbor Laboratory) · 2022-07-30 · 1 citations

  preprintOpen access

  Abstract Tailocins are ribosomally synthesized bacteriocins, encoded by bacterial genomes, but originally derived from bacteriophage tails. As with both bacteriocins and phage, tailocins are largely thought to be species-specific with killing activity often assumed to be directed against closely-related strains. Previous investigations into interactions between tailocin host range and sensitivity across phylogenetically diverse isolates of the phytopathogen Pseudomonas syringae have demonstrated that many strains possess intraspecific tailocin activity and that this activity is highly precise and specific against subsets of strains. However, here we demonstrate that at least one strain of P. syringae , USA011R, defies both expectations and current overarching dogma because tailocins from this strain possess broad killing activity against other agriculturally significant phytopathogens such as Erwinia amylovora and Xanthomonas perforans as well as against the clinical human pathogen Salmonella choleraesuis . Moreover, we show that the full spectrum of this interspecific killing activity is not conserved across closely related strains with data suggesting that even if tailocins can target different species, they do so with different efficiencies. Our results reported herein highlight the potential for and phenotypic divergence of interspecific killing activity of P. syringae tailocins and establish a platform for further investigations into the evolution of tailocin host range and strain specificity.

  PublisherOA PDFDOI

• Transcriptional Profiles of a Foliar Fungal Endophyte ( <i>Pestalotiopsis</i> , Ascomycota) and Its Bacterial Symbiont ( <i>Luteibacter</i> , <i>Gammaproteobacteria</i> ) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction

  mSystems · 2022 · 25 citations

  • Biology
  • Botany
  • Chemistry

  .

  PublisherDOI

• Draft Genome Sequences of Multiple <i>Streptomyces</i> Isolates from Arizona

  Microbiology Resource Announcements · 2021-07-01

  articleOpen accessSenior author

  Streptomyces strains are bacteria that are well known for their distinctive physiology, behaviors, and ecology, as well as for being prodigious producers of diverse antibiotics. Here, we report draft genome sequences for eight Streptomyces strains that were isolated from multiple sky islands in Arizona and sequenced using an Oxford Nanopore Technologies Flongle adapter and MinION system.

  PublisherDOI

• Transcriptional profiles of a foliar fungal endophyte ( <i>Pestalotiopsis</i> , Ascomycota) and its endohyphal bacterium ( <i>Luteibacter</i> , Gammaproteobacteria) in co-culture support sulfur exchange and growth regulation

  bioRxiv (Cold Spring Harbor Laboratory) · 2021-11-25 · 1 citations

  preprintOpen access

  ABSTRACT Symbiosis with bacteria is widespread among eukaryotes, including fungi. Bacteria that live within fungal mycelia (endohyphal bacteria) occur in many plant-associated fungi, including diverse Mucoromycota and Dikarya. Pestalotiopsis sp. 9143 is a filamentous ascomycete isolated originally as a foliar endophyte of Platycladus orientalis (Cupressaceae). It is infected naturally with the endohyphal bacterium Luteibacter sp. 9143, which influences auxin and enzyme production by its fungal host. Previous studies have used transcriptomics to examine similar symbioses between endohyphal bacteria and root-associated fungi such as arbuscular mycorrhizal fungi and plant pathogens. However, currently there are no gene expression studies of endohyphal bacteria of Ascomycota, the most species-rich fungal phylum. We developed methods for assessing gene expression by Pestalotiopsis sp. and Luteibacter sp. when grown in co-culture and when each was grown axenically. Our assays showed that the density of Luteibacter sp. in co-culture was greater than in axenic culture, but the opposite was true for the Pestalotiopsis sp. Dual RNA-seq data demonstrate that growing in co-culture modulates developmental and metabolic processes in both the fungus and bacterium, potentially through changes in the balance of organic sulfur via methionine acquisition. Our analyses also suggest an unexpected, potential role of the bacterial type VI secretion system in symbiosis establishment, expanding current understanding of the scope and dynamics of fungal-bacterial symbioses. TWEET When in co-culture, Luteibacter downregulates motility and upregulates a T6SS. Gene expression changes in its host, Pestalotiopsis , suggest the bacterium impacts fungal cell structure and methionine availability. IMPORTANCE Interactions between microbes and their hosts have important outcomes for host- and environmental health. Foliar fungal endophytes that infect healthy plants can harbor facultative endosymbionts called endohyphal bacteria, which can influence the outcome of plant-fungus interactions. These bacterial-fungal interactions can be influential but are poorly understood, particularly from a transcriptome perspective. Here, we report on a comparative, dual RNA-seq study examining the gene expression patterns of a foliar fungal endophyte and a facultative endohyphal bacterium when cultured together vs. separately. Our findings support a role for the fungus in providing organic sulfur to the bacterium, potentially through methionine acquisition, and potential involvement of a bacterial type VI secretion system in symbiosis establishment. This work adds to the growing body of literature characterizing endohyphal bacterial-fungal interactions, with a focus on a model facultative bacterial-fungal symbiosis in two species-rich lineages, the Ascomycota and Proteobacteria.

  PublisherOA PDFDOI

• Experimental evolution of the megaplasmid pMPPla107 in <i>Pseudomonas stutzeri</i> enables identification of genes contributing to sensitivity to an inhibitory agent

  Philosophical Transactions of the Royal Society B Biological Sciences · 2021-11-29 · 5 citations

  articleOpen access

  Abstract Horizontally transferred elements, such as plasmids, can burden host cells with various metabolic and fitness costs and may lead to other potentially detrimental phenotypic effects. Acquisition of the Pseudomonas syringae megaplasmid pMPPla107 by various Pseudomonads causes sensitivity to a growth-inhibiting substance that is produced in cultures by Pseudomonads during growth under standard laboratory conditions. After approximately 500 generations of laboratory passage of Pseudomonas stutzeri populations containing pMPPla107, strains from two out of six independent passage lines displayed resistance to this inhibitory agent. Resistance was transferable and is, therefore, associated with mutations occurring on pMPPla107. Resequencing experiments demonstrated that resistance is likely due to a large deletion on the megaplasmid in one line, and to a nonsynonymous change in an uncharacterized megaplasmid locus in the other strain. We further used allele exchange experiments to confirm that resistance is due to this single amino acid change in a previously uncharacterized megaplasmid protein, which we name SkaA. These results provide further evidence that costs and phenotypic changes associated with horizontal gene transfer can be compensated through single mutational events and emphasize the power of experimental evolution and resequencing to better understand the genetic basis of evolved phenotypes. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

  PublisherOA PDFDOI

• Genomic Background Governs Opposing Responses to Nalidixic Acid upon Megaplasmid Acquisition in <i>Pseudomonas</i>

  mSphere · 2021-02-23 · 5 citations

  articleOpen accessSenior author

  Numerous studies have demonstrated that gene transfer events (e.g., plasmid acquisition) can entail a variety of costs that arise as by-products of the incorporation of foreign DNA into established physiological and genetic systems. These costs can be ameliorated through evolutionary time by the occurrence of compensatory mutations, which stabilize the presence of a horizontally transferred region within the genome but which also may skew future adaptive possibilities for these lineages. Here, we demonstrate another possible outcome, that phenotypic changes arising as a consequence of the same horizontal gene transfer (HGT) event are costly to some strains but may actually be beneficial in other genomic backgrounds under the right conditions. These results provide a new viewpoint for considering conditions that promote plasmid maintenance and highlight the influence of genomic and environmental contexts when considering amelioration of fitness costs after HGT events.

  PublisherDOI

• Complete Genome Sequences for <i>Pseudomonas</i> sp. Strains 29A and 43A

  Microbiology Resource Announcements · 2020-09-23

  articleOpen access

  Pseudomonas sp. strains 29A and 43A were originally isolated from the phyllosphere of individual plants of Cardamine cordifolia (Brassicaceae). Here, we report complete genome sequences for these two closely related strains, assembled using a hybrid approach combining Illumina paired-end reads and longer reads sequenced on an Oxford Nanopore MinION flow cell.

  PublisherDOI

Frequent coauthors

• David A. Baltrus

  32 shared

• Brian A. Smith

  University of Minnesota

  13 shared

• Caitlin Smith

  University of Arizona

  11 shared

• Kevin Dougherty

  Foundation Medicine (United States)

  10 shared

• Joseph E. Spraker

  Paragon Genomics (United States)

  10 shared

• Kevin L. Hockett

  Pennsylvania State University

  9 shared

• Madison Mollico

  University of Arizona

  7 shared

• Courtney Leligdon

  University of Arizona

  5 shared