Biology subjects

Hayes, M. M.

Publications and source records attributed to Hayes, M. M..

3 recordsLinked to original sources

bioRxiv2026

Bridge recombinase enables versatile rewriting of bacterial genomes

Bacteria drive crucial processes across ecosystems and impact human health, yet tools to rewrite microbiomes remain limited. Here, we show that bridge recombinase enables versatile and programmable genome editing across the bacterial tree of life. In Escherichia coli, we achieved 142 kb insertions at >90% efficiency, megabase-scale inversions (2.3 Mb), and pathway-scale 50 kb excisions. With a single ortholog and bridge RNA (bRNA), we edited bacterial isolates spanning five phyla and diverse members of two human gut communities. We overcame cross-reactivity between co-expressed bRNAs to establish search-and-replace Targetable Recombinase Assisted DNA Exchange (TRADE) editing and demonstrated capture and interphylum transfer of chromosomal pathways, enabling programmable horizontal gene transfer. These advances establish bridge recombinase as a foundation for reprogramming gene flow in complex microbial communities.

synthetic biology↗

bioRxiv2022

Validating methods to eradicate Select Agent and phylotype I Ralstonia solanacearum strains reveals that growth in planta increases bacterial stress tolerance

Ralstonia solanacearum is a destructive pathogen that causes bacterial wilt disease of diverse crops. Wilt disease prevention and management is difficult because R. solanacearum persists in soil, water, and plant material. Growers need practical methods to kill R. solanacearum in irrigation water, a common source of disease outbreaks. Additionally, the Race 3 biovar 2 (R3bv2) subgroup is a quarantine pest in many countries and a highly regulated U.S. Select Agent. Plant protection officials and researchers need validated protocols to eradicate R. solanacearum for regulatory compliance. To meet these needs, we measured survival of four R3bv2 and three phylotype I R. solanacearum strains following treatment with hydrogen peroxide, stabilized hydrogen peroxide (HuwaSan), active chlorine, heat, ultraviolet radiation, and desiccation. No surviving R. solanacearum cells were detected after cultured bacteria were exposed for ten minutes to 400 ppm hydrogen peroxide, 50 ppm HuwaSan, 50 ppm active chlorine, or temperatures above 50{degrees}C. R. solanacearum cells on agar plates were eradicated by 30s UV irradiation and killed by desiccation on most biotic and all abiotic surfaces tested. R. solanacearum did not survive the cell lysis steps of four nucleic acid extraction protocols. However, bacteria in planta were more difficult to kill. Stems of infected tomato plants contained a subpopulation of bacteria with increased tolerance of heat and UV light, but not oxidative stress. This result has significant management implications. We demonstrate the utility of these protocols for compliance with Select Agent research regulations and for management of a bacterial wilt outbreak in the field. ImportanceRalstonia solanacearum, a globally distributed wilt pathogen of many high-value crops, is spread via diseased plant material and contaminated soil, tools, and irrigation water. The Race 3 biovar 2 Select Agent subgroup of R. solanacearum is subject to stringent and constantly evolving regulations intended to prevent pathogen introduction or release. We validated eradication and inactivation methods that can be used by: 1) growers seeking to disinfest water and manage bacterial wilt disease outbreaks; 2) researchers who must remain in compliance with regulations; and 3) regulators who are expected to define containment practices. Relevant to all these stakeholders, we show that while cultured R. solanacearum cells are sensitive to relatively low levels of oxidative chemicals, dessication, and heat, more aggressive treatment such as autoclaving or incineration is required to eradicate R. solanacearum cells growing inside plant material.

microbiology↗

bioRxiv2019

A Hotspot Atop: Rivers of the Guyana Highlands Hold High Diversity of Endemic Pencil Catfish

AimThe Pakaraima Mountains are an ancient mountain range along the borders of Guyana, Brazil, and Venezuela. The high plateau is drained by multiple river systems in all directions. Although hypotheses have been presented for the biogeographic relationships of lowland rivers, the interconnectivity of rivers on the top of the plateau is unknown. With multiple complex rivers in a small, upland area we predicted a high level of endemism for stream fishes and complex biogeographic relationships. We explore this with the incredibly diverse pencil catfish genus Trichomycterus. Only two species are known from the region. In this study, we 1) confirm the discovery of multiple endemic Trichomycterus species in the region, 2) determine the phylogenetic placement of our samples to posit biogeographical scenarios, and 3) provide clarification for the identification of T. guianensis based on morphology.\n\nLocationPakaraima Mountains, a part of the Guiana Shield in Guyana, South America\n\nTaxonPencil catfish genus Trichomycterus\n\nMethodsUsing collections from recent expeditions to the Pakaraima Mountains of Guyana, we amplified three mitochondrial (16S, COI, and cytb) and two nuclear markers (myh6 and RAG2). We constructed individual gene trees as well as a concatenated tree to determine the placement of these taxa within the Trichomycterus of the Trans-andean/Amazonian clade.\n\nResultsOur results identify six unique lineages in the highlands of Guyana. Only two species, Trichomycterus guianensis and T. conradi, were previously known to science.\n\nMain ConclusionsThe Pakaraima Mountains of South America are a region of high endemism, as demonstrated here in Trichomycterus catfishes. We find two species occupying multiple basins, suggesting that Pakaraima streams either maintain or had some degree of recent connectivity. We identify six endemic lineages of Trichomycterus from the highlands of the Pakaraima Mountains. The upper portions of the study rivers have been connected either through surface flow or by stream capture. Both processes have occurred on multiple time scales and are independent of the patterns seen in the lowlands.

zoology↗