Graduation Date

Spring 2024

Document Type

Thesis

Program

Master of Science degree with a major in Biology

Committee Chair Name

Mark Wilson

Committee Chair Affiliation

HSU Faculty or Staff

Second Committee Member Name

Catalina Cuellar-Gempeler

Second Committee Member Affiliation

HSU Faculty or Staff

Third Committee Member Name

Karen Kiemnec-Tyburczy

Third Committee Member Affiliation

HSU Faculty or Staff

Fourth Committee Member Name

Yoon Kim

Fourth Committee Member Affiliation

HSU Faculty or Staff

Keywords

Northern California, Humboldt County, Streptomyces, Bacteria, Phylogenetics, Scale, Habitat, Measurements

Subject Categories

Biology

Abstract

Bacteria in the genus Streptomyces are detected in most soils around the world, as well as on and in seeds, plants, animals, insects and the wind. Currently, more than 700 valid species of Streptomyces have been identified worldwide. Streptomyces produce the majority of antibiotics, antivirals and antifungals, as well as important agricultural bioactive molecules due to their unique genetic capabilities. Their distinct genetic abilities allow them to produce an unlimited amount of biosynthetic gene clusters, or BGC’s. Although many compounds come from Streptomyces, scientists have not discovered the biogeographic patterns of this genus. The biogeography of Streptomyces is a valuable research topic for many reasons. Current Streptomyces biogeographic studies have shown that the community structures in Streptomyces vary greatly, depending on the two components: scale size and the habitat sampled. New methods such as multi-locus sequence typing (MLST), in which several protein-coding genes are sequenced, concatenated, and used to build genetic phylogenies are useful in understanding community structure. Comprehending Streptomyces phylogeny has been improved by using MLST and other new methods. Understanding Streptomyces biogeographic patterns might locate Streptomyces with novel BGC’s, including stronger antibiotics and antifungals, safer and non-toxic herbicides, and bioactive compounds that promote soil regeneration quickly. The largest continental-scale MLST biogeography study of Streptomyces analyzed over 1,000 Streptomyces soil isolates from across North America, and found that these isolates exhibited a latitudinal biogeography gradient in which phylogroups were found at specific latitudes. The present study examined the biogeography of Streptomyces on a regional/local scale from a range of various of habitats. Forty-four isolates were collected from seven different habitats within Humboldt County, California. Five housekeeping genes were isolated and sequenced. MLST was performed using these five housekeeping genes, and the resulting sequences were analyzed using phylogenetic trees and distance matrices. The resulting individual gene and MLST phylogenetic trees have unique and different branching patterns, and did not shown evidence for dispersal limitation. As well, widespread horizontal gene transfer was identified among the Humboldt isolates. Humboldt isolates were compared with the continental-scale MLST study isolates. Few Humboldt isolates were in the same phylotypes as isolates from the continental-scale study, and the distribution of those phylotypes was consistent with that found in large study. This study contributes an understanding of the distribution patterns of Streptomyces sampled from various habitats from within the small/regional area of Humboldt County.

Citation Style

ACS

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