Biology subjects

Testerman, T.

Publications and source records attributed to Testerman, T..

5 recordsLinked to original sources

bioRxiv2026

Succession and Shifting Identities in Freshwater, Built Environment Biofilm Communities

Biofilms on aquaculture infrastructure harbor diverse microbial communities that may influence water quality and fish health, yet the temporal dynamics of these communities remain poorly characterized. Here, we used 16S rRNA gene amplicon sequencing to profile biofilm communities on concrete raceway surfaces across an 80-day rainbow trout (Oncorhynchus mykiss) indoor hatch-house production period. One hundred twenty-three wall swab samples from 19 raceways at six time points (9, 23, 38, 53, 65, and 80 days) were analyzed after stringent quality control. Beta diversity analyses revealed that biofilm communities at each time point were significantly distinct (PERMANOVA, p < 0.001 for all pairwise comparisons), with early communities exhibiting greater variability than late-stage biofilms. Total bacterial load increased approximately 2.5-fold from early to late stages (qPCR, p < 0.001). Differential abundance testing (ANCOM-BC) identified 57 differentially abundant genera between early-and late-stage biofilms, and random forest classification distinguished early from late communities with over 93% test accuracy. A clear successional trajectory emerged: early biofilms were dominated by pioneer taxa including Pseudomonas, Caulobacter, and Flavobacterium; mid-succession communities featured predatory Bdellovibrio and the methylotroph Methylotenera; and mature biofilms were enriched in saprophytic Saprospiraceae and Haliscomenobacter, polysaccharide-degrading Verrucomicrobiaceae, and cooperative predatory myxobacteria. Flavobacterium columnare, a pathogen of concern in aquaculture, was detected at low levels throughout the production period. These results demonstrate predictable ecological succession in freshwater built environment biofilms and provide a foundation for understanding the role of surface-associated microbial communities in hatchery management.

microbiology↗

bioRxiv2025

From Biofilms to Biocontrol: Aquaculture Biofilms as a Reservoir of Pseudomonas spp. with Activity Against Fish and Human Pathogens

The antimicrobial resistance crisis, driven by excessive use of antimicrobials in medical and agricultural settings, has spurred the search for alternative strategies. In the present study, we investigated surface biofilms from a rainbow trout aquaculture facility to identify bacteria with inhibitory activity against fish and human pathogens. A total of 906 isolates were obtained, of which 478 were taxonomically classified using full-length 16S rRNA gene sequencing, revealing Pseudomonas, Aeromonas, and Flavobacterium as the most abundant genera. Twenty-nine isolates, predominantly novel Pseudomonas species, inhibited one or more fish pathogen strains, with two P. aphyarum strains inhibiting every fish pathogen tested. All human pathogen strains were inhibited by at least one trout farm isolate. A biofilm assay identified strains capable of excluding F. columnare from established biofilms. Numerous strains reduced biofilm colonization, with P. aphyarum and P. idahonensis strains exhibiting the greatest reduction. Genome analysis and biosynthetic gene cluster (BGC) identification from a subset of isolates revealed shared and unique clusters with strong potential for antimicrobial production, correlating in part with observed inhibition patterns. Metabolomics profiling identified a suite of strain-specific siderophores that may mediate biofilm disruption. Additionally, co-culture of these isolates with the human pathogen Pseudomonas aeruginosa enhanced the production of specialized metabolites with reported antimicrobial activities. Collectively, these findings highlight trout farm biofilms as a promising source of bacteria that could be developed as probiotics or investigated for novel antimicrobial discovery. ImportanceDisease outbreaks in aquaculture facilities pose significant threats to food security and often rely on antibiotic treatments, contributing to antimicrobial resistance. This study identifies Pseudomonas isolates from native biofilms of a trout aquaculture facility that are capable of disrupting biofilms and inhibiting a wide range of fish and human pathogens. These Pseudomonas isolates produce a variety of siderophores that may mediate biofilm disruption, offering a promising avenue for developing probiotic applications or the discovery of new antimicrobials to improve aquaculture health and reduce reliance on antibiotics. The discovery of these biofilm-disrupting bacteria holds potential significance for combating antimicrobial resistance in both aquaculture and clinical settings.

microbiology↗

bioRxiv2022

Pseudomonas apudapuas sp. nov., Pseudomonas fontis sp. nov., Pseudomonas idahonensis sp. nov., and Pseudomonas rubra sp. nov. isolated from in, and around, a rainbow trout farm

During a large-scale bacterial culturing effort of biofilms in the vicinity of a rainbow trout aquaculture facility in Idaho, USA, ten isolates were identified as having pathogen inhibiting activity and were characterized further. These isolates were shown to be Gram negative, rod-shaped bacteria belonging to the genus Pseudomonas. Whole genome comparisons and multi-locus sequence analysis using four housekeeping genes (16S rDNA, gyrA, rpoB, rpoD) showed that these 10 isolates clustered into four distinct species groups. These comparisons also indicated that these isolates were below the established species cutoffs for the genus Pseudomonas. Further phenotypic characterization using API 20NE, API ZYM, and BioLog GENIII assays and chemotaxonomic analysis of cellular fatty acids were carried out. Based on the genomic, physiological, and chemotaxonomic properties of these isolates, we concluded that these strains composed four novel species of Pseudomonas. The proposed names are: Pseudomonas apudapuas sp. nov. consisting of strains ID233, ID386T, and ID387 with ID386T (DSM 114641) as the type strain; Pseudomonas rubra sp. nov. consisting of strains ID291T, ID609, and ID1025 with ID291T (DSM 114640) as the type strain; Pseudomonas idahonensis sp. nov. consisting of strains ID357T and ID1048 with ID357T (DSM 114609) as the type strain; and Pseudomonas fontis sp. nov. consisting of strains ID656T and ID681 with ID656T (DSM 114610) as the type strain.

microbiology↗

bioRxiv2022

Large-Scale, Multi-Year Microbial Community Survey of a Freshwater Trout Aquaculture Facility

Aquaculture is an important tool for solving growing worldwide food demand, but infectious diseases of the farmed animals represent a serious roadblock to continued industry growth. Therefore, it is essential to understand the microbial communities that reside within the built environments of aquaculture facilities to identify reservoirs of bacterial pathogens and potential correlations between commensal species and specific disease agents. Here, we present the results from three years of sampling a commercial rainbow trout aquaculture facility. The sampling was focused on the early-life stage hatchery building and included sampling of the facility source water and outdoor production raceways. We observed that the microbial communities residing on the abiotic surfaces within the hatchery were distinct from those residing on the surfaces of the facility water source as well as the production raceways, despite similar communities in the water column at each location. Within the hatchery building, most of the microbial classes and families within surface biofilms were also present within the water column, suggesting that these biofilms are seeded by a unique subgroup of microbial taxa from the water. Lastly, we detected a common fish pathogen, Flavobacterium columnare, within the hatchery, including at the source water inlet. Importantly, the relative abundance of this pathogen was correlated with clinical disease. Our results characterized the microbial communities in an aquaculture facility, established that the hatchery environment contains a unique community composition, and demonstrated that a specific fish pathogen resides within abiotic surface biofilms and is seeded from the natural source water. ImportanceThe complex microbial consortium residing in the built environment of aquaculture facilities is poorly understood. In this study, we provide a multi-year profile of the surface- and water-associated microbial communities of this biome. The results demonstrated that distinct community structures exist in the water and on surfaces. Furthermore, it was shown that a common and economically impactful bacterial pathogen, F. columnare, is continually introduced via the source water, is widespread within surface biofilms in the hatchery environment, and is likely amplified within these raceways but does not always cause disease despite being present. These results advance our understanding of pathogen localization at fish farms, show the interplay between host and environmental microbiomes, and reveal the importance of microbial community sequencing in aquaculture for identifying potential beneficial and harmful microbes. This study adds to the aquaculture microecology dataset and enhances our ability to understand this environment from a "One Health" perspective.

microbiology↗

bioRxiv2021

Detecting Flavobacterial Fish Pathogens in the Environment Using High-Throughput Community Analysis

Diseases caused by the fish pathogens Flavobacterium columnare and Flavobacterium psychrophilum are major contributors of preventable losses in the aquaculture industry. The persistent and difficult to control infections caused by these bacteria make timely intervention and prophylactic elimination of pathogen reservoirs important measures to combat these disease-causing agents. In the present study, we present two independent assays for detecting these pathogens in a range of environmental samples. Natural water samples were inoculated with F. columnare and F. psychrophilum cells, and pathogen levels were detected using Illumina MiSeq sequencing and droplet digital PCR. Both detection methods accurately identified pathogen-positive samples and showed good agreement in quantifying each pathogen. Additionally, the real-world application of these approaches was demonstrated using environmental samples collected at a rainbow trout aquaculture facility. These results show that both methods can serve as useful tools for surveillance efforts in aquaculture facilities, where the early detection of these flavobacterial pathogens may direct preventative measures to reduce disease occurrence. ImportanceEarly detection of a deadly disease outbreak in a population can be the difference between mass fatality or mitigated effects. In the present study, we evaluated and compared two techniques for detecting economically impactful aquaculture pathogens. We demonstrate that one of these techniques, 16S rRNA gene sequencing using Illumina MiSeq technology, provides the ability to accurately detect two fish pathogens, F. columnare and F. psychrophilum, while simultaneously profiling the native microbial community. The second technique, droplet digital PCR, is commonly used for pathogen detection, and the results obtained using the assays we designed with this method served to validate those obtained using the MiSeq method. These two methods offer distinct advantages. The MiSeq method pairs pathogen detection and microbial community profiling to answer immediate and long-term fish health concerns, while droplet digital PCR method provides fast and highly sensitive detection that is useful for surveillance and rapid clinical responses.

molecular biology↗