Biology subjects

Lane, T. W.

Publications and source records attributed to Lane, T. W..

4 recordsLinked to original sources

bioRxiv2026

Characterizing Industrial Pond Ecology Timeline in DISCOVR Cultivation Trials for Early Detection of Pond Crashes

For sustainable algal biomass cultivation, we need substantial improvement in annualized productivity by reducing the frequency of crop failure and improved growth in open raceway pond systems. In this study, high-performing strains were identified and optimized for biomass productivity. We utilized next-generation sequencing methods to quantify the ecological features of open raceway systems cultivated at in Arizona. We utilized data from several months of cultivation runs to construct a rich time-series of the ecology dynamics using amplicon sequencing and used custom anomaly detection, "PondSentry", for the early prediction of pond crashes. PondSentry uses tensor decomposition of higher-order joint moments to detect incipient anomalies in multivariate data and displays significant improvements from standard knowledge-based anomaly detection methods. The PondSentry strategy identifies signs of deteriorating pond health at an average of three days before an actual crash event, with rank order of the ecological features plausible for crop failures driven by organisms such as Amoeboaphelidium occidentale FD01. These findings are independently confirmed with PCR and microscopy studies at an Arizona cultivation site. PondSentrys time-series-based anomaly detection of crashes provides a suitable monitoring strategy for eukaryotic crash agents in unialgal culture. The early warnings can be used to time interventions or harvests to prevent biomass loss. The PondSentry strategy strengthens the role of data science and data-driven methods in algal cultivation and can increase the feasibility of algal-biomass based products.

ecology↗

bioRxiv2026

Protection of algae grown for biofuel using a consortium of environmentally harvested bacteria

Crop loss due to infection by pests and pathogens is a major barrier to the large-scale production of algal biofuels. Test systems have seen loss of green algae crops due to infection by the fungus-like Amoeboaphelidium occidentale FD01. While current antifungal compounds are effective in inhibiting the infection, their application raises the overall cost of the crop and lowers its economic viability as a biofuel source. Here we show that co-culturing environmentally harvested bacteria alongside algae crops can drastically lower the rate of infection in two different green algae species of interest for biofuel production. These bacteria-algae consortia increase the mean time to crop failure (MTTF) by up to 350% when tested under environmentally relevant conditions. While there was an increase in diversity over time, there was no statistically significant correlation between an increase in diversity and a longer MTTF. Community composition analysis reveals similarities between the bacterial genera growing alongside both green algae species even as bacterial harvest locations differed, although there was not a single dominant genus responsible for the increase in crop protection. These results show a promising new method of anti-fungal crop protection that can be applied to algal biofuels with no increase in fuel cost. HighlightsO_LIBacteria-algal cocultures protect against fungal pests without impact to productivity C_LIO_LIBacterial community composition is variable over time even as protection persists C_LIO_LIBacterial consortia can increase mean time to failure by 350% C_LI

microbiology↗

bioRxiv2025

Multi-omic and phenotypic analysis of growth and resilience of open raceway pond production of Monoraphidium minutum 26B-AM

BackgroundGreen microalgae, such as Monoraphidium minutum 26B-AM, have garnered significant commercial interest due to their high biomass production and lipid yield, providing promising candidates for various bioprocessing applications. However, the economic viability of large-scale algal cultivation in open raceway ponds is limited by biocontamination and environmental stressors, necessitating deeper understanding of the molecular mechanisms that underpin resilience and productivity in these systems. We hypothesized that the molecular signature associated with the cellular responses of M. minutum to environmental stressors will reveal critical information for the timely prediction of resilience and productivity in algal cultures within open pond systems. ResultsTo test this hypothesis, we conducted a longitudinal multi-omic study, integrating transcriptomics, proteomics, metabolomics, and phenomics, to monitor the acclimation, growth dynamics, and pathogen responses of algal cultures in two 1000 L raceway ponds, before and after the introduction of a pathogen as a stressor. We identified a number of molecular patterns that correlate with changes in the algal environment, and we can track these changes within the ponds per time. Furthermore, we identify scale-up and infection-specific molecular pathways through integrated multi-omics, showing that most patterns are unique to each studied stressor/transition. ConclusionsUltimately, this study demonstrates the utility of multi-omics observations at scale, revealing unique signatures and laying the groundwork for developing molecular detection techniques and predictive models that can improve the sustainability and efficiency of large-scale algae biomass production.

molecular biology↗

bioRxiv2020

Computational front end to diverse therapeutic phage cocktails

New therapies are necessary to combat increasingly antibiotic-resistant bacterial pathogens. We have developed a technology platform of computational, molecular biology, and microbiology tools which together enable on-demand production of phages that target virtually any given bacterial isolate. Two complementary computational tools that identify and precisely map prophages and other integrative genetic elements (IGEs) in bacterial genomes are used to identify prophage-laden bacteria that are close relatives of the target strain. Phage genomes are engineered to disable lysogeny, through use of long amplicon PCR and Gibson assembly. Finally, the engineered phage genomes are introduced into host bacteria for phage production. As an initial demonstration, we used this approach to produce a phage cocktail against the opportunistic pathogen Pseudomonas aeruginosa PAO1. Two prophage-laden P. aeruginosa strains closely related to PAO1 were identified, ATCC 39324 and ATCC 27853. Deep sequencing revealed that mitomycin C treatment of these strains induced seven phages that grow on P. aeruginosa PAO1. The most diverse five of these were engineered for non-lysogeny by deleting the integrase gene (int), which is readily identifiable and typically conveniently located at one end of the prophage. The {Delta}int phages, individually and in cocktails, showed killing of P. aeruginosa PAO1 in vitro as well as in a waxworm (Galleria mellonella) model of infection. SIGNIFICANCE STATEMENTThe antibiotic-resistance crisis in medicine and agriculture has led to renewed interest in phage therapy as an alternative means of treating infection. However, conventional methods for isolating pathogen-specific phage are slow, labor-intensive, and frequently unsuccessful. We have demonstrated that prophages carried by near-neighbor bacteria can serve as starting material for production of engineered phages that kill the target pathogen. Our approach and technology platform offer new opportunity for rapid development of phage therapies against most, if not all, bacterial pathogens, a foundational advance for use of phage in treating infectious disease.

microbiology↗