Biology subjects

Lear, G.

Publications and source records attributed to Lear, G..

6 recordsLinked to original sources

bioRxiv2025

An experimental approach to understanding plastic leachate impacts on marine microorganisms

Plastics in the worlds oceans are exposed to diverse environmental stressors that fragment them, accelerating the leaching of associated additives. The impact of potentially toxic plastic degradation products and additives on marine microorganisms remains poorly understood. We assessed the impact of plastic leachate on marine microbial communities in vitro by exposure to one of four plastic leachates (from linear low-density polyethylene [LLPDE], polyamide-6 [or polycaprolactam; PA6], polyethylene terephthalate [PET] and polylactic acid [PLA]), prepared by immersing plastics in artificial seawater salts broth for three months at 80 {degrees}C. Microbial communities were then exposed to different leachates, noting that lower concentrations of plastic additives leached from the more inert plastic types (LLDPE and PET), as determined by GC-MS. PLA-leachate exposed communities differed significantly in composition from other plastic-leachate-exposed communities (PERMANOVA, P=0.001) as assessed by 16S rRNA gene and ITS region amplicon sequencing. Communities exposed to PLA-leachate contained a higher proportion of Proteobacteria, specifically Halomonas spp., previously reported to degrade LDPE and common plasticisers. Greater relative abundances of Psathyrellaceae fungi also distinguished these communities from those exposed to other plastic leachates. However, despite significant differences in the structure of communities exposed to PLA-leachate, we found no difference in the relative abundances of gene transcripts associated with plastic degradation. While biodegradable plastics such as PLA may persist for shorter times in the environment than more inert plastics, our study indicates greater consequences for marine microbial communities.

microbiology↗

bioRxiv2025

Molecular mechanisms of plastic biodegradation by the fungus Clonostachys rosea

Microbial degradation provides an avenue for the remediation of select plastic polymers contributing to the urgent environmental problem of global plastic pollution. We demonstrate the degradation of polycaprolactone (PCL) by Clonostachys rosea and elucidate its underlying molecular mechanisms. We constructed the genome of this fungal strain and monitored changes in gene expression when exposed to PCL. Twelve genes linked to PCL degradation were found in the genome of C. rosea, and some of them were upregulated in the presence of the plastic, including genes coding for two cutinases. We heterologously expressed the enzymes coded by both genes and confirmed their activity against PCL polymers. We also demonstrate that one of the enzymes was active against polyethylene terephthalate (PET) polymers. Glucose inhibited the expression of both genes, completely halting the plastic biodegradation process, possibly serving as a preferred and readily metabolisable carbon source compared with PCL. We confirm the presence of key metabolic pathways linked to PCL degradation in C. rosea, including fatty acid degradation, providing further evidence of the mechanisms central to plastic biodegradation.

microbiology↗

bioRxiv2024

Resource Recovery from Wastewater By Directing Microbial Metabolism Toward Production of Value-added Biochemicals

Transitioning wastewater treatment from mere pollutant removal to resource recovery necessitates exploiting the metabolic capabilities of microbial communities. Studies suggest that under low-oxygen conditions, microbes activate oxygen-responsive regulons that suppress the tricarboxylic acid (TCA) cycle, diverting carbon flux towards biosynthetic pathways and accumulating valuable organic metabolites. We hypothesized that dynamically altering dissolved oxygen levels in activated sludge would disrupt aerobic metabolic equilibrium, enhancing the production of valuable biochemicals like amino acids and fatty acids. To test this, batch experiments were conducted with activated sludge under constant aeration and rapid cycling between oxygen-rich and oxygen-poor states. Fluctuating oxygen concentrations between 0 and 2 mg/L significantly increased valuable biochemical production compared to constant aeration (P<0.05). Continuous oxygen perturbations increased free amino acids by 35.7{+/-}7.6% and free fatty acids by 76.4{+/-}13.0%, while intermittent perturbations with anoxic periods enhanced free amino acids by 42.4{+/-}8.1% and free fatty acids by 39.3{+/-}7.7%. Notably, 14 standard amino acids showed significant increases, and most fatty acids had carbon chain lengths between C12-C22. Mechanistically, compared to stable oxygen, oxygen perturbations activated the FNR and ArcA regulons, resulting in lower relative abundances of TCA cycle enzymes such as malate dehydrogenase, isocitrate dehydrogenase, and 2-oxoglutarate dehydrogenase, while higher relative abundances of amino acid (ilv cluster) and fatty acid (acc cluster) biosynthetic enzymes. Our findings demonstrate that introducing controlled oxygen fluctuations in wastewater treatment can enhance the biochemical value of activated sludge with minimal process modifications, facilitating resource recovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/614227v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@181590corg.highwire.dtl.DTLVardef@fd51c3org.highwire.dtl.DTLVardef@102ddd1org.highwire.dtl.DTLVardef@130dc73_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

Genome sequence of Pseudopithomyces chartarum, causal agent of facial eczema (pithomycotoxicosis) in ruminants, and identification of the putative sporidesmin toxin gene cluster

Facial eczema (FE) in grazing ruminants is a debilitating liver syndrome induced by ingestion of sporidesmin, a toxin belonging to the epipolythiodioxopiperazine class of compounds. Sporidesmin is produced in spores of the fungus Pseudopithomyces chartarum, a microbe which colonises leaf litter in pastures. New Zealand has a high occurrence of FE in comparison to other countries as animals are fed predominantly on ryegrass, a species that supports high levels of Pse. chartarum spores. The climate is also particularly conducive for Pse. chartarum growth. Here, we present the genome of Pse. chartarum and identify the putative sporidesmin gene cluster. The Pse. chartarum genome was sequenced using single molecule real-time sequencing (PacBio) and gene models identified. Loci containing genes with homology to the aspirochlorine, sirodesmin PL and gliotoxin cluster genes of Aspergillus oryzae, Leptosphaeria maculans and Aspergillus fumigatus, respectively, were identified by tBLASTn. We identified and annotated an epipolythiodioxopiperazine cluster at a single locus with all the functionality required to synthesise sporidesmin. HighlightsO_LIThe whole genome of Pseudopithomyces chartarum has been sequenced and assembled. C_LIO_LIThe genome is 39.13 Mb, 99% complete, and contains 11,711 protein coding genes. C_LIO_LIA putative sporidesmin A toxin (cause of facial eczema) gene cluster is described. C_LIO_LIThe genomes of Pse. chartarum and the Leptosphaerulina chartarum teleomorph differ. C_LIO_LIComparative genomics is required to further resolve the Pseudopithomyces clade. C_LI

genomics↗

bioRxiv2019

Induction of microbial oxidative stress as a new strategy to enhance the enzymatic degradation of organic micropollutants in wastewater

Organic micropollutants (OMPs) are pervasive anthropogenic contaminants of fresh and marine waters with known potential to adversely affect aquatic life (e.g. endocrine disruption). Their ubiquitous environmental occurrence is primarily attributed to wastewater treatment plant discharges following their incomplete removal by common biological treatment processes. This study assesses a new strategy for promoting the degradation of six model OMPs (i.e. sulfamethoxazole, carbamazepine, tylosin, atrazine, naproxen and ibuprofen) by stimulating microbial oxidoreductase production to counter the effects of oxidative stress caused by oxygen perturbation. Microbial cultures from dairy farm wastewater were exposed to a cyclical ON-OFF perturbations of oxygen supply, ranging from 0.16 to 2 cycles per hour (i.e. 2, 1, 0.5, 0.25 and 0.16 cycles/hour), in laboratory bioreactors. The activity and relative abundances of microbial oxidoreductases (such as peroxidases, cytochromes P450) were upregulated by oxygen perturbation. In comparison to controls subjected to constant oxygen levels, OMP concentrations in perturbed cultures decreased by 70{+/-}9% (mean {+/-} SD). A distance-based linear model confirmed strong positive correlations between the relative abundance of the bacterial families, Rhodocyclaceae, Syntrophaceae and Syntrophobacteraceae, and oxygen perturbations. Our results confirm that intentional perturbation of oxygen supply to induce microbial oxidative stress can improve OMP removal efficiencies in wastewater treatment bioreactors.

bioengineering↗

bioRxiv2018

Multivariate methods for testing hypotheses of temporal community dynamics

For ecological research to make important contributions towards understanding and managing temporally-variable global change processes, such as responses to land-use and climatic change, we must have effective and comparable ways to quantify and analyse compositional change over time in biological communities. These changes are the sum of local colonisation and extinction events, or changes in the biomass and relative abundance of taxa within and among samples. We conducted a quantitative review of currently available methods for the analysis of multivariate datasets collected at temporal intervals. This review identified the need for the application of quantitative, hypothesis-based approaches to understand temporal change in community composition, particularly for small datasets with less than 15 temporal replicates. To address this gap, we: (1) conceptually present how temporal patterns in community dynamics can be framed as specific, testable hypotheses; (2) provide three fully-worked case-studies, complete with R code, demonstrating multivariate analysis methods for temporal hypothesis testing and pattern visualisation; and (3) present a road map for testing specific, quantitative hypotheses relating to the underlying mechanisms of temporal community dynamics.

ecology↗