Biology subjects

Weaver, L.

Publications and source records attributed to Weaver, L..

4 recordsLinked to original sources

bioRxiv2026

Isolation of thermophilic plastic-degrading bacteria from hot springs of Aotearoa-New Zealand

Geothermal springs are unique environments that harbor diverse populations of microorganisms. As a result of their environmental and geochemical variability, different springs can support distinct heterogeneous communities of organisms with unique functional adaptations and metabolic capabilities. A recent molecular survey of Aotearoa-New Zealand hot springs indicated that these springs may support thermophilic microorganisms be able to degrade plastics. To test this, we applied a cultivation-centered approach via an in situ enrichment of putative plastic-degraders using high surface are polyethylene terephthalate (PET), polylactic acid (PLA), and polyhydroxybutyrate (PHB) substrates in a diversity of New Zealand hot springs. The plastic associated microbial communities were characterized via marker gene and analyses. Finally, plastic-associated biofilms were used as inoculum to isolate thermophilic plastic degraders. Via this process, we confirm that there are plastic degrading bacteria are present in springs across Aotearoa-New Zealand. Moreover, we isolated two PHB degrading strains (Cuprividus sp. and Rubrobacter sp.) and demonstrated their capability to metabolize plastic under thermophilic conditions in vitro. While the pathways identified in our plastic degrading isolates suggest they may be able to metabolize plastics for carbon, the primary use of plastics by geothermal microbial communities does not appear to be as an energy source. Instead, they appear to mainly serve as surfaces for microbial attachment, composed primarily of non-plastic degrading taxa.

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↗

bioRxiv2021

Metabolic diversity and aero-tolerance in anammox bacteria from geochemically distinct aquifers

BackgroundAnaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon poor environments. Yet, the diversity and prevalence of anammox bacteria in the terrestrial subsurface - a typically oligotrophic environment - is little understood across different geochemical conditions. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analysed 16S rRNA genes, metagenomes and metatranscriptomes, and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells distributed over 1 240 km2. ResultsData indicate that anammox-associated bacteria (class Brocadiae) and the anammox process are prevalent in aquifers (identified in aquifers with sandy-gravel, sand-silt and volcanic lithologies). While Brocadiae diversity decreased with increasing DO, Brocadiae 16S rRNA genes and hydrazine synthase genes and transcripts (hydrazine synthase, hzsB) were detected across a wide range of bulk groundwater dissolved oxygen (DO) concentrations (0 - 10 mg/L). Anammox genes and transcripts (hzsB) correlated significantly with those involved in bacterial and archaeal ammonia oxidation (ammonia monooxygenase, amoA), which could represent a major source of nitrite for anammox. Differences in anammox community composition were strongly associated with DO and bore depth (and to a lesser extent pH and phosphate), revealing niche differentiation among anammox bacteria in groundwater that was largely driven by water oxygen contents, and not ammonium/nitrite. Eight Brocadiae genomes (63-95% estimated completeness) reconstructed from a subset of groundwater sites belong to 2 uncharacterized families and 6 novel species (based on average nucleotide identity). Distinct groups of these genomes dominated the anammox-associated community at dysoxic and oxic sites, further reflecting the influence of DO on Brocadiae composition. Six of the genomes (dominating dysoxic or oxic sites) have genes characteristic of anammox (hydrazine synthase and/or dehydrogenase). These genes, in addition to aerotolerance genes, belonging to four Brocadiae genomes, were transcriptionally active, although transcript numbers clearly highest in dyoxic groundwater. ConclusionsOur findings indicate anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, and that this is likely supported by nitrite from aerobic ammonia oxidation. Results provide an insight into the distribution and activity of anammox bacteria across distinct aquifer physicochemisties.

microbiology↗

bioRxiv2019

PIKfyve deficiency in myeloid cells impairs lysosomal homeostasis in macrophages and promotes systemic inflammation in mice

Macrophages are professional phagocytes that are essential for host defense and tissue homeostasis. Proper membrane trafficking and degradative functions of the endolysosomal system is known to be critical for the function of these cells. We have found that PIKfyve, the kinase that synthesizes the endosomal phosphoinositide PI(3,5)P2, is an essential regulator of lysosomal biogenesis and degradative functions in macrophages. Genetically engineered mice lacking PIKfyve in their myeloid cells (PIKfyvefl/fl LysM-Cre) develop diffuse tissue infiltration of foamy macrophages, hepatosplenomegaly, and systemic inflammation. PIKfyve loss in macrophages causes enlarged endolysosomal compartments and impairs the lysosomal degradative function. Moreover, PIKfyve deficiency increases the cellular levels of lysosomal proteins. Although PIKfyve deficiency reduced the activation of mTORC1 pathway and was associated with increased cleavage of TFEB proteins, this does not translate into transcriptional activation of lysosomal genes, suggesting that PIKfyve modulates the abundance of lysosomal proteins by affecting the degradation of these proteins. Taken together, our study shows that PIKfyve modulation of lysosomal degradative activity and protein expression is essential to maintain lysosomal homeostasis in macrophages.

cell biology↗