Biology subjects

Sweeney, C.

Publications and source records attributed to Sweeney, C..

3 recordsLinked to original sources

bioRxiv2024

Prochlorococcus predation by a globally abundant filter feeder

Prochlorococcus is the most abundant photosynthetic cell on Earth and is critical to primary productivity and biogeochemical cycles of the open ocean. Appendicularians are ubiquitous gelatinous filter-feeding zooplankton that feed on marine microorganisms including Prochlorococcus. However, the details of this feeding interaction are extremely understudied relative to its potential importance in top-down controls on Prochlorococcus. This is the first study to experimentally examine several dimensions of the feeding interaction between cultivated appendicularians and Prochlorococcus. We found that Prochlorococcus retention rates by the appendicularian Oikopleura dioica increased with prey concentration and predator age. We found that appendicularians grazed equally on the two most globally abundant Prochlorococcus ecotypes HLI and HLII and that the presence of larger diatom prey did not change Prochlorococcus retention rates. The quantitative insight and retention rates provided by this study will help fill gaps in models of the marine carbon cycle and marine microbial community dynamics and biogeography, and expand the knowledge of Prochlorococcus ecology. ImportanceAppendicularians are a known predator of picocyanobacteria, but the details of their feeding on the globally abundant picocyanobacterium Prochlorococcus have not been investigated. We quantified Prochlorococcus retention rates over a range of ecologically relevant conditions, which will inform microbial community predictions and carbon flux models and lead to improved understanding of carbon transfer in the ocean, microbial ecology, and microbial communities.

ecology↗

bioRxiv2019

De Novo Growth Of Methanogenic Granules Indicates A Biofilm Life-Cycle With Complex Ecology

Methanogenic sludge granules are densely packed, small (diameter, approx. 0.5-2.0 mm) spherical biofilms found in anaerobic digesters used to treat industrial wastewaters, where they underpin efficient organic waste conversion and biogas production. A single digester contains millions of individual granules, each of which is a highly-organised biofilm comprised of a complex consortium of likely billions of cells from across thousands of species - but not all granules are identical. Whilst each granule theoretically houses representative microorganisms from all of the trophic groups implicated in the successive and interdependent reactions of the anaerobic digestion process, parallel granules function side-by-side in digesters to provide a meta-organism of sorts. Granules from a full-scale bioreactor were size-separated into small, medium and large granules. Laboratory-scale bioreactors were operated using only small (0.6-1 mm), medium (1-1.4 mm) or large (1.4-1.8 mm) granules, or unfractionated (naturally distributed) sludge. After >50 days of operation, the granule size distribution in each of the small, medium and large bioreactor types had diversified beyond - to both bigger and smaller than - the size fraction used for inoculation. New granules were analysed by studying community structure based on high-throughput 16S rRNA gene sequencing. Methanobacterium, Aminobacterium, Propionibacteriaceae and Desulfovibrio represented the majority of the community in new granules. H2-using, and not acetoclastic, methanogens appeared more important, and were associated with abundant syntrophic bacteria. Multivariate integration analyses identified distinct discriminant taxa responsible for shaping the microbial communities in different-sized granules, and along with alpha diversity data, indicated a possible biofilm life cycle.\n\nImportanceMethanogenic granules are spherical biofilms found in the built environment, where despite their importance for anaerobic digestion of wastewater in bioreactors, little is understood about the fate of granules across their entire life. Information on exactly how, and at what rates, methanogenic granules develop will be important for more precise and innovative management of environmental biotechnologies. Microbial aggregates also spark interest as subjects in which to study fundamental concepts from microbial ecology, including immigration and species sorting affecting the assembly of microbial communities. This experiment is the first, of which we are aware, to compartmentalise methanogenic granules into discrete, size-resolved fractions, which were then used to separately start up bioreactors to investigate the granule life cycle. The evidence, and extent, of de novo granule growth, and the identification of key microorganisms shaping new granules at different life-cycle stages, is important for environmental engineering and microbial ecology.

microbiology↗

bioRxiv2017

Identification of Novel Breast Tumor Expression Dimensions within the PAM50 and Discovery of a Breast Cancer Susceptibility Locus at 12q15

It is well-known that breast tumors exhibit different expression patterns that can be used to assign intrinsic subtypes - the PAM50 assay, for example, categorizes tumors into: Luminal A, Luminal B, HER2-enriched and Basal-like - yet tumors are often more complex than categorization can describe. We used 911 sporadic breast tumors to reparameterize expression from the PAM50 genes to five orthogonal tumor dimensions using principal components (PC). Three dimensions captured intrinsic subtype, two dimensions were novel, and all replicated in 945 TCGA tumors. By definition dimensions are independent, an important attribute for inclusion in downstream studies exploring effects of tumor diversity. One application where tumor subtyping has failed to provide impact is susceptibility genetics. Germline genetic heterogeneity reduces power for gene-finding. The identification of heritable tumor characteristics has potential to increase homogeneity. We compared 238 breast tumors from high-risk pedigrees not attributable to BRCA1 or BRCA2 to 911 sporadic breast tumors. Two PC dimensions were significantly enriched in the pedigrees (intrinsic subtypes were not). We performed proof-of-concept gene-mapping in one enriched pedigree and identified a 0.5 Mb genomewide significant region at 12q15 that segregated to the 8 breast cancer cases with the most extreme PC tumors through 32 meioses (p=2.6x10-8). In conclusion, our study: suggests a new approach to describe tumor diversity; supports the hypothesis that tumor characteristics are heritable providing new avenues for germline studies; and proposes a new breast cancer locus. Reparameterization of expression patterns may similarly inform other studies attempting to model the effects of tumor heterogeneity.

genetics↗