Biology subjects

van der Gast, C.

Publications and source records attributed to van der Gast, C..

3 recordsLinked to original sources

bioRxiv2025

Rapid Assembly and Functional Differentiation of the Soil Surface Microbiome in Temperate Agricultural soil

The surface of dryland soils is typically covered by biological soil crusts (BSC) dominated by cyanobacteria, lichens or moss which contribute key ecosystem functions. However, while photosynthetic biota have been observed on the surface of temperate agricultural soils, understanding of the development, biodiversity and functional significance of these communities is extremely limited. We investigated the temporal development of the soil surface community following tillage and during subsequent growth of a wheat crop. Amplicon analysis showed that establishment of the soil surface microbiome was rapid over the winter period, with distinct communities of phototrophs, bacteria and protists detected 60 days after tillage. There was rapid succession with yellow-green algae (Xanthophyceae) dominating early stages of development, followed by Cyanobacteria and Charophytes and finally moss. Temporal dynamics of fungal and protist communities was influenced by eDNA deposition from plant pathogens inhabiting the crop canopy and wild animal parasites. For all groups, assembly processes in the surface soil became increasingly dominated by dispersal limitation over time while assembly of bulk soil communities became predominantly influenced by drift. Metagenome analysis showed that the soil surface had developed a distinct functional profile relative to bulk soil after 9 months, enriched in photosynthetic processes which were largely from eukaryotic algae rather than cyanobacteria. Additionally the 3-Hydroxypropionate bicycle and reductive TCA carbon fixation pathways were enriched in surface soil. The abundance of genes involved in heterotrophic carbon, nitrogen, phosphorus and sulphur cycling processes were also enriched in surface soil. This included reads of carbohydrate active enzymes, nitrification, denitrification and sulphate reduction genes, largely attributed to the enrichment of Actinobacteria, Bacteroidetes and Proteobacteria in the soil surface. Overall, we show overlap in dominant phototrophic taxa between temperate agricultural and BSC in arid soils, but with notable differences, including abundance of Xanthphycae and Charophytes. Furthermore, the functional signatures of the soil surface communities indicate that they may play an important role in the delivery of ecosystem functions in temperate agricultural systems.

microbiology↗

bioRxiv2025

Investigating microbiota differences across chronic pancreatitis, influenced by lifestyle and genetic determinants

BackgroundChronic pancreatitis (CP) is a multifaceted and irreversible inflammatory condition that impacts both endocrine and exocrine pancreatic functions. Whilst there is evidence of a general intestinal microbial dysbiosis, differences across CP resulting from diverse triggers remains poorly elucidated. MethodsIn this study, we investigated how different CP triggers, namely alcohol-induced CP (AIP) and CFTR-related CP (CFRP), might undermine differences across microbiota structure and predicted function. Faecal samples from 25 CP participants were collected, alongside 9 healthy controls for microbiota analyses. Both full and short (V4) 16S rRNA sequencing was performed, including predicted functionality using PICRUSt2. Clinical metadata was integrated to investigate relationships with microbiota structure and predicted functionality with ordination-based approaches. ResultsMicrobiota diversity patterns between groups varied slightly by sequencing approach, with differences across common core and rarer satellite taxa diversity evident. Importantly, microbiota compositional profiles were shared between approaches, with control samples clustering closer than CP samples. Between groups, significant differences in microbiota composition were apparent, with the AIP group significantly different to both control and CFRP groups across various microbiota partitions (P < 0.05). Notable genera drove the observed dissimilarity, including Bifidobacterium, Faecalibacterium, and Ruminococcus, which were decreased in relative abundance across CP. Predictive functional analyses further demonstrated increased similarity of controls as compared to CP groups. Significant variation across both microbiota structure and predicted function was explained by CP subtype (P < 0.01). When compared back to controls, the relative abundance of various predicted functional pathways from both the core and satellite taxa was significantly different across groups (P < 0.05). ConclusionsOverall, we demonstrate that gut microbiota structure and predicted function differs between not only healthy controls and CP, including across CP subtypes themselves. Various taxa with important physiological roles were implicated across CP. Differences in predicted functionality of the core and satellite taxa were evident, relating to microbial processes that may have downstream consequences at the site of the GI tract. Future studies will employ larger cohorts with the incorporation of additional omics-based approaches. This will better elucidate differences in microbiota structure and functionality across CP, including relationships with pancreatic-based clinical outcomes.

microbiology↗

bioRxiv2021

Mild CF Lung Disease is Associated with Bacterial Community Stability

Microbial communities in the airways of persons with CF (pwCF) are variable, may include genera that are not typically associated with CF, and their composition can be difficult to correlate with long-term disease outcomes. Leveraging two large datasets characterizing sputum communities of 167 pwCF and associated metadata, we identify five bacterial community types. These communities explain 24% of the variability in lung function in this cohort, far more than single factors like Simpson diversity, which explains only 4%. Subjects with Pseudomonas-dominated communities tended to be older and have reduced percent predicted FEV1 (ppFEV1) than subjects with Streptococcus-dominated communities, consistent with previous findings. To assess the predictive power of these five communities in a longitudinal setting, we used random forests to classify 346 additional samples from 24 subjects observed 8 years on average in a range of clinical states. Subjects with mild disease were more likely to be observed at baseline, that is, not in the context of a pulmonary exacerbation, and community structure in these subjects was more self-similar over time, as measured by Bray-Curtis distance. Interestingly, we found that subjects with mild disease were more likely to remain in a mixed Pseudomonas community, providing some support for the climax-attack model of the CF airway. In contrast, patients with worse outcomes were more likely to show shifts among community types. Our results suggest that bacterial community instability may be a risk factor for lung function decline and indicates the need to better understand factors that drive shifts in community composition.

microbiology↗