Biology subjects

Mason, O.

Publications and source records attributed to Mason, O..

3 recordsLinked to original sources

bioRxiv2023

Diversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes

Sulfur-oxidizing and sulfate-reducing bacteria in salt marsh sediments are major controllers of ecosystem-scale carbon cycling. Cross-site comparisons of S-cycling communities are difficult given the rampant uncultured microbial diversity in sediment, yet comparisons are essential for revealing biogeographic, phylogenetic and functionally significant variation. Here, we use deep shotgun metagenomic sequencing data to construct and compare metagenome-assembled genomes (MAGs) of sulfur-cycling bacteria from Massachusetts and Alabama salt marshes that contrast in seasonality and sediment organic matter content. Samples were collected from sediments under Sporobolus alterniflorus and Sporobolus pumilus in separate MA vegetation zones, and under Sporobolus alterniflorus and Juncus roemerianus co-rooted in AL marsh. We grouped metagenomic data by plant species and site and identified 38 MAGs that included pathways for dissimilatory sulfate reduction or sulfide oxidation. Phylogenetic analyses indicated that 30 of the 38 were affiliated with uncultivated lineages. Read-mapping to MAGs showed significant differentiation of AL and MA samples, differentiation of samples taken in S. alterniflorus and S. pumilus vegetation zones in MA, but no differentiation of samples taken under S. alterniflorus and J. roemerianus that were rooted together in AL marsh. Pangenomic analyses of eight ubiquitous MAGs also detected site- and vegetation-specific genomic features, including varied sulfur-cycling operons, carbon fixation pathways, fixed single nucleotide variants, and active diversity-generating retroelements. This genetic diversity, detected at multiple scales even within uncultured groups, suggests evolutionary relationships affected by distance and local environment, and demonstrates differential microbial capacities for sulfur and carbon cycling in salt marsh sediments. ImportanceSalt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are the major decomposers in salt marsh systems, and sulfur-oxidizing bacteria remove sulfide, a toxic byproduct of sulfate reduction, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here we use comparative genomics to overcome these challenges and provide an in-depth characterization of microbial diversity in salt marshes. We characterize sulfur-cycling communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with sulfur-cycling uncultivated lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.

ecology↗

bioRxiv2021

Plant host shift: The viability and persistence of a polyphagous non-native insect

Assessing the effects of a plant-host shift is important for monitoring insect populations over long time periods and for interventions in a conservation or pest management framework. In a heterogeneous environment, individuals may disperse between sources and sinks in order to persist. Here we propose a single-species two-patch model that aims to capture the generational movement of an insect that exhibits density-dependent dispersal, to see how shifting between hosts could alter its viability and asymptotic dynamics. We then analyse the stability and persistence properties of the model and further validate it using parameter estimates derived from laboratory experiments. In order to evaluate the potential of this model, we applied it to Drosophila suzukii (Diptera: Drosophilidae), which has become a harmful pest in several countries around the world. Although many studies have investigated the preference and attractiveness of potential hosts on this invasive drosophilid, no studies thus far have investigated whether a shift of fruit host could affect such a species ecological viability or spatiotemporal persistence. The model results show that a shift in host choice can significantly affect the growth potential and fecundity of a species such as D. suzukii, which ultimately could aid such invasive populations in their ability to persist within a changing environment.

ecology↗

bioRxiv2018

Extent of the annual Gulf of Mexico hypoxic zone influences microbial community structure

Rich geochemical datasets generated over the past 30 years have provided fine-scale resolution on the northern Gulf of Mexico (nGOM) coastal hypoxic ([≤] 2 mg of O2 L-1) zone. In contrast, little is known about microbial community structure and activity in the hypoxic zone despite the implication that microbial respiration is responsible for forming low dissolved oxygen (DO) conditioXSns. Here, we hypothesized that the extent of the hypoxic zone is a driver in determining microbial community structure, and in particular, the abundance of ammonia-oxidizing archaea (AOA). Samples collected across the shelf for two consecutive hypoxic seasons in July 2013 and 2014 were analyzed using 16S rRNA gene sequencing, oligotyping, microbial co-occurrence analysis and quantification of thaumarchaeal 16S rRNA and archaeal ammonia-monooxygenase (amoA) genes. In 2014 Thaumarchaeota were enriched and inversely correlated with DO while Cyanobacteria, Acidimicrobiia and Proteobacteria where more abundant in oxic samples compared to hypoxic. Oligotyping analysis of Nitrosopumilus 16S rRNA gene sequences revealed that one oligotype was significantly inversely correlated with dissolved oxygen (DO) in both years and that low DO concentrations, and the high Thaumarchaeota abundances, influenced microbial co-occurrence patterns. Taken together, the data demonstrated that the extent of hypoxic conditions could potentially influence patterns in microbial community structure, with two years of data revealing that the annual nGOM hypoxic zone is emerging as a low DO adapted AOA hotspot.

microbiology↗