Biology subjects

Muratore, D. J.

Publications and source records attributed to Muratore, D. J..

3 recordsLinked to original sources

bioRxiv2024

Diel Partitioning in Microbial Phosphorus Acquisition in the Sargasso Sea

The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. According to temporal niche partitioning theory, competition for scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism structuring uptake of limiting nutrients and facilitating coexistence of diverse microbes in open ocean ecosystems.

ecology↗

bioRxiv2022

Microbial and Viral Genome and Proteome Nitrogen Demand Varies Across Multiple Spatial Scales Within a Marine Oxygen Minimum Zone

Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter- and even micron-level spatial scales. It is unclear if such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions distinguishing free-living versus particle-associated microbes. We find a substantial increase in nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size-fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in modulating the C:N ratio of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCEThe genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses using metagenomes from the nitracline of the eastern tropical North Pacific OMZ including both particle-associated and non-associated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micro- to millimeter scale associated with particle-associated versus free-living lifestyles.

microbiology↗

bioRxiv2018

Re-evaluating the salty divide: phylogenetic specificity of transitions between marine and freshwater systems

Marine and freshwater microbial communities are phylogenetically distinct and transitions between habitat types are thought to be infrequent. We compared the phylogenetic diversity of marine and freshwater microorganisms and identified specific lineages exhibiting notably high or low similarity between marine and freshwater ecosystems using a meta-analysis of 16S rRNA gene tag-sequencing datasets. As expected, marine and freshwater microbial communities differed in the relative abundance of major phyla and contained habitat-specific lineages; at the same time, however, many shared taxa were observed in both environments. Betaproteobacteria and Alphaproteobacteria sequences had the highest similarity between marine and freshwater sample pairs. Gammaproteobacteria and Alphaproteobacteria contained the highest number of Minimum Entropy Decomposition nodes shared by marine and freshwater samples. Shared nodes included lineages of the abundant alphaproteobacterial group SAR11 that have not previously been reported in 16S rRNA gene surveys of freshwater lakes. Our results suggest that shared taxa are numerous, but tend to occur sporadically and at low relative abundance in one habitat type, leading to an underestimation of transition frequency between marine and freshwater habitats. Lineages with a high degree of shared taxa or habitat-specific diversification represent targets for genome-scale investigations into microbial adaptations and evolutionary innovations. Rare taxa with abundances near or below detection, including lineages that appear to have crossed the salty divide relatively recently, may have novel adaptations enabling them to exploit opportunities for niche expansion when environments are disturbed or conditions change.\n\nImportanceThe distribution of microbial diversity across environments yields insight into processes that create and maintain this diversity as well as potential to infer how communities will respond to future environmental changes. We integrated datasets from dozens of freshwater lake and marine samples to compare diversity across open water habitats differing in salinity. Our novel combination of sequence-based approaches revealed phyla and proteobacterial classes inferred to include more or less recent transitions across habitat types as well as specific lineages that are shared by marine and freshwater environments at the level of 16S rRNA sequence types. Our findings contribute to understanding the ecological and evolutionary controls on microbial distributions, and open up new questions regarding the plasticity and adaptability of particular lineages.

microbiology↗