Biology subjects

Held, N. A.

Publications and source records attributed to Held, N. A..

8 recordsLinked to original sources

bioRxiv2026

Shifting resource limitation explains multiphasic patterns of density dependence

Several recent studies have presented sublinear density dependence as a universal phenomenon across species, driven by factors unrelated to resource limitation (e.g. predation or non-resource based inhibition). Through a combination of bacterial growth experiments and mathematical modelling, we instead show that regimes of sublinear density dependence readily emerge under sequential shifts in resource limitation, without the need to invoke other processes. We nevertheless predict that superlinear density dependence, driven by standard resource limitation, will still predominate at both high and low densities.

ecology↗

bioRxiv2024

Marine Bacteria Alteromonas spp. Require UDP-glucose-4-epimerase for Aggregation and Production of Sticky Exopolymer

The physiology and ecology of particle-associated marine bacteria are of growing interest, but our knowledge of their aggregation behavior and mechanisms controlling their association with particles remains limited. We have found that a particle-associated isolate, Alteromonas sp. ALT199 strain 4B03, and the related type-strain A. macleodii 27126 both form large (>500 m) aggregates while growing in rich medium. A non-clumping variant (NCV) of 4B03 spontaneously arose in the lab, and whole genome sequencing revealed a partial deletion in the gene encoding UDP-glucose-4-epimerase (galE{Delta}308-324). In 27126, a knock-out of galE ({Delta}galE::kmr) resulted in a loss of aggregation, mimicking the NCV. Microscopic analysis shows that both 4B03 and 27126 rapidly form large aggregates, whereas their respective galE mutants remain primarily as single planktonic cells or clusters of a few cells. Strains 4B03 and 27126 also aggregate chitin particles, but their galE mutants do not. Alcian Blue staining shows that 4B03 and 27126 produce large transparent exopolymer particles (TEP), but their galE mutants are deficient in this regard. This study demonstrates the capabilities of cell-cell aggregation, aggregation of chitin particles, and production of TEP in strains of Alteromonas, a widespread particle-associated genus of heterotrophic marine bacteria. A genetic requirement for galE is evident for each of the above capabilities, expanding the known breadth of requirement for this gene in biofilm-related processes. ImportanceHeterotrophic marine bacteria have a central role in the global carbon cycle. Well-known for releasing CO2 by decomposition and respiration, they may also contribute to particulate organic matter (POM) aggregation, which can promote CO2 sequestration via the formation marine snow. We find that two members of the prevalent particle-associated genus Alteromonas can form aggregates comprising cells alone or cells and chitin particles, indicating their ability to drive POM aggregation. In line with their multivalent aggregation capability, both strains produce TEP, an excreted polysaccharide central to POM aggregation in the ocean. We demonstrate a genetic requirement for galE in aggregation and large TEP formation, building our mechanistic understanding of these aggregative capabilities. These findings point toward a role for heterotrophic bacteria in POM aggregation in the ocean and support broader efforts to understand bacterial controls on the global carbon cycle based on microbial activities, community structure, and meta-omic profiling.

microbiology↗

bioRxiv2023

Spatial and Temporal Resolution of Cyanobacterial Bloom Chemistry Reveals an Open-Ocean Trichodesmium thiebautii as a Talented Producer of Specialized Metabolites

While the ecological role that Trichodesmium sp. play in nitrogen fixation has been widely studied, little information is available on potential specialized metabolites that are associated with blooms and standing stock Trichodesmium colonies. While a collection of biological material from a T. thiebautii bloom event from North Padre Island, TX in 2014 indicated that this species was a prolific producer of chlorinated specialized metabolites, additional spatial and temporal resolution was needed. We have completed these metabolite comparison studies, detailed in the current report, utilizing LC-MS/MS-based molecular networking to visualize and annotate the specialized metabolite composition of these Trichodesmium blooms and colonies in the Gulf of Mexico (GoM) and other waters. Our results showed that T. thiebautii blooms and colonies found in the GoM have a remarkably consistent specialized metabolome. Additionally, we isolated and characterized one new macrocyclic compound from T. thiebautii, trichothilone A (1), which was also detected in three independent cultures of T. erythraeum. Genome mining identified genes predicted to synthesize certain functional groups in the T. thiebautii metabolites. These results provoke intriguing questions of how these specialized metabolites affect Trichodesmium ecophysiology, symbioses with marine invertebrates, and niche development in the global oligotrophic ocean. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/569781v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@7bce53org.highwire.dtl.DTLVardef@26d052org.highwire.dtl.DTLVardef@36d44aorg.highwire.dtl.DTLVardef@1ab85fb_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Quantifying nutrient colimitation of microbial growth

Resource availability dictates how fast and how much microbial populations grow. Quantifying the relationship between microbial growth and resource concentrations makes it possible to promote, inhibit, and predict microbial activity. Microbes require many resources, including macronutrients (e.g., carbon and nitrogen), micronutrients (e.g., metals), and complex nutrients like vitamins and amino acids. When multiple resources are scarce, as occurs in nature, microbes may experience resource colimitation in which more than one resource limits growth simultaneously. Despite growing evidence for colimitation, the data is difficult to interpret and compare due to a lack of quantitative measures of colimitation and systematic tests of resource conditions. We hypothesize that microbes experience a continuum of nutrient limitation states and that nutrient colimitation is common in the laboratory and in nature. To address this, we develop a quantitative theory of resource colimitation that captures the range of possible limitation states and describes how they can change dynamically with resource conditions. We apply this approach to clonal populations of Escherichia coli to show that colimitation occurs in common laboratory conditions. We also show that growth rate and growth yield are colimited differently, reflecting their different underlying biology. Finally, we analyze environmental data to provide intuition for the continuum of limitation and colimitation conditions in nature. Altogether our results provide a quantitative framework for understanding and quantifying colimitation of microbes in biogeochemical, biotechnology, and human health contexts.

microbiology↗

bioRxiv2022

Effects of interspecies interactions on marine community ecosystem function

Microbial communities perform key ecosystem processes collectively. One such process is the degradation of carbohydrate polymers, which are the dominant pool of organic carbon in natural environments. Carbohydrate polymers are often degraded in a stepwise manner. Individual steps are performed by different microbial species, which form trophic cascades with carbon polymers at the bottom and fully oxidised carbon at the top. It is widely believed that these trophic cascades are hierarchically organised, where organisms at each level rely on organisms at the levels below. However, whether and how the higher-level organisms can also affect processes at the lower levels is not well understood. Here we studied how carbohydrate polymer degradation mediated by secreted enzymes is affected by species at higher trophic levels, i.e., species that cannot produce the enzymes for polymer degradation but can grow in presence of the polymer degraders. We used growth and enzyme assays in combination with transcriptomics to study how chitin degradation by a number of Vibrio strains is affected by the presence of different cross-feeders that consume metabolic by-products. We found that interactions between the degraders and cross-feeders influence the rate of chitin degradation by the community. Furthermore, we show that this is a result of changes in chitinase expression by degraders. Overall, our results demonstrate that interactions between species can influence key ecosystem functions performed by individuals within microbial communities. These results challenge the perspective that trophic cascades based on metabolically coupled microbial communities are unidirectional and provide mechanistic insights into these downstream interactions.

microbiology↗

bioRxiv2022

Microbial population dynamics decouple nutrient affinity from environmental concentration

How the growth rate of a microbial population responds to the environmental availability of chemical nutrients and other resources is a fundamental question in microbiology. Models of this response, such as the widely-used Monod model, are generally characterized by a maximum growth rate and a half-saturation concentration of the resource. What values should we expect for these half-saturation concentrations, and how should they depend on the environmental concentration of the resource? We survey growth response data across a wide range of organisms and resources. We find that the half-saturation concentrations vary across orders of magnitude, even for the same organism and resource. To explain this variation, we develop an evolutionary model to show that demographic fluctuations (genetic drift) can constrain the adaptation of half-saturation concentrations. We find that this effect fundamentally differs depending on the type of population dynamics: populations undergoing periodic bottlenecks of fixed size will adapt their half-saturation concentration in proportion to the environmental resource concentration, but populations undergoing periodic dilutions of fixed size will evolve half-saturation concentrations that are largely decoupled from the environmental concentration. Our model not only provides testable predictions for laboratory evolution experiments, but it also reveals how an evolved half-saturation concentration may not reflect the organisms environment. In particular, this explains how organisms in resource-rich environments can still evolve fast growth at low resource concentrations. Altogether our results demonstrate the critical role of population dynamics in shaping fundamental ecological traits.

microbiology↗

bioRxiv2020

Development of an Ocean Protein Portal for Interactive Discovery and Education

Proteins are critical in catalyzing chemical reactions, forming key cellular structures, and in regulating cellular processes. Investigation of marine microbial proteins by metaproteomics methods enables the discovery of numerous aspects of microbial biogeochemistry processes. However, these datasets present big-data challenges as they often involve many samples collected across broad geospatial and temporal scales, resulting in thousands of protein identifications, abundances, and corresponding annotation information. The Ocean Protein Portal (OPP) was created to enable data sharing and discovery among multiple scientific domains and serve both research and education functions. The portal focuses on three use case questions: "Where is my protein of interest?", "Who makes it?", and "How much is there?", and provides profile and section visualizations, real-time taxonomic analysis, and links to metadata, sequence analysis, and other external resources to enabling connections to be made between biogeochemical and proteomics datasets.

systems biology↗

bioRxiv2020

METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies - Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses

We present METATRYP version-2 software that identifies shared peptides across organisms within environmental metaproteomics studies to enable accurate taxonomic attribution of peptides during protein inference. Improvements include: ingestion of complex sequence assembly data categories (metagenomic and metatranscriptomic assemblies, single cell amplified genomes, and metagenome assembled genomes), prediction of the Least Common Ancestor (LCA) for a peptide shared across multiple organisms, increased performance through updates to the backend architecture, and development of a web portal (https://metatryp.whoi.edu). Major expansion of the marine database confirms low occurrence of shared tryptic peptides among disparate marine microorganisms, implying tractability for targeted metaproteomics. METATRYP was designed for ocean metaproteomics and has been integrated into the Ocean Protein Portal (https://oceanproteinportal.org); however, it can be readily applied to other domains. We describe the rapid deployment of a coronavirus-specific web portal (https://metatryp-coronavirus.whoi.edu/) to aid in use of proteomics on coronavirus research during the ongoing pandemic. A Coronavirus-focused METATRYP database identified potential SARS-CoV-2 peptide biomarkers and indicated very few shared tryptic peptides between SARS-CoV-2 and other disparate taxa, sharing 0.1% peptides or less (1 peptide) with the Influenza A & B pan-proteomes, establishing that taxonomic specificity is achievable using tryptic peptide-based proteomic diagnostic approaches. Statement of significanceWhen assigning taxonomic attribution in bottom-up metaproteomics, the potential for shared tryptic peptides among organisms in mixed communities should be considered. The software program METATRYP v 2 and associated interactive web portals enables users to identify the frequency of shared tryptic peptides among taxonomic groups and evaluate the occurrence of specific tryptic peptides within complex communities. METATRYP facilitates phyloproteomic studies of taxonomic groups and supports the identification and evaluation of potential metaproteomic biomarkers.

genomics↗