Biology subjects

Bulseco, A. N.

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

3 recordsLinked to original sources

bioRxiv2025

Microbial consortia in salt marsh sediments are sequentially buried over millennia and genomic complementarity analysis indicates an important role in complex carbon decomposition

Salt marsh sediments contain high levels of microbial diversity and function that reflect the heterogeneity of available nutrients, dynamic hydrology, and layers of organic matter developed over millennia. However, the microbially mediated processes involved in the cycling of complex carbon in these sediments are still largely undescribed. We used genome reconstruction, cooccurrence networks, and genome scale metabolic modeling to identify the functional capacity for organic matter decomposition among cooccurring microbes from 240 cm of sediment in a Spartina patens dominated salt marsh, representing over 3000 years of sediment accumulation. Microbial communities were structured according to depth, and the network identified significant positive cooccurrence within the community. We identified an active subnetwork of cooccurring subsurface metagenomic assembled genomes (MAGs) capable of decomposing complex carbon and aromatics. The Wood-Ljungdahl pathway was central to most of the MAGs within the subnetwork and metabolism of aromatics was potentially enabled through metabolic handoffs and the Benzoyl-CoA pathway. Variant analysis indicates that these subsurface populations are stratified with depth, suggesting high selection coupled with spatial isolation. These results provide evidence of microbial populations that persist under energy limited conditions and contribute to the transformation of organic matter within salt marsh sediment.

ecology↗

bioRxiv2024

Growth characteristics of natural microbial populations are skewed towards bacteria with low specific growth rates

Microbes are often functionally characterized by traits that specify their optimum environmental conditions for growth, such as temperature or pH, as well as upper and lower bounds where growth is possible. While any given microbe will have a narrow environmental window where growth can occur, a diverse community can span a much larger range of conditions where growth is possible by at least some members of the community. One important trait of microbes is maximum specific growth rate, as this trait determines if a microbe can persist in environments with short residence times. In this study, we conducted a chemostat experiment with natural microbial communities and manipulated dilution rate to test how it would act as a selective force controlling community dynamics and microbial diversity. Using both experimental chemostats and trait-based modeling, we examine how the composition of a microbial community collected from a coastal meromictic pond changes as dilution rate increases from 0.1 to 10 d-1. We compare experimental results from 16S rRNA gene amplicon sequences to the output from two different simulations of the trait-based model, one in which maximum specific growth rate is initially evenly distributed across the community and another where maximum specific growth rate traits are pulled from a beta probability distribution that is skewed towards low specific growth rates. Our experimental results match the simulation where the initial natural population is dominated by slow-growing microbes. Our results also highlight the importance of initial trait distributions in modeling community response to environmental changes. ImportanceAll living organisms are constrained by environmental boundaries that govern where growth is possible, such as minimum and maximum temperature or pH. An organisms maximum specific growth rate places a lower bound on the residence or turnover time of a system where an organism can persist without being removed from the system. While we have good bounds on the maximum specific growth rate of culturable organisms, such as Escherichia or Vibrio species, information is lacking on how the maximum specific growth rate trait is distributed in natural microbial communities. This information is critical for understanding how a community will respond to changes in residence time. Using chemostats and trait-based modeling, this study assesses how maximum specific growth rate is distributed in a natural community collected from a coastal, salinity-stratified pond.

microbiology↗

bioRxiv2021

Microbial dark carbon fixation fueled by nitrate enrichment

Anthropogenic nitrate amendment to coastal marine sediments can increase rates of heterotrophic mineralization and autotrophic dark carbon fixation (DCF). DCF may be favored in sediments where organic matter is biologically unavailable, leading to a microbial community supported by chemoautotrophy. Niche partitioning among DCF communities and adaptations for nitrate metabolism in coastal marine sediments remain poorly characterized, especially within salt marshes. We used genome-resolved metagenomics, phylogenetics, and comparative genomics to characterize the potential niche space, phylogenetic relationships, and adaptations important to microbial communities within nitrate enriched sediment. We found that nitrate enrichment of sediment from discrete depths between 0-25 cm supported both heterotrophs and chemoautotrophs that use sulfur oxidizing denitrification to drive the Calvin-Benson-Bassham (CBB) or reductive TCA (rTCA) DCF pathways. Phylogenetic reconstruction indicated that the nitrate enriched community represented a small fraction of the phylogenetic diversity contained in coastal marine environmental genomes, while pangenomics revealed close evolutionary and functional relationships with DCF microbes in other oligotrophic environments. These results indicate that DCF can support coastal marine microbial communities and should be carefully considered when estimating the impact of nitrate on carbon cycling in these critical habitats. ImportanceSalt marshes store carbon at one of the fastest rates of any blue carbon system and buffer coastal marine waters from eutrophication. Dark carbon fixation (DCF) conducted by microbes within the sediment can influence the carbon storage capacity, but little is known about the ecology or genomic potential of these organisms. Our study identifies a potential niche space for several functionally distinct groups of chemoautotrophs which primarily use sulfur oxidizing denitrification to fuel DCF under high nitrate concentrations. These findings fill an important gap in our understanding of microbial contributions to carbon storage within salt marsh sediments and how this critical blue carbon system responds to anthropogenic nitrate enrichment.

ecology↗