Biology subjects

Vineis, J. H.

Publications and source records attributed to Vineis, J. H..

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↗

bioRxiv2023

Machined silicon traps for capturing novel bacterial communities and strains in-situ

We tested the feasibility of a novel machined silicon nanopore enrichment device to recover individual microbial taxa from anaerobic sediments. Unlike other environmental isolation devices that have multiple entry points for bacteria or require the sample to be manually placed inside of a culturing chamber, our silicon device contains 24 precisely sized and spaced nanopores, each of which is connected to one culturing well, thereby providing only one entry point for bacteria. The culturing wells allow nutrient transport, so the bacteria that enter continue to experience their natural chemical environment, allowing collection of microbes without manipulating the environment. The device was deployed in marsh sediment and subsequently returned to the laboratory for bacterial culturing and analysis. 16S rRNA marker gene and metagenomic sequencing was used to quantify the number of different microbial taxa cultured from the device. The 16S rRNA sequencing results indicate that each well of the device contained between 1 and 62 different organisms from several taxonomic groups, including likely novel taxa. We also sequenced the metagenome from 8 of the 24 wells, enabling the reconstruction of 56 metagenomic assembled genomes (MAGs), and 44 of these MAGs represented non-redundant genome reconstructions. These results demonstrate that our novel silicon nanofluidic device can be used for isolating and culturing consortia containing a small number of microbial taxa from anaerobic sediments, which can be very valuable in determining their physiological potential. ImportanceThere are very few methods that can remove a few bacterial cells from a complex environment and keep the cells alive so that they can propagate sufficiently to be analyzed in a laboratory. Such methods are important to develop because the physiological functions of individual species of bacteria are often unknown, cannot be determined directly in the complex sample, and many bacterial cells cannot be grown outside of their natural environment. A novel bacterial isolation device has been made tested in a salt marsh. The results show that the device successfully isolated small groups of bacterial species from the incredibly diverse surroundings. The communities of bacteria were easily removed from the device in the laboratory and analyzed.

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↗