Biology subjects

Friesen, M. L.

Publications and source records attributed to Friesen, M. L..

5 recordsLinked to original sources

bioRxiv2024

NFixDB (Nitrogen Fixation DataBase) - A Comprehensive Integrated Database for Robust 'Omics Analysis of Diazotrophs

Biological nitrogen fixation is a fundamental biogeochemical process that transforms that provides fixed biologically available nitrogen by diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which has three different gene clusters: 1) molybdenum nitrogenase (nifDHK) is the most abundant, followed by its alternatives 2) vanadium nitrogenase (vnfDHK), and 3) iron nitrogenase (anfDHK). Multiple databases have been constructed as resources for diazotrophic omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFixDB (Nitrogen Fixation DataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (nifDHK, vnfDHK, anfDHK) and nitrogenase-like enzymes (e.g., nflDH) linked to ribosomal operons (16S-5.8S-23S). NFixDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFixDB to nifH databases from Buckley, Zehr, Mise, and FunGene finding extensive evidence of nifH, in addition to vnfH and nflH. NFixDB contains more than 4,000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NFixDB offers the first comprehensive nitrogenase database available to researchers.

bioinformatics↗

bioRxiv2022

MerCat2: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from omics data

SummaryMerCat2 ("Mer - Catenate2") is a versatile, parallel, scalable and modular property software package for robustly analyzing features in omics data. Using massively parallel sequencing raw reads, assembled contigs, and protein sequences from any platform as input, MerCat2 performs k-mer counting of any length k, resulting in feature abundance counts tables, quality control reports, protein feature metrics, ecological diversity metrics, and graphical representation (i.e., PCA). MerCat2 allows for direct analysis of data properties in a database-independent manner that initializes all data, which other profilers and assembly-based methods cannot perform. MerCat2 represents an integrated tool to illuminate omics data within a sample for rapid cross-examination and comparisons. Availability and implementationMerCat2 is written in Python and distributed under a BSD-3 license. The source code of MerCat2 is freely available at https://github.com/raw-lab/mercat2. MerCat2 is compatible with Python 3 on Mac OS X and Linux. MerCat2 can also be easily installed using bioconda: conda install MerCat2. ContactRichard Allen White III, UNC Charlotte, rwhit101@uncc.edu Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2021

Multiple Mutualist Effects generate synergistic selection and strengthen fitness alignment in a tripartite interaction between legumes, rhizobia, and mycorrhizal fungi

Nearly all organisms interact with multiple mutualists, and complementarity within these complex interactions can result in synergistic fitness effects. However, it remains largely untested how multiple mutualists impact eco-evolutionary dynamics. We tested how multiple microbial mutualists-- N-fixing bacteria and mycorrrhizal fungi-- affected selection and heritability in their shared host plant (Medicago truncatula), as well as fitness alignment between partners. Our results demonstrate for the first time that multispecies mutualisms synergistically affect selection and heritability of host traits and enhance fitness alignment between mutualists. Specifically, we found that multiple mutualists doubled the strength of selection on a plant architectural trait, resulted in 2-3-fold higher heritability of reproductive success, and more than doubled the strength of fitness alignment between N-fixing bacteria and plants. Taken together, these findings show that synergism generated by multiple mutualisms extends to key components of microevolutionary change, and emphasizes the importance of multiple mutualist effects in understanding evolutionary trajectories.

ecology↗

bioRxiv2019

Switchgrass Rhizosphere Metabolite Chemistry Driven by Nitrogen Availability

Plants and soil microorganisms interact closely in the rhizosphere where plants may exchange carbon (C) for functional benefits from the microbial community. For example, the bioenergy crop, switchgrass (Panicum virgatum) is thought to exchange root-exuded C for nitrogen (N) fixed by diazotrophs (free-living N-fixers). However, this interaction is not well characterized and it is not known how or if switchgrass responds to diazotrophs or their activity. To explore this question, we assessed rhizosphere metabolite chemistry of switchgrass grown in a hydroponic system under two N levels and under inoculated or uninoculated conditions. We found switchgrass root exudate chemistry to be more responsive to N availability than to diazotroph presence. Total metabolite concentrations were generally greater under high N versus low N and unaffected by inoculation. Examination of rhizosphere chemical fingerprints indicates metabolite chemistry was also driven strongly by N availability with a greater relative abundance of carbohydrates under high N and greater relative abundance of organic acids under low N. We also found evidence of changes in rhizosphere chemical fingerprints by inoculation treatment suggesting a potential for switchgrass to respond or even recruit diazotrophs. However, we found little evidence of N treatment and inoculation interaction effects which suggests switchgrass response to diazotroph presence is not mediated by N availability.

ecology↗

bioRxiv2017

Widespread Negative Frequency-Dependent Selection Maintains Diversity in the Legume-Rhizobia Symbiosis: Balancing nodulation may explain the paradox of rhizobium diversity

The evolutionary origin and ecological maintenance of biodiversity is a central problem in biology. For diversity to be stable through time, each genotype or species must have an advantage when rare. This negative frequency-dependence prevents deterministic extinction and mitigates the stochastic loss of diversity (1-4). However, models of mutualism typically generate positive frequency-dependence that reduces diversity (5-8). Here, we report empirical evidence for negative frequency-dependence in the legume-rhizobium mutualism within a single host generation, a phenomenon that we term balancing nodulation. Balancing nodulation increases rare rhizobia across all 13 legume genera investigated to date, at high and low inoculum densities, and with minimal genetic differentiation between rhizobia strains. While the mechanism generating this phenomenon is currently unknown, balancing nodulation could actively maintain variation in the rhizobia-legume symbiosis.

plant biology↗