Biology subjects

Denef, V. J.

Publications and source records attributed to Denef, V. J..

6 recordsLinked to original sources

bioRxiv2024

Tracking Microcystis viruses and infection dynamics across distinct phases of a Microcystis-dominated bloom

Given the impact of viruses on microbial community composition and function, viruses have the potential to play a significant role in the fate of freshwater cyanobacterial harmful algal blooms (cHABs). Yet the role of viruses in cHABs remains poorly understood. We sought to address this knowledge gap with a metagenomic analysis of viruses of bloom-forming Microcystis aeruginosa across cHAB phases in the western basin of Lake Erie. Size-fractionation of the water allowed us to identify significant fraction-specific trends in viral diversity, which corresponded with Microcystis genetic diversity. Using a new machine-learning model, we predicted infections between viral and microbial host populations. We predicted hundreds of viral populations with infection histories including Microcystis and non-Microcystis hosts, suggesting extensive interconnectivity and the potential for virus-mediated cross-species exchange of genetic material within cHABs communities. Infection predictions revealed a broad host range for Lake Erie Microcystis viruses, challenging previous notions of "narrow" host-virus interactions in cHABs. Abundant viral genes belonging to predicted Microcystis viruses revealed their potential role in key metabolic pathways and adaptation to environmental changes. We observed significant turnover of predicted Microcystis virus populations across time. Viral diversity was highest in the viral fraction and lowest in the colony-associated fraction, suggesting that Microcystis colony formation and growth during cHABs leads to bottlenecks in viral diversity. These findings advance our understanding of uncultivated Microcystis virus diversity, their potential effects on host metabolism, potential influence on species interactions, and potential coevolutionary processes between microbial hosts and their viral predators within Microcystis-dominated cHABs. ImportanceUnderstanding interactions between viruses, their hosts, and environmental parameters may be key to identifying the mechanisms underlying the persistence and demise of cyanobacterial harmful algal blooms (cHABs). In this study we describe the viral diversity and host ranges of viruses predicted to infect Microcystis, describing the distribution of these properties across time, space, and different bloom-associated size fractions. Additionally, the study highlights abundant genes belonging to predicted Microcystis viruses and their potential roles in key metabolic pathways and adaptation to environmental changes. The observed turnover of Microcystis virus populations, with the highest diversity in viral fractions and the lowest in colony-associated fractions, suggests that Microcystis colony formation during blooms plays an important role in shaping viral diversity and community turnover. These findings contribute to a better understanding of the interplay between viruses, Microcystis, and their accompanying bacterial communities, shedding light on mechanisms driving bloom dynamics, species interactions, and coevolutionary processes.

microbiology↗

bioRxiv2022

The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome

Cyanobacteria harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 unialgal Microcystis cultures collected from western Lake Erie between 2017-2019. While some cultures isolated in different years have a high degree of genetic similarity (Average Nucleotide Identity >99%), genomic data shows that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only 5 isolates contained all the genes required for microcystin synthesis while 2 isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 g L-1) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America, which is changing rapidly due to climate change. HighlightsO_LITwenty one xenic Microcystis cultures were isolated from western Lake Erie and capture the diversity of Microcystis strains observed in natural populations as well as their associated bacteria C_LIO_LIMicrocystis strains show variability in core and accessory gene content, and genetically similar strains produce varying concentrations and congeners of microcystins C_LIO_LIThis collection is a valuable resource for studying strain diversity and interactions between Microcystis and associated bacteria C_LIO_LIOur collection increases the availability of environmentally relevant strains from temperate North America, which is historically underrepresented in culture collections. C_LI

microbiology↗

bioRxiv2019

To dereplicate or not to dereplicate?

Our ability to reconstruct genomes from metagenomic datasets has rapidly evolved over the past decade, leading to publications presenting 1,000s, and even more than 100,000 metagenome-assembled genomes (MAGs) from 1,000s of samples. While this wealth of genomic data is critical to expand our understanding of microbial diversity, evolution, and ecology, various issues have been observed in some of these datasets that risk obfuscating scientific inquiry. In this perspective we focus on the issue of identical or highly similar genomes assembled from independent datasets. While obtaining multiple genomic representatives for a species is highly valuable, multiple copies of the same or highly similar genomes complicates downstream analysis. We analyzed data from recent studies to show the levels of redundancy within these datasets, the highly variable performance of commonly used dereplication tools, and to point to existing approaches to account and leverage repeated sampling of the same/similar populations.

microbiology↗

bioRxiv2019

Temperature and nutrient gradients correspond with lineage-specific microdiversification in the ubiquitous and abundant Limnohabitans freshwater genus

Most freshwater bacterial communities are characterized by a few dominant taxa, which are often ubiquitous across freshwater biomes worldwide. Our understanding of the genomic basis underlying this pattern is limited to a subset of taxa. Here, we investigated the genomic basis that enables Limnohabitans, a freshwater genus key in funneling carbon from primary producers to higher trophic levels, to achieve abundance and ubiquity. We reconstructed eight metagenome assembled genomes (MAGs) from this genus along broad environmental gradients existing in Lake Michigan, part of Earths largest surface freshwater system. De novo strain inference analysis resolved a total of 23 strains from these MAGs, which strongly partitioned into two habitat-specific clusters with co-occurring strains from different lineages. The largest number of strains belonged to the abundant LimB lineage, for which robust in situ strain-delineation had not previously been achieved. Our data show that temperature and nutrient levels may be two of the primary drivers of microdiversification within the Limnohabitans genus. Additionally, strains predominant in low and high phosphorus conditions had larger genomic divergence than strains abundant under different temperatures. Comparative genomics and gene expression analysis yielded evidence for the ability of LimB populations to exhibit cellular motility and chemotaxis, a phenotype not yet associated with cultured Limnohabitans strains. Our findings broaden historical marker gene-based surveys of Limnohabitans microdiversification, and provide in situ evidence of genome diversity and its functional implications across freshwater gradients.

microbiology↗

bioRxiv2018

Using machine learning to associate bacterial taxa with functional groups through flow cytometry, 16S rRNA gene sequencing, and productivity data

High-(HNA) and low-nucleic acid (LNA) bacteria are two operational groups identified by flow cytometry (FCM) in aquatic systems. HNA cell density often correlates strongly with heterotrophic production, while LNA cell density does not. However, which taxa are specifically associated with these groups, and by extension, productivity has remained elusive. Here, we addressed this knowledge gap by using a machine learning-based variable selection approach that integrated FCM and 16S rRNA gene sequencing data collected from 14 freshwater lakes spanning a broad range in physicochemical conditions. There was a strong association between bacterial heterotrophic production and HNA absolute cell abundances (R2 = 0.65), but not with the more abundant LNA cells. This solidifies findings, mainly from marine systems, that HNA and LNA could be considered separate functional groups, the former contributing a disproportionately large share of carbon cycling. Taxa selected by the models could predict HNA and LNA absolute cell abundances at all taxonomic levels, with the highest performance at the OTU level. Selected OTUs ranged from low to high relative abundance and were mostly lake system-specific (89.5%-99.2%). A subset of selected OTUs was associated with both LNA and HNA groups (12.5%-33.3%) suggesting either phenotypic plasticity or within-OTU genetic and physiological heterogeneity. These findings may lead to the identification of systems-specific putative ecological indicators for heterotrophic productivity. Generally, our approach allows for the association of OTUs with specific functional groups in diverse ecosystems in order to improve our understanding of (microbial) biodiversity-ecosystem functioning relationships. ImportanceA major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Research is limited by the ability to readily culture most bacteria present in the environment and the difference in bacterial physiology in situ compared to in laboratory culture. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are associated with heterotrophic productivity in freshwater lakes and indicated that the key contributors were highly system-specific, regularly rare members of the community, and that some could switch between being low and high contributors. Our approach provides a promising framework to identify taxa that contribute to ecosystem functioning and can be further developed to explore microbial contributions beyond heterotrophic production.

ecology↗

bioRxiv2017

Microhabitats shape diversity-productivity relationships in freshwater bacterial communities

Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on richness, evenness, or phylogenetic diversity, and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake. Diversity measures, and not environmental variables, were the best predictors of particle-associated heterotrophic production. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened with evenness. There were no observable BEF trends in free-living bacterial communities. Across both habitats, communities with more phylogenetically related taxa had higher per-capita heterotrophic production than communities of phylogenetically distantly related taxa. Our findings show that heterotrophic bacterial productivity is positively correlated with evenness and richness, negatively with phylogenetic diversity, and that BEF relationships are contingent on microhabitats. Our work adds to the understanding of the highly distinct contributions to community diversity and ecosystem functioning contributed by bacteria in free-living and particle-associated aquatic habitats.

ecology↗