Biology subjects

McNichol, J.

Publications and source records attributed to McNichol, J..

7 recordsLinked to original sources

bioRxiv2026

Estimating absolute microbial abundances from metabarcoding anchored to cytometry data

Over the past decades, metabarcoding and automated cell-counting approaches have greatly advanced our understanding of marine microbial communities. Metabarcoding provides high taxonomic resolution and comprehensive community characterization, typically as relative gene abundances, whereas flow cytometry provides absolute cell abundances but lower taxonomic coverage. Here, we assess whether concurrent flow-cytometry observations can calibrate metabarcoding data to derive absolute gene abundances across four basin-scale Atlantic and Pacific Ocean transects. We first show that flow-cytometry-anchored calibration reproduces absolute abundances of Prochlorococcus and Synechococcus with performance comparable (R2 = 0.87) to internal DNA standard-based quantification. For datasets lacking internal standards, the choice of cytometric "anchor" species introduces systematic offsets in absolute abundance estimates, although spatial patterns remain robust. These offsets may reflect underestimation of cytometric counts or variation in rRNA gene copy numbers among actively dividing cells. We therefore recommend the use of multiple anchors where possible to diagnose systematic uncertainty. Applying this framework, we derive absolute gene concentrations for diverse plankton taxa from compositional metabarcoding data. For taxa with known rRNA gene copy numbers, calibration further enables estimation of absolute cell concentrations. We also resolve ecotype-level absolute abundances of Prochlorococcus along a longitudinal temperature gradient, revealing ecological patterns not apparent from compositional or cytometric data alone. Our results demonstrate that calibrated metabarcoding provides a practical quantitative bridge between molecular and cytometric observations, yielding high taxonomic resolution together with absolute gene concentrations and quantified uncertainties.

ecology↗

bioRxiv2026

Maximum Unified Fatty Acid Signature Analysis: a new approach to QFASA

Accurately estimating predator diets is crucial for understanding and predicting ecosystem changes. The desire for non-lethal but accurate diet estimation techniques has led to new approaches such as quantitative fatty acid signature analysis (QFASA), a now widely accepted method for estimating the diets of marine predators. We propose a novel alternative to QFASA, namely maximum unified fatty acid signature analysis (MUFASA), to estimate dietary proportions using fatty acid signatures. MUFASA is based on maximum likelihood estimation principles and consequently offers several theoretical advantages over QFASA, including estimates that possess desirable properties when model assumptions hold. In addition, the availability of a likelihood function enables the use of a broad range of existing methodologies that may have the capacity to address current well-known challenges associated with diet estimation via fatty acids. MUFASA and QFASA are compared using simulations based on wide-ranging diets, as well as real-life data from a captive study of harbour seals, for which diets are known. Estimates derived from QFASA and MUFASA are similar, suggesting that diet estimation in this context can potentially be viewed through an MLE framework. While not the primary focus of this work, bootstrap confidence intervals are also developed and preliminary results yield high coverage probabilities when the diet proportions are not near 0 or 1.

ecology↗

bioRxiv2025

Induced pathogenicity toward open-ocean diatoms by a newly isolated filterable bacterium Ekhidna algicida sp. nov.

Phytoplankton are the base of marine food webs. They form intricate interactions with heterotrophic bacteria ranging from mutualistic to pathogenic that together impact oceanic carbon and nutrient cycling. Our understanding of these interactions in marine environments remains primarily limited to laboratory-based studies of model organisms. Here, we report the discovery and characterization of Ekhidna algicida sp. nov. strain To15, isolated from the oligotrophic Pacific Ocean (16{degrees}N, 140{degrees}W) based on its algicidal effect on the pelagic diatom Thalassiosira oceanica. Subsequent co-culture experiments demonstrate that E. algicida is lethal within days to a diverse array of diatoms, with the effect mediated by bacterial exudates that remain algicidal on their own against axenic T. oceanica cultures. Twenty additional algicidal Ekhidna strains were subsequently isolated from the Pacific Ocean. Our findings reveal E. algicida as a potentially widespread pathogen of diatoms, that can alter microbial community composition dynamics in pelagic ecosystems. TeaserA newly discovered Pacific Ocean bacterium can kill diatoms, revealing a hidden pathogenic role in open-ocean ecosystems.

ecology↗

bioRxiv2025

A Multidomain Lens on the Temporal Dynamics of Surface Microbial Communities in the Southern Ocean (2013-2019)

Marine microorganisms are vital to biogeochemical cycles and food web dynamics, with their community structure shaped by environmental factors such as temperature, light, and salinity. While microbial dynamics in the western Antarctic Peninsula are relatively well- studied, the northwestern region remains underexplored, particularly in long-term, multidomain analyses. To fill this gap, we investigated microbial communities encompassing all three domains of life (Bacteria, Archaea, and Eukarya) in the Northwestern Antarctic Peninsula. Using the universal primer set 515Y/926R, we sequenced unfractionated seawater from ten sites over a six-year period (2013-2019). Environmental parameters, temperature and salinity, showed minimal variation across the study. However, microbial diversity and composition, especially among eukaryotic phytoplankton, displayed significant temporal changes among seasons and years. The prokaryotic community, by contrast, was relatively stable, with Gammaproteobacteria-- particularly the Nitrincolaceae family--maintaining high relative abundance throughout all sampling periods, but a few distinct ASVs. In contrast, no eukaryotic group exhibited consistently high relative abundance across sampling periods. The summer of 2016, marked by a strong El Nino event, presented the most distinct microbial community structure, underscoring the sensitivity of these communities to extreme climatic conditions. These results highlight the importance of integrated, long-term studies to better understand the dynamics, interactions, and resilience of microbial ecosystems in the rapidly changing Antarctic environment. IMPORTANCEThis study provides a unique long-term perspective on microbial community dynamics in the Northwestern Antarctic Peninsula, a region still poorly explored through a multidomain lens. By investigating the temporal variability of Bacteria, Archaea, and Eukaryotes over six years, we reveal distinct stability patterns between these groups, with phytoplankton showing the highest variability and prokaryotes remaining relatively stable. The strong response of the microbial community to the 2016 El Nino event highlights its sensitivity to extreme climate conditions, reinforcing the importance of understanding how Antarctic ecosystems will respond to future climate shifts. The consistent presence of Nitrincolaceae, a key bacterial taxon, suggests its ecological relevance in the region, while fluctuations in phytoplankton composition may impact food web dynamics. These findings emphasize the need for continued long-term monitoring to predict how microbial communities will adapt to environmental changes, which is crucial for assessing the future functioning of polar marine ecosystems.

microbiology↗

bioRxiv2024

Variational inference for microbiome survey data with application to global ocean data

Linking sequence-derived microbial taxa abundances to host (patho-)physiology or habitat characteristics in a reproducible and interpretable manner has remained a formidable challenge for the analysis of microbiome survey data. Here, we introduce a flexible probabilistic modeling framework, VI-MIDAS (Variational Inference for MIcrobiome survey DAta analysiS), that enables joint estimation of context-dependent drivers and broad patterns of associations of microbial taxon abundances from microbiome survey data. VI-MIDAS comprises mechanisms for direct coupling of taxon abundances with covariates and taxa-specific latent coupling which can incorporate spatio-temporal information and taxon-taxon interactions. We leverage mean-field variational inference for posterior VI-MIDAS model parameter estimation and illustrate model building and analysis using Tara Ocean Expedition survey data. Using VI-MIDAS latent embedding model and tools from network analysis, we show that marine microbial communities can be broadly categorized into five modules, including SAR11-, Nitrosopumilus-, and Alteromondales-dominated communities, each associated with specific environmental and spatiotemporal signatures. VI-MIDAS also finds evidence for largely positive taxon-taxon associations in SAR11 or Rhodospirillales clades, and negative associations with Alteromonadales and Flavobacteriales classes. Our results indicate that VI-MIDAS provides a powerful integrative statistical analysis framework for discovering broad patterns of associations between microbial taxa and context-specific covariate data from microbiome survey data.

bioinformatics↗

bioRxiv2024

Predictable functional biogeography of marine microbial heterotrophs

Heterotrophic bacteria and archaea ( heteroprokaryotes) drive global carbon cycling, but how to quantitatively organize their functional complexity remains unclear. We generated a global-scale understanding of marine heteroprokaryotic functional biogeography by synthesizing genetic sequencing data with a mechanistic marine ecosystem model. We incorporated heteroprokaryotic diversity into the trait-based model along two axes: substrate lability and growth strategy. Using genetic sequences along three ocean transects, we compiled 21 heteroprokaryotic guilds and estimated their degree of optimization for rapid growth (copiotrophy). Data and model consistency indicated that gradients in grazing and substrate lability predominantly set biogeographical patterns, and identified deep-ocean slow copiotrophs whose ecological interactions control the surface accumulation of dissolved organic carbon.

ecology↗

bioRxiv2019

Reconciling a Model of Core Metabolism with Growth Yield Predicts Biochemical Mechanisms and Efficiency for a Versatile Chemoautotroph

Obligately chemoautotrophic Campylobacteria dominate productivity in dark, sulfidic, and oxygen-depleted environments. However, biochemical mechanisms underlying their growth remain poorly known, limiting understanding of their physiology, ecology, and biogeochemical impact. In this study, we used comparative genomics, conceptual modeling of core metabolism, and chemostat growth yields to derive a model of energy conservation consistent with experimental data for the versatile chemoautotroph Sulfurimonas denitrificans. Our model rests on three core mechanisms: Firstly, to allow electrogenic sulfur-based denitrification, we predict that the campylobacterial-type sulfur oxidation enzyme complex must donate electrons to the membrane quinone pool, possibly via a sulfide:quinone oxidoreductase. Secondly, to account for the unexpectedly low growth efficiency of aerobic sulfur oxidation compared to denitrification, we posit the high-affinity campylobacterial-type cbb3 cytochrome c oxidase has a relatively low H+/e- of 1, likely due to a lack of proton pumping under physiological conditions. Thirdly, we hypothesize that reductant for carbon fixation by the reverse tricarboxylic acid cycle is produced by a non-canonical complex I that reduces both ferredoxin and NAD(P)H. This complex is conserved among related Campylobacteria and may have allowed for the radiation of organisms like S. denitrificans into sulfur-rich environments that became available after the great oxidation event. Our theoretical model has two major implications. Firstly, it sets the stage for future experimental work by providing testable hypotheses about the physiology, biochemistry, and evolution of chemoautotrophic Campylobacteria. Secondly, it provides constraints on the carbon fixation potential of chemoautotrophic Campylobacteria in sulfidic environments worldwide by predicting theoretical ranges of chemosynthetic growth efficiency.\n\nSignificanceChemoautotrophic Campylobacteria are abundant in many low-oxygen, high-sulfide environments where they contribute significantly to dark carbon fixation. Although the overall redox reactions they catalyze are known, the specific biochemical mechanisms that support their growth are mostly unknown. Our study combines conceptual modeling of core metabolic pathways, comparative genomics, and measurements of physiological growth yield in a chemostat to infer the most likely mechanisms of chemoautotrophic energy conservation in the model organism Sulfurimonas denitrificans. The hypotheses proposed herein are novel, experimentally falsifiable, and will guide future biochemical, physiological, and environmental modelling studies. Ultimately, investigating the core mechanisms of energy conservation will help us better understand the evolution and physiological diversification of chemoautotrophic Campylobacteria and their role in modern ecosystems.

microbiology↗