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McMahon, K.

Publications and source records attributed to McMahon, K..

At least 19 recordsLinked to original sources
bioRxiv2026

Not-so-great tits: early-life environment drives long-term decrease in adult body mass in a wild bird population

Body mass is a key organismal characteristic that impacts many physiological and ecological processes and often a strong determinant of fitness. Recent studies have documented temporal phenotypic changes in this trait in many populations, but identifying the mechanisms underpinning these changes can be difficult. Here, we use 47 years of data to analyse how adult and nestling body mass have changed over time in a great tit Parus major population in Wytham Woods (UK). Further, we link those changes to three environmental variables previously recognised as drivers of body mass: temperature, intra- and inter-specific competition and temporal mismatch with a key prey during breeding, winter moth Operophtera brumata caterpillars. Temporal analyses of adult body mass revealed contrasting dynamics at the between- and within-cohort levels, mirroring Simpsons Paradox. At the population level we report a marked decrease in body mass in adults between 1978 and 2024 (-0.042 Haldanes), and show that this results from phenotypic plasticity, driven by a negative between-cohort trend likely reflecting carry-over effects of the early environment. Within cohorts, however, trends were consistently positive likely reflecting an age-dependent mass increase. The change in adults was paralleled by a change in nestling body mass (-0.036 Haldanes). Nestling mass was negatively associated with estimated intensity of intraspecific competition, as well as inter-specific competition from blue tits Cyanistes caeruleus, as quantified by local population density. These effects carried over to adulthood, as shown by a negative association between adult mass and the population density experienced at early life. Temperature during development and mismatch with the caterpillar food supply, despite being associated with adult and nestling mass, did not explain the observed declines in mass, largely because these have not changed over time. Overall, our results illustrate the potential for effects mediated early in development to carry-over into long-term phenotypic change at later life history stages, and emphasise the value of considering multiple effects as drivers of phenotypic change in natural populations.

evolutionary biology↗
bioRxiv2025

Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem

Giant viruses represent key ecological players in aquatic ecosystems, yet their evolutionary dynamics in response to environmental change remain poorly understood, particularly in freshwater environments. We leveraged an unprecedented 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1,512 high-quality giant virus metagenome-assembled genomes (GVMAGs), providing a unique framework to track viral genome evolution across decades. Viruses in the order Imitervirales dominated the Lake Mendota virome, exhibiting consistent presence across all seasons and years. We identified gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as drivers of genomic innovation in giant viruses. Co-occurrence network analysis between viral DNA polymerase B and eukaryotic 18S rRNA sequences revealed significantly increased virus-host associations following the 2009 invasion of a predatory zooplankton. Genome-wide single nucleotide polymorphism analysis demonstrated predominantly purifying selection across viral genes, but revealed a significant increase in positively selected genes post-invasion, including in functions related to host infection (such as protein translation). Comparative evolutionary analyses revealed that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, positioning them as evolutionary intermediates with bacterial-like genomic stability but virus-like adaptive capacity. By analyzing a vicennial (20-year) time series, we show that freshwater giant viruses employ sophisticated evolutionary strategies. They broaden their host range without abandoning established partners and maintain stable genomic backbones while rapidly adapting infection-related genes. These dynamics highlight their critical yet previously underappreciated role in freshwater ecosystem dynamics and resilience to environmental change.

microbiology↗
bioRxiv2025

Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats

From its earliest beginnings, lifes expansion into new habitats has been profoundly shaped by its reciprocal interactions with Earths changing environments. Understanding how ancient metabolisms co-evolved with their environments requires uncovering the ecological and evolutionary processes that structured the functionally linked genes and networks underlying these metabolisms. Here, we focus on nitrogen (N2) fixation, one of lifes most critical metabolisms, and investigate the drivers of complexity in its associated gene machinery today. We used a large-scale comparative genomics framework to construct a comprehensive catalog of extant N2 fixation-associated genes and assessed their distribution across diverse microbial genomes and environmental backgrounds. Genomes enriched in N2 fixation genes generally have larger genome sizes, broader metabolic capabilities, wider habitat ranges, and are predominantly associated with mesophilic and aerobic lifestyles. Evolutionary reconstructions reveal a pattern of early gene gains in ancestral diazotrophs followed by lineage-specific gene losses in later diverging taxa, suggesting evolutionary trade-offs shaped by changing environments. These findings demonstrate that the evolution of N2 fixation has been intertwined with the composition and organization of the genes supporting the overarching N2 metabolism, driven by feedback between genome evolution and shifting environmental and ecological conditions.

microbiology↗
bioRxiv2024

Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake

The genetic potential for extracellular electron transfer (EET)-based metabolism has been shown to be a prevailing feature of humic lakes where bacterioplankton may be able to use EET to cycle dissolved organic matter (DOM) extracellularly between oxidized and reduced states, but measurable abiotic features resulting from this phenomenon have yet to be demonstrated. We observed an anoxygenic photosynthetic Chlorobium sp. bloom each summer in Trout Bog Lake in northern WI, USA. Given this blooms characteristics, we hypothesized that EET-based metabolisms of Chlorobium sp. and accompanying bacteria cycle DOM between oxidized and reduced states with seasonal or diel-timescale oscillations; therefore, we anticipated this could be measured by weekly and subdaily sampling. We collected vertical profiles on these timescales using a multiparameter sonde, including oxidation-reduction potential measurement, and we assayed for inorganic electron donors. We also developed and deployed a buoy to measure electric current flow between many pairs of electrodes simultaneously. Using metagenomics analyses, we examined the EET genes and other oxidoreductases of bacteria from water column samples at select depths and from biofilms that developed on electrodes at similar depths. Our results indicate the occurrence of diel electron cycling between phototrophic oxidation (electrotrophic metabolism) and anaerobic respiration (electrogenic metabolism), likely involving DOM. We also observed a gradual seasonal increase in hypolimnion oxidation-reduction potential. These diel and seasonal patterns have implications for carbon emissions and the ecology of electroactive bacteria in lakes. IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.

microbiology↗
bioRxiv2024

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

BackgroundProtists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the worlds best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last twenty years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community, and to hypothesize about their interactions with bacteria. ResultsBased on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Further, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g. ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. ConclusionsWe demonstrate that metagenomic sequence-based community analysis can complement existing eorts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes, and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

ecology↗
bioRxiv2024

A 20-year time-series of a freshwater lake reveals seasonal dynamics and environmental drivers of viral diversity, ecology, and evolution

Long-term ecological studies are powerful tools to investigate microbiomes and ecosystem change but have mostly ignored viruses. Here, we leveraged a 20-year time-series of a freshwater lake to characterize 1.3 million viral genomes over time, seasonality, and environmental factors. We identified 578 auxiliary metabolic gene (AMG) clusters representing over 150,000 AMGs, the most abundant of which, including psbA for photosynthesis, pmoC for methane oxidation, and katG for hydrogen peroxide decomposition, were consistently represented in viruses across decades and seasons. We observed positive associations and niche differentiation between virus-host pairs during seasonal change including in keystone taxa, Cyanobacteria, methanotrophs, and Nanopelagicales. Environmental constraints, specifically inorganic carbon and ammonium influenced viral abundances over time, and highlighted roles of viruses in both "top-down" and "bottom-up" interactions. Key evolutionary processes shaping gene and genome-wide selection included favored fitness genes, reduced genomic heterogeneity, and dominant sub-populations carrying specific genes. Overall, our study advances understanding of diversity, ecological dynamics, and evolutionary trajectories of viruses in Earths microbiomes and ecosystems.

microbiology↗
bioRxiv2023

Refinement of the "Candidatus Accumulibacter" Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration

Members of the "Candidatus Accumulibacter" genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 "Ca. Accumulibacter" species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most "Ca. Accumulibacter" MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the "Ca. Accumulibacter" diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium and high-quality MAGs for 5 of the 18 "Ca. Accumulibacter" species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized "Ca. Accumulibacter" species for which we propose the new species designation "Ca. Accumulibacter jenkinsii" sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, "Ca. A. necessarius" and "Ca. A. propinquus" accounted for more than 40% of the "Ca. Accumulibacter" community, whereas the newly proposed "Ca. A. jenkinsii" accounted for about 5% of the "Ca. Accumulibacter" community. IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the "Candidatus Accumulibacter" genus in pilot-scale plants operating with minimal aeration. We identified the "Ca. Accumulibacter" species enriched under these conditions, including one novel species for which we propose "Ca. Accumulibacter jenkinsii" sp. nov. as its designation. Furthermore, the MAGs obtained for 5 additional "Ca. Accumulibacter" species further refine the phylogeny of the "Ca. Accumulibacter" genus and provide new insight into its diversity within unconventional biological nutrient removal systems.

microbiology↗
bioRxiv2023

Social network centrality predicts dietary decisions in a wild bird population

How individuals balance costs and benefits of group living remains central to understanding sociality. In relation to diet, social foraging provides many advantages but also increases competition. Nevertheless, social individuals may offset increased competition by broadening their diet and consuming novel foods. Despite the expected relationships between social behaviour and dietary decisions, how sociality shapes individuals novel food consumption remains largely untested in natural populations. Here, we use wild, RFID-tracked, great tits to experimentally test how sociality predicts dietary decisions. We show that individuals with more social connections have higher propensity to use novel foods compared to socially-peripheral individuals, and this is unrelated to neophobia, observations, and demographic factors. These findings indicate sociable individuals may offset potential costs of competition by foraging more broadly. We discuss how social environments may drive behavioural change in natural populations, and the implications for the causes and consequences of social strategies and dietary decisions.

ecology↗
bioRxiv2023

Viral impacts on microbial activity and biogeochemical cycling in a seasonally anoxic freshwater lake

Microbial biogeochemical cycling relies on alternative electron acceptors when oxygen is unavailable, yet the role of viruses (bacteriophages) in these processes is understudied. We investigated how seasonal anoxia impacts viral and microbial biogeochemical cycling, by using paired total metagenomes, viromes, and metatranscriptomes, that were collected weekly. Stratification and anoxia drove microbial community composition, but dataset origin impacted the interpretation of viral community structure, activity, and function. Importantly, taxa abundance did not correlate with activity for both microbes and viruses. We identified virus-host linkages for 116 phages across 55 distinct hosts, many of which expressed genes for aerobic methane oxidation, nitrogen fixation, denitrification, and sulfate reduction. Overall, this work demonstrates the breadth and dynamics of virus-host interactions in mediating biogeochemistry. Additionally, we propose that viral community detection, functional potential, and activity are sensitive to pre-sequencing decisions, which must be kept in mind when interpreting genomic data in a biologically meaningful way.

microbiology↗
bioRxiv2022

Signatures of Microbial Diversity at Multiple Scales of Resolution within Engineered Enrichment Communities

Microbial community dynamics are dictated by both abiotic environmental conditions and biotic interactions. These communities consist of individual microorganisms across the continuum of phylogenetic diversity, ranging from coexisting members of different domains of life and phyla to multiple strains with only a handful of single nucleotide variants. Ecological forces act on a shifting template of population-level diversity that is shaped by evolutionary processes. However, understanding the ecological and evolutionary forces contributing to microbial community interactions and overall ecosystem function is difficult to interrogate for complex, naturally occurring microbial communities. Here, we use two time series of lab-scale engineered enrichment microbial communities simulating phosphorus removal to explore signatures of microbial diversity at multiple phylogenetic scales. We characterized microbial community dynamics and diversity over the course of reactor start-up and long-term dynamics including periods of eubiosis and dysbiosis as informed by the intended ecosystem function of phosphorus removal. We then compared these signatures to lineages from full-scale WWTPs performing phosphorus removal. We found that enriched lineages in lab-scale bioreactors harbor less intra-population diversity than lineages from the full-scale WWTP overall. Our work establishes a foundation for using engineered enrichment microbial communities as a semi-complex model system for addressing the fundamental ecological and evolutionary processes necessary for developing stable microbiome based biotechnologies.

microbiology↗
bioRxiv2022

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

microbiology↗
bioRxiv2021

Multi T1-weighted contrast imaging and T1 mapping with Compressed sensing FLAWS at 3T

The Fluid And White matter Suppression (FLAWS) MRI sequence allows for the acquisition of multiple T1-weighted contrasts in a single sequence acquisition. However, its acquisition time is prohibitive for use in clinical practice when the k-space is linearly downsampled and reconstructed using the Generalized Autocalibrating Partially Parallel Acquisition (GRAPPA) technique. This study proposes a FLAWS sequence optimization tailored to allow for the acquisition of FLAWS images with a Cartesian phyllotaxis k-space undersampling and compressed sensing (CS) reconstruction at 3T. The CS FLAWS sequence parameters were determined using a method previously employed to optimize FLAWS imaging at 1.5T and 7T. In-vivo experiments show that the proposed CS FLAWS optimization allows to reduce the FLAWS sequence acquisition time from 8 mins to 6 mins without decreasing the FLAWS image quality. In addition, this study demonstrates for the first time that T1-weighted imaging with low B1 sensitivity and T1 mapping can be performed with the FLAWS sequence at 3T for both GRAPPA and CS reconstructions. The FLAWS T1 mapping was validated using in-silico, in-vitro and in-vivo experiments with comparison against the inversion recovery turbo spin echo and MP2RAGE T1 mappings. These new results suggest that the recent advances in FLAWS imaging allow to combine the MP2RAGE imaging benefits (T1-weigthed imaging with low B1 sensitivity and T1 mapping) and with the previous version of FLAWS imaging benefits (multi T1-weighted contrast imaging) in a single 6 mins sequence acquisition. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

neuroscience↗
bioRxiv2021

Stratification in Microbial Communities with Depth and Redox Status in a Eutrophic Lake Across Two Years

Bacteria have a profound impact on many key biogeochemical cycles in freshwater lake ecosystems; in turn, the composition of bacteria in the lake is contingent on the chemistry of the water. Many parameters that affect bacterial growth in freshwater ecosystems, such as water temperature, nutrient levels, and redox status, exhibit notable inter-annual differences in addition to seasonal changes. However, little is known about the impact of these inter- and intra-annual differences on the freshwater microbiome, especially in anoxic bottom waters. In this study, we paired biogeochemical field data with 16S rRNA gene amplicon sequencing of depth-discrete samples from a dimictic lake across two open-water seasons to observe variation in the microbiome relative to differences in water chemistry between two years. We found differences in the timing anoxia onset and the redox status in the water column across the two years. Changes in redox status led to major shifts in the microbial community composition. While there was little variation between years in the microbial taxonomic composition at the phyla level, there was substantial interannual variation at more resolved taxonomic levels. Some interannual differences can be explained by links between the predicted metabolic potential of those lineages and the different redox conditions between the two years. These results emphasize the need for repeated monitoring to deduce long-term trends in microbial communities in natural ecosystems and the importance of a comprehensive evaluation of environmental conditions contemporary with any microbiome analysis. ImportanceThe results of this study add to the growing body of evidence that microbial communities in natural systems are temporally dynamic on multiple scales, and even more so at highly resolved taxonomic levels. By correlating our analysis of the microbial community with the redox status of the water column we find that many community differences between the years can be in part explained by these parameters. As collecting 16S rRNA data over many years is critical to understanding long term trends in microbial ecology, our study suggests that corresponding water chemistry data could be a powerful tool to help explain microbiome trends.

microbiology↗
bioRxiv2021

Investigating the chemolithoautotrophic and formate metabolism of Nitrospira moscoviensis by constraint-based metabolic modeling and 13C-tracer analysis

Nitrite-oxidizing bacteria belonging to the genus Nitrospira mediate a key step in nitrification and play important roles in the biogeochemical nitrogen cycle and wastewater treatment. While these organisms have recently been shown to exhibit metabolic flexibility beyond their chemolithoautotrophic lifestyle, including the use of simple organic compounds to fuel their energy metabolism, the metabolic networks controlling their autotrophic and mixotrophic growth remain poorly understood. Here, we reconstructed a genome-scale metabolic model for Nitrospira moscoviensis (iNmo686) and used constraint-based analysis to evaluate the metabolic networks controlling autotrophic and formatotrophic growth on nitrite and formate, respectively. Subsequently, proteomic analysis and 13C-tracer experiments with bicarbonate and formate coupled to metabolomic analysis were performed to experimentally validate model predictions. Our findings support that N. moscoviensis uses the reductive tricarboxylic acid cycle for CO2 fixation. We also show that N. moscoviensis can indirectly use formate as a carbon source by oxidizing it first to CO2 followed by reassimilation, rather than direct incorporation via the reductive glycine pathway. Our study offers the first measurements of Nitrospiras in vivo central carbon metabolism and provides a quantitative tool that can be used for understanding and predicting their metabolic processes. ImportanceNitrospira are globally abundant nitrifying bacteria in soil and aquatic ecosystems and wastewater treatment plants, where they control the oxidation of nitrite to nitrate. Despite their critical contribution to nitrogen cycling across diverse environments, detailed understanding of their metabolic network and prediction of their function under different environmental conditions remains a major challenge. Here, we provide the first constraint-based metabolic model of N. moscoviensis representing the ubiquitous Nitrospira lineage II and subsequently validate this model using proteomics and 13C-tracers combined with intracellular metabolomic analysis. The resulting genome-scale model will serve as a knowledge base of Nitrospira metabolism and lays the foundation for quantitative systems biology studies of these globally important nitrite- oxidizing bacteria.

microbiology↗
bioRxiv2020

Freshwater Chlorobia exhibit metabolic specialization among cosmopolitan and endemic populations

Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on their functional ecology and local adaptations came from isolates and merely 26 sequenced genomes that are poor representatives of natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-cell genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs) or "species". Of the 71 mOTUs, 57 were classified as genus Chlorobium and these mOTUs varied in relative abundance up to ~60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many were lacking genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian Chlorobium clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insights into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems. ImportanceThe reconstruction of genomes from metagenomes has enabled unprecedented insights into the ecology and evolution of environmental microbiomes. We applied this powerful approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and pinpoint nutrients that likely fuel their electron chains. Being photoautotrophs, these Chlorobia organisms also have the potential to serve as carbon sources that support metalimnetic and hypolimnetic food webs.

ecology↗
bioRxiv2020

Expanded Phylogenetic Diversity and Metabolic Flexibility of Microbial Mercury Methylation

Methylmercury is a potent, bioaccumulating neurotoxin that is produced by specific microorganisms by methylation of inorganic mercury released from anthropogenic sources. The hgcAB genes were recently discovered to be required for microbial methylmercury production in diverse anaerobic bacteria and archaea. However, the full phylogenetic and metabolic diversity of mercury methylating microorganisms has not been fully explored due to the limited number of cultured, experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury methylating microorganisms identified by hgcA sequence identity from publicly available isolate genomes and metagenome-assembled genomes (MAGs), as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known, and the distribution of hgcA is most likely due to several independent horizontal gene transfer events. Identified methylating microorganisms possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. Using a metatranscriptomic survey of a thawing permafrost gradient from which we identified 111 putative mercury methylators, we demonstrate that specific methylating populations may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify methylators based upon hgcA presence and describe their putative functions in the environment. IMPORTANCESpecific anaerobic microorganisms among the Deltaproteobacteria, Firmicutes, and Euryarchaeota have been shown to produce the bioaccumulating neurotoxin methylmercury. Accurately assessing the sources of microbial methylmercury production in the context of phylogenetic identification, metabolic guilds, and activity in the environment is crucial for understanding the constraints and effects of mercury impacted sites. Advances in next-generation sequencing technologies have enabled large-scale, cultivation-independent surveys of diverse and poorly characterized microorganisms of numerous ecosystems. We used genome-resolved metagenomics and metatranscriptomics to highlight the vast phylogenetic and metabolic diversity of putative mercury methylators, and their depth-discrete activities in the environment. This work underscores the importance of using genome-resolved metagenomics to survey specific putative methylating populations of a given mercury-impacted ecosystem.

microbiology↗
bioRxiv2019

metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways

SummaryAdvances in high-throughput sequencing technologies and bioinformatic pipelines have exponentially increased the amount of data that can be obtained from uncultivated microbial lineages inhabiting diverse ecosystems. Various annotation tools and databases currently exist for predicting the functional potential of sequenced genomes or microbial communities based upon sequence identity. However, intuitive, reproducible, and user-friendly tools for further exploring and visualizing functional guilds of microbial community metagenomic sequencing datasets remains lacking. Here, we present metabolisHMM, a series of workflows for visualizing the distribution of curated and user-provided Hidden Markov Models (HMMs) to understand metabolic characteristics and evolutionary histories of microbial lineages. metabolisHMM performs functional annotations with a set of curated or user-defined HMMs to 1) construct ribosomal protein and single marker gene phylogenies, 2) summarize the presence/absence of metabolic pathway markers, and 3) create heatmap visualizations of presence/absence summaries. Availability and ImplementationmetabolisHMM is freely available on Github at https://github.com/elizabethmcd/metabolisHMM and on PyPi at https://pypi.org/project/metabolisHMM/ under the GNU General Public License v3.0.

bioinformatics↗
bioRxiv2018

acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively-synthesized Retinal

Freshwater lakes harbor complex microbial communities, but these ecosystems are often dominated by acI Actinobacteria from three clades (acI-A, acI-B, acI-C). Members of this cosmopolitan lineage are proposed to bolster heterotrophic growth using phototrophy because their genomes encode actino-opsins (actR). This model has been difficult to experimentally validate because acI are not consistently culturable. In this study, using genomes from single cells and metagenomes, we provide a detailed biosynthetic route for many acI-A and -B members to synthesize retinal and its carotenoid precursors. Accordingly, these acI should be able to natively assemble light-driven actinorhodopsins (holo-ActR) to pump protons, in contrast to acI-C members and other bacteria that encode opsins but lack retinal-production machinery. Moreover, we show that all acI clades contain genes for a complex carotenoid pathway that starts with retinal precursors. Transcription analysis of acI in a eutrophic lake shows that all retinal and carotenoid pathway operons are transcribed and that actR is among the most highly-transcribed of all acI genes. Furthermore, heterologous expression of retinal pathway genes shows that lycopene, retinal, and ActR can be made. Model cells producing ActR and the key acI retinal-producing {beta}-carotene oxygenase formed acI-holo-ActR and acidified solution during illumination. Our results prove that acI containing both ActR and retinal-production enzymes have the capacity to natively synthesize a green light-dependent outward proton-pumping rhodopsin.\n\nIMPORTANCEMicrobes play critical roles in determining the quality of freshwater ecosystems that are vital to human civilization. Because acI Actinobacteria are ubiquitous and abundant in freshwater lakes, clarifying their ecophysiology is a major step in determining the contributions that they make to nitrogen and carbon cycling. Without accurate knowledge of these cycles, freshwater systems cannot be incorporated into climate change models, ecosystem imbalances cannot be predicted, and policy for service disruption cannot be planned. Our work fills major gaps in microbial light utilization, secondary metabolite production, and energy cycling in freshwater habitats.

microbiology↗