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1. Gut Microbiomes of Freshwater Mussels (Unionidae) Are Taxonomically and Phylogenetically Variable across Years but Remain Functionally Stable

   https://doi.org/10.3390/microorganisms9020411  

   McCauley, Mark; Chiarello, Marlène; Atkinson, Carla L.; Jackson, Colin R. (February 2021, Microorganisms)

   null (Ed.)

   Freshwater mussels perform essential ecosystem functions, yet we have no information on how their microbiomes fluctuate over time. In this study, we examined temporal variation in the microbiome of six mussel species (Lampsilis ornata, Obovaria unicolor, Elliptio arca, Fusconaia cerina, Cyclonaias asperata, and Tritogonia verrucosa) sampled from the same river in 2016 and 2019. We examined the taxonomic, phylogenetic, and inferred functional (from 16S rRNA sequences) facets of their microbiome diversity. Significant differences between the two years were identified in five of the six species sampled. However, not all species that exhibited a temporally variable microbiome were functionally distinct across years, indicating functional redundancy within the mussel gut microbiome. Inferred biosynthesis pathways showed temporal variation in pathways involved in degradation, while pathways involved in cellular metabolism were stable. There was no evidence for phylosymbiosis across any facet of microbiome biodiversity. These results indicate that temporal variation is an important factor in the assembly of the gut microbiomes of freshwater mussels and provides further support that the mussel gut microbiome is involved in host development and activity. 

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2. Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost

   https://doi.org/10.1038/s43705-023-00326-5  

   Romanowicz, Karl J; Crump, Byron C; Kling, George W (December 2023, ISME Communications)

   Abstract Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost–climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0–50 cm), transition-zone (50–70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3–5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra. 

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3. Barren to green in a single application: Revitalizing brownfield soil with simulated root exudates

   https://doi.org/10.1016/j.eti.2024.103735  

   Vaidya, Bhagyashree P; Krisak, Sarah E; Krumins, Jennifer Adams; Goodey, Nina M (November 2024, Environmental Technology & Innovation)

   Barren, metal-contaminated soils lack plants and root exudate inputs, exhibit low microbial abundance and functioning, and often require soil revitalization to revegetate. While the effects of simulated root exudates (SRE) have been investigated in uncontaminated, vegetated soils, their potential for remediating post-industrial barren, contaminated soils has not been examined or leveraged. We asked whether priming brownfield soils with a laboratory-prepared SRE solution stimulates native soil microbial metabolism and functioning and how long the effects last. Moreover, we compared a cost-effective single SRE addition to repeated SRE additions. We collected soils from a metal-contaminated, abandoned industrial rail yard (barren and vegetated sites) and a vegetated agricultural reference site, established microcosms, and treated the soils with either a single or repeated SRE addition/s. By day 30, SRE-enriched barren, brownfield soils showed significantly higher soil respiration rates than the untreated control soils. Phosphatase activities were significantly higher even 210 days after a single SRE addition. Plants were introduced 282 days after the single SRE addition. The average shoot height (16 ± 0.3 cm) and total plant biomass (0.5 ± 0.02 g) of plants grown in single addition SRE enriched barren soil were significantly higher than the controls (9 ± 0.9 cm and 0.3 ± 0.02 g, respectively). The increased soil microbial functioning and productivity indicate that a single SRE application holds promise as a field-ready technology to revitalize barren, poorly functioning brownfield soils. SRE application may also be a pragmatic and innovative approach to enable successful phytoremediation and re-greening of industrial barrens. 

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4. Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets

   https://doi.org/10.1111/1755-0998.70062  

   Vilonen, Leena; Thompson, Andrew; Adams, Byron; Ayres, Edward; Franco, André_L C; Wall, Diana H (January 2026, Molecular Ecology Resources)

   ABSTRACT Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under‐characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long‐term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom‐built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large‐scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America. 

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5. Pangenomes suggest ecological-evolutionary responses to experimental soil warming

   https://doi.org/10.1128/msphere.00059-25  

   Choudoir, Mallory J; Narayanan, Achala; Rodriguez-Ramos, Damayanti; Simoes, Rachel; Efroni, Alon; Sondrini, Abigail; DeAngelis, Kristen M (April 2025, mSphere)

   Tringe, Susannah Green (Ed.)

   ABSTRACT Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoingin situsoil warming experiment where, for over three decades, temperate forest soils are continuously heated at 5°C above ambient. We hypothesize that across generations of chronic warming, genomic signatures within diverse bacterial lineages reflect adaptations related to growth and carbon utilization. From our bacterial culture collection isolated from experimental heated and control plots, we sequenced genomes representing dominant taxa sensitive to warming, including lineages of Actinobacteria, Alphaproteobacteria, and Betaproteobacteria. We investigated genomic attributes and functional gene content to identify signatures of adaptation. Comparative pangenomics revealed accessory gene clusters related to central metabolism, competition, and carbon substrate degradation, with few functional annotations explicitly associated with long-term warming. Trends in functional gene patterns suggest genomes from heated plots were relatively enriched in central carbohydrate and nitrogen metabolism pathways, while genomes from control plots were relatively enriched in amino acid and fatty acid metabolism pathways. We observed that genomes from heated plots had less codon bias, suggesting potential adaptive traits related to growth or growth efficiency. Codon usage bias varied for organisms with similar 16Srrnoperon copy number, suggesting that these organisms experience different selective pressures on growth efficiency. Our work suggests the emergence of lineage-specific trends as well as common ecological-evolutionary microbial responses to climate change.IMPORTANCEAnthropogenic climate change threatens soil ecosystem health in part by altering below-ground carbon cycling carried out by microbes. Microbial evolutionary responses are often overshadowed by community-level ecological responses, but adaptive responses represent potential changes in traits and functional potential that may alter ecosystem function. We predict that microbes are adapting to climate change stressors like soil warming. To test this, we analyzed the genomes of bacteria from a soil warming experiment where soil plots have been experimentally heated 5°C above ambient for over 30 years. While genomic attributes were unchanged by long-term warming, we observed trends in functional gene content related to carbon and nitrogen usage and genomic indicators of growth efficiency. These responses may represent new parameters in how soil ecosystems feedback to the climate system. 

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