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1. Long-Term Nutrient Enrichment of an Oligotroph-Dominated Wetland Increases Bacterial Diversity in Bulk Soils and Plant Rhizospheres

   https://doi.org/10.1128/mSphere.00035-20  

   Bledsoe, Regina B.; Goodwillie, Carol; Peralta, Ariane L. (June 2020, mSphere)

   Campbell, Barbara J. (Ed.)

   ABSTRACT In nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return, plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast-growing copiotrophs, slow-growing oligotrophs) and plant (C 3 forb, C 4 grass) communities residing in a nutrient-poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized versus unfertilized) and plant association (bulk versus rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass versus forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease-suppressive bacterial taxa, and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling. IMPORTANCE Over the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorus deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline, and the abundance of copiotrophic taxa is anticipated to increase in bacterial communities. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter diversity and metabolism of rhizosphere bacterial communities in unexpected ways. 

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2. 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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3. Conserved pathway for homarine catabolism in environmental bacteria

   https://doi.org/10.21203/rs.3.rs-7359689/v1  

   Ferrer-Gonzalez, Frank; Heal, Katherine; Sacks, Joshua; Romero-Maysonet, Yarinet; Finch, Anna; Carlson, Laura; Coe, Lisa; Bartolek, Zinka; Luthy, Claudia; Gaffney, Moira; et al (August 2025, Research Square)

   Abstract Homarine (N-methylpicolinic acid) is a ubiquitous marine metabolite produced by phytoplankton and noted for its bioactivity in marine animals, yet its microbial degradation pathways are uncharacterized. Here, we identify a conserved operon (homABCDER) that mediates homarine catabolism in bacteria using comparative transcriptomics, mutagenesis, and targeted knockouts. Phylogenetic and genomic analyses show this operon distributed across abundant bacterial clades, including coastal copiotrophs (e.g., Rhodobacterales) and open-ocean oligotrophs (e.g., SAR11, SAR116). High-resolution mass spectrometry revealed N-methylglutamic acid and glutamic acid as key metabolic products of homarine in both model and natural systems, with N-methylglutamate dehydrogenase catalyzing their conversion. Metatranscriptomics showed responsive and in situ expression of hom genes aligned with homarine availability. These findings uncover the genetic and metabolic basis of homarine degradation, establish its ecological relevance, and highlight homarine as a versatile growth substrate that feeds into central metabolism via glutamic acid in diverse marine bacteria. 

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4. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization

   https://doi.org/10.1111/gcb.16073  

   See, Craig R.; Keller, Adrienne B.; Hobbie, Sarah E.; Kennedy, Peter G.; Weber, Peter K.; Pett‐Ridge, Jennifer (January 2022, Global Change Biology)

   Abstract Associations between soil minerals and microbially derived organic matter (often referred to as mineral‐associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non‐rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere–bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non‐random colonization of mineral surfaces by hyphae‐associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals. 

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5. An Examination of Fungal and Bacterial Assemblages in Bulk and Rhizosphere Soils under Solanum tuberosum in Southeastern Wyoming, USA

   https://doi.org/10.3390/applmicrobiol1020013  

   Custer, Gordon; van Diepen, Linda; Stump, William (September 2021, Applied Microbiology)

   Solanum tuberosum, commonly known as potato, is the most important non-cereal crop in the world. However, its cultivation is prone to disease and other issues. In recent years, a newfound interest in the soil microbiome and the potential benefits it may convey has led researchers to study plant–microbe interactions in great detail and has led to the identification of putative beneficial microbial taxa. In this survey, we examined fungal and bacterial diversity using high-throughput sequencing in soils under a potato crop in southeastern Wyoming, USA. Our results show decreased microbial diversity in the rhizosphere, with increases in the abundances of arbuscular mycorrhizal fungi as well as pathogenic microbes. We show coarse taxonomic differences in microbial assemblages when comparing the bulk and rhizosphere soils for bacteria but not for fungi, suggesting that the two kingdoms respond differently to the selective pressures of the rhizosphere. Using cooccurrence network analysis, we identify microbes that may serve as keystone taxa and provide benefits to their host plants through competitive exclusion of detrimental pathogenic taxa and increased nutrient availability. Our results provide additional information on the structure and complexity of the potato rhizosphere microbiome and highlight candidate taxa for microbial isolation and inoculation. 

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