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microbial ecology

  • Open Access
    Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats
    Minireview | Applied and Environmental Science
    Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats

    Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen.

    Chequita N. Brooks, Erin K. Field
  • Open Access
    Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)
    Research Article | Applied and Environmental Science
    Generation of Comprehensive Ecosystem-Specific Reference Databases with Species-Level Resolution by High-Throughput Full-Length 16S rRNA Gene Sequencing and Automated Taxonomy Assignment (AutoTax)

    High-throughput 16S rRNA gene amplicon sequencing is an essential method for studying the diversity and dynamics of microbial communities. However, this method is presently hampered by the lack of high-identity reference sequences for many environmental microbes in the public 16S rRNA gene reference databases and by the absence of a systematic and comprehensive taxonomy for the uncultured majority. Here, we demonstrate how high-...

    Morten Simonsen Dueholm, Kasper Skytte Andersen, Simon Jon McIlroy, Jannie Munk Kristensen, Erika Yashiro, Søren Michael Karst, Mads Albertsen, Per Halkjær Nielsen
  • Open Access
    Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth
    Research Article | Applied and Environmental Science
    Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

    Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole...

    John I. Miller, Stephen Techtmann, Dominique Joyner, Nagissa Mahmoudi, Julian Fortney, James A. Fordyce, Nargiz GaraJayeva, Faig S. Askerov, Claudio Cravid, Maarten Kuijper, Oliver Pelz, Terry C. Hazen
  • Open Access
    A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems
    Research Article | Host-Microbe Biology
    A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

    Diagnosing diseases using machine learning (ML) is rapidly being adopted in microbiome studies. However, the estimated performance associated with these models is likely overoptimistic. Moreover, there is a trend toward using black box models without a discussion of the difficulty of interpreting such models when trying to identify microbial biomarkers of disease. This work represents a step toward developing more-reproducible ML...

    Begüm D. Topçuoğlu, Nicholas A. Lesniak, Mack T. Ruffin, Jenna Wiens, Patrick D. Schloss
  • Open Access
    Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA
    Research Article | Applied and Environmental Science
    Prokaryotic and Viral Community Composition of Freshwater Springs in Florida, USA

    Aquifer systems may hold up to 40% of the total microbial biomass on Earth. However, little is known about the composition of microbial communities within these critical freshwater ecosystems. Here, we took advantage of Florida’s first-magnitude springs (the highest spring classification based on water discharge), each discharging at least 246 million liters of water each day from the Floridan aquifer system (FAS), to investigate...

    Kema Malki, Karyna Rosario, Natalie A. Sawaya, Anna J. Székely, Michael J. Tisza, Mya Breitbart
  • Open Access
    Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison
    Research Article | Host-Microbe Biology
    Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison

    Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly...

    Andrzej Tkacz, Eloïne Bestion, Zhiyan Bo, Marion Hortala, Philip S. Poole
  • Open Access
    Microbial Life Deep Underfoot
    Commentary | Ecological and Evolutionary Science
    Microbial Life Deep Underfoot

    Soil is one of the most diverse microbial habitats on Earth. While the distribution and abundance of microbial taxa in surface soils have been well described, the phylogenetic and functional diversity of bacteria and archaea in deep-soil strata remains unexplored.

    Jay T. Lennon
  • Open Access
    Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria
    Research Article | Ecological and Evolutionary Science
    Maintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial Bacteria

    Due to the promiscuous exchange of genetic material and asexual reproduction, delineating microbial species (and, by extension, populations) remains challenging. Because of this, the vast majority of microbial studies assessing population structure often compare divergent strains from disparate environments under varied selective pressures. Here, we investigated the population structure within a single bacterial ecotype, a unit...

    Alexander B. Chase, Philip Arevalo, Eoin L. Brodie, Martin F. Polz, Ulas Karaoz, Jennifer B. H. Martiny
  • Open Access
    Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons

    Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly...

    Tess E. Brewer, Emma L. Aronson, Keshav Arogyaswamy, Sharon A. Billings, Jon K. Botthoff, Ashley N. Campbell, Nicholas C. Dove, Dawson Fairbanks, Rachel E. Gallery, Stephen C. Hart, Jason Kaye, Gary King, Geoffrey Logan, Kathleen A. Lohse, Mia R. Maltz, Emilio Mayorga, Caitlin O’Neill, Sarah M. Owens, Aaron Packman, Jennifer Pett-Ridge, Alain F. Plante, Daniel D. Richter, Whendee L. Silver, Wendy H. Yang, Noah Fierer
  • Open Access
    Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
    Author Reply | Applied and Environmental Science
    Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
    Xiaoquan Su, Gongchao Jing, Daniel McDonald, Honglei Wang, Zengbin Wang, Antonio Gonzalez, Zheng Sun, Shi Huang, Jose Navas, Rob Knight, Jian Xu

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