microbial ecology
Research Article | Applied and Environmental ScienceGeneration 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-...
Research Article | Applied and Environmental ScienceMicrobial Communities across Global Marine Basins Show Important Compositional Similarities by DepthMarine 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...
Research Article | Host-Microbe BiologyA Framework for Effective Application of Machine Learning to Microbiome-Based Classification ProblemsDiagnosing 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...
Research Article | Applied and Environmental ScienceProkaryotic and Viral Community Composition of Freshwater Springs in Florida, USAAquifer 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...
Research Article | Host-Microbe BiologyInfluence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom ComparisonGlobal 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...
Commentary | Ecological and Evolutionary ScienceMicrobial Life Deep UnderfootSoil 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.
Research Article | Ecological and Evolutionary ScienceMaintenance of Sympatric and Allopatric Populations in Free-Living Terrestrial BacteriaDue 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...
Editor's Pick Research Article | Ecological and Evolutionary ScienceEcological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil HorizonsSoil 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...
Author Reply | Applied and Environmental ScienceReply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”
Research Article | Ecological and Evolutionary ScienceMicrobial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial SignaturesHumans leave behind a microbial trail, regardless of intention. This may allow for the identification of individuals based on the “microbial signatures” they shed in built environments. In a shared living environment, these trails intersect, and through interaction with common surfaces may become homogenized, potentially confounding our ability to link individuals to their associated microbiota. We sought to understand the factors that...