Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire.

We examined the dynamics of soil microbiomes under heat press disturbance from an underground coal mine fire in Centralia, PA. Here, we present metagenomic sequencing and assembly data from soil microbiomes across seven consecutive years at repeatedly sampled fire-affected sites along with unaffected reference sites.

Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance.

Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions.

Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling.

Soil viruses are important components of the carbon (C) cycle, yet we still know little about viral ecology in soils. We added diverse C-labelled carbon sources to soil and we used metagenomic-SIP to detect C assimilation by viruses and their putative bacterial hosts. These data allowed us to link a C-labelled bacteriophage to its C-labelled Streptomyces putative host, and we used qPCR to track the dynamics of the putative host and phage in response to C inputs.

Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing.

Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized.

Tracing Carbon Metabolism with Stable Isotope Metabolomics Reveals the Legacy of Diverse Carbon Sources in Soil.

Tracking the metabolic activity of whole soil communities can improve our understanding of the transformation and fate of carbon in soils. We used stable isotope metabolomics to trace C from nine labeled carbon sources into the water-soluble metabolite pool of an agricultural soil over time. Soil was amended with a mixture of all nine sources, with one source isotopically labeled in each treatment.

Bacterial community dynamics explain carbon mineralization and assimilation in soils of different land-use history.

Soil dwelling microorganisms are key players in the terrestrial carbon cycle, driving both the degradation and stabilization of soil organic matter. Bacterial community structure and function vary with respect to land use; yet the ecological drivers of this variation remain poorly described and difficult to predict. We conducted a multi-substrate DNA-stable isotope probing experiment across cropland, old-field, and forest habitats to link carbon mineralization dynamics with the dynamics of bacterial growth and carbon assimilation.

Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling.

Soil microorganisms determine the fate of soil organic matter (SOM), and their activities compose a major component of the global carbon (C) cycle. We employed a multisubstrate, DNA-stable isotope probing experiment to track bacterial assimilation of C derived from distinct sources that varied in bioavailability. This approach allowed us to measure microbial contributions to SOM processing by measuring the C assimilation dynamics of diverse microorganisms as they interacted within soil.

Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils.

Soil pH has shown to predict bacterial diversity, but mechanisms are still poorly understood. To investigate how bacteria distribute themselves as a function of soil pH, we assessed community composition, diversity, assembly, and gene abundance across local (ca. 1 km) scale gradients in soil pH from ~ 3.

Simulating metagenomic stable isotope probing datasets with MetaSIPSim.

Background: DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies.

Evidence for phylogenetically and catabolically diverse active diazotrophs in deep-sea sediment.

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. However, we know little about the identity and activity of diazotrophs in deep-sea sediments, a habitat covering nearly two-thirds of the planet. Here, we identify candidate diazotrophs from Pacific Ocean sediments collected at 2893 m water depth using N-DNA stable isotope probing and a novel pipeline for nifH sequence analysis.

Soil characteristics and land-use drive bacterial community assembly patterns.

Land-use and soil characteristics drive variation in soil community composition, but the influences of these factors on dispersal and community assembly at regional scale remain poorly characterized. Land-use remains a consistent driver of soil community composition even when exhibiting patchy spatial distribution at regional scale. In addition, disturbed and early successional soils often exhibit stochastic community assembly patterns.

Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP.

DNA stable isotope probing (DNA-SIP) allows for the identification of microbes that assimilate isotopically labeled substrates into DNA. Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP). MW-HR-SIP has improved accuracy over other methods and is easily implemented on the statistical platform R.

Diverse genotypes of the amphibian-killing fungus produce distinct phenotypes through plastic responses to temperature.

Phenotypes are the target of selection and affect the ability of organisms to persist in variable environments. Phenotypes can be influenced directly by genes and/or by phenotypic plasticity. The amphibian-killing fungus Batrachochytrium dendrobatidis (Bd) has a global distribution, unusually broad host range, and high genetic diversity.

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs.

HTSSIP: An R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments.

Combining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (qSIP), and ΔBD.

Inhibition of Fungal Pathogens across Genotypes and Temperatures by Amphibian Skin Bacteria.

Symbiotic bacteria may dampen the impacts of infectious diseases on hosts by inhibiting pathogen growth. However, our understanding of the generality of pathogen inhibition by different bacterial taxa across pathogen genotypes and environmental conditions is limited. Bacterial inhibitory properties are of particular interest for the amphibian-killing fungal pathogens ( and ), for which probiotic applications as conservation strategies have been proposed.