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Whitman, T.

Publications and source records attributed to Whitman, T..

22 records · Page 2Linked to original sources

Microbial community shifts reflect losses of native soil carbon with pyrogenic and fresh organic matter additions and are greatest in low-carbon soils

Soil organic carbon (SOC) plays an important role in regulating global climate change, carbon and nutrient cycling in soils, and soil moisture. Organic matter (OM) additions to soils can affect the rate at which SOC is mineralized by microbes, with potentially important effects on SOC stocks. Understanding how pyrogenic organic matter (PyOM) affects the cycling of native SOC (nSOC) and the soil microbes responsible for these effects is important for fire-affected ecosystems as well as for biochar-amended systems. We used an incubation trial with five different soils from National Ecological Observatory Network sites across the US and 13C-labelled 350{degrees}C corn stover PyOM and fresh corn stover OM to trace nSOC-derived CO2 emissions with and without PyOM and OM amendments. We used high-throughput sequencing of rRNA genes to characterize bacterial, archaeal, and fungal communities and their response to PyOM and OM. We found that the effects of amendments on nSOC-derived CO2 reflected the unamended soil C status, where amendments increased C mineralization the most in low-C soils. OM additions produced much greater effects on nSOC-CO2 emissions than PyOM additions. Furthermore, the magnitude of microbial community composition change mirrored the magnitude of increases in nSOC-CO2, indicating a specific subset of microbes were likely responsible for the observed changes in nSOC mineralization. However, PyOM responders differed across soils and did not necessarily reflect a common "charosphere". Overall, this study suggests that soils that already have low SOC may be particularly vulnerable to short-term increases in SOC loss with OM or PyOM additions. ImportanceSoil organic matter (SOM) has an important role in global climate change, carbon and nutrient cycling in soils, and soil moisture dynamics. Understanding the processes that affect SOM stocks is important for managing these functions. Recently, understanding how fire-affected, or "pyrogenic" organic matter (PyOM) affects existing SOM stocks has become increasingly important, both due to changing fire regimes, and to interest in "biochar" - pyrogenic organic matter that is produced intentionally for carbon management or as an agricultural soil amendment. We found that soils with less SOM were more prone to increased losses with PyOM (and fresh organic matter) additions, and that soil microbial communities changed more in soils that also had greater SOM losses with PyOM additions. This suggests that soils that already have low SOM content may be particularly vulnerable to short-term increases in SOM loss, and that a subset of the soil microbial community is likely responsible for these effects.

microbiology↗

Soil Bacterial and Fungal Response to Wildfires in the Canadian Boreal Forest Across a Burn Severity Gradient

Global fire regimes are changing, with increases in wildfire frequency and severity expected for many North American forests over the next 100 years. Fires can result in dramatic changes to C stocks and can restructure plant and microbial communities, with long-lasting effects on ecosystem functions. We investigated wildfire effects on soil microbial communities (bacteria and fungi) in an extreme fire season in the northwestern Canadian boreal forest, using field surveys, remote sensing, and high-throughput amplicon sequencing. We found that fire occurrence, along with vegetation community, moisture regime, pH, total carbon, and soil texture are all significant predictors of soil microbial community composition. Communities become increasingly dissimilar with increasingly severe burns, and the burn severity index (an index of the fractional area of consumed organic soils and exposed mineral soils) best predicted total bacterial community composition, while burned/unburned was the best predictor for fungi. Globally abundant taxa were identified as significant positive fire responders, including the bacteria Massilia sp. (64x more abundant with fire) and Arthrobacter sp. (35x), and the fungi Penicillium sp. (22x) and Fusicladium sp. (12x). Bacterial and fungal co-occurrence network modules were characterized by fire responsiveness as well as pH and moisture regime. Building on the efforts of previous studies, our results identify specific fire-responsive microbial taxa and suggest that accounting for burn severity improves our understanding of their response to fires, with potentially important implications for ecosystem function.

microbiology↗

Microbial community assembly differs by mineral type in the rhizosphere

Inputs of root carbon (C) fuel growth of nearby soil microorganisms. If these microbes associate with soil minerals, then mineral-microbiome complexes near roots could be a gateway towards stabilization of soil carbon and may influence the quantity and quality of persistent SOM. To investigate the interactions between roots, soil minerals, and microbes, we incubated three types of minerals (ferrihydrite, kaolinite, quartz) and a native soil mineral fraction near roots of a common Californian annual grass, Avena barbata, growing in its resident soil. We followed microbial colonization of these minerals for 2.5 months - the plants lifespan. Bacteria and fungi that colonized mineral surfaces during this experiment differed across mineral types and differed from those in the background soil, implying microbial colonization was the result of processes in addition to passive movement with water to mineral surfaces. Null model analysis revealed that dispersal limitation was a dominant factor structuring mineral-associated microbial communities for all mineral types. Once bacteria arrived at a mineral surface, capacity for rapid growth appeared important, as ribosomal copy number was significantly correlated with relative enrichment on minerals. Glomeromycota (a phylum associated with arbuscular mycorrhizal fungi) appeared to preferentially associate with ferrihydrite surfaces. The mechanisms enabling colonization of soil minerals may be foundational to the overall soil microbiome composition and partially responsible for the persistence of C entering soil via plant roots.

microbiology↗

Spatiotemporal Dynamics of the Bacterial Microbiota and Methanotrophic Bacteria on Lotic Cladophora glomerata (Chlorophyta)

The branched periphytic green alga Cladophora glomerata, often abundant in nearshore waters of lakes and rivers worldwide, plays important ecosystem roles, some mediated by epibiotic microbiota that benefit from host-provided surface, organic C, and O2. Previous microscopy and high throughput sequencing studies have indicated surprising epibiont taxonomic and functional diversity, but have not included adequate consideration of sample replication or the potential for spatial and temporal variation. Here we report the results of 16S rRNA amplicon-based phylum-to-genus taxonomic analysis of Cladophora-associated bacterial epibiota sampled in replicate from three microsites and at six times during the open-water season of 2014, from the same lake locale (Picnic Point, Lake Mendota, Dane Co., WI, USA) explored by high throughput sequencing studies in two previous years. Statistical methods were used to test null hypotheses that the bacterial community: 1) is homogeneous across microsites tested, and 2) does not change over the course of a growth season or among successive years. Results indicated a dynamic microbial community that is more strongly influenced by sampling day during the growth season than by microsite variation. A surprising diversity of bacterial genera known to be associated with the key function of methane-oxidation (methanotrophy)-including relatively high-abundance of Crenothrix, Methylomonas, and Methylocaldum-showed intra-seasonal and inter-annual variability possibly related to temperature differences, and microsite preferences possibly related to variation in methane abundance. By contrast, a core assemblage of bacterial genera seems to persist over a growth season and from year-to-year, possibly transmitted by a persistent attached host resting stage.

microbiology↗