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  1. Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon

    Rempfert, Kaitlin R. ; Bell, Sheryl L. ; Kasanke, Christopher P. ; ... - Soil Biology and Biochemistry
    There is an emerging consensus that microorganisms are a primary source of persistent, slow-cycling soil organic matter (SOM), however which microbial residues contribute to SOM and what controls their accumulation remains unresolved. Lipids are a commonly overlooked biomolecular pool that could contribute significantly to stable SOM. While current estimates for phospholipid degradation in soils are rapid, lipids are structurally heterogeneous molecules that could turnover at different rates. Through a year-long soil incubation and compound-specific, stable isotope probing (SIP)-lipidomics, we were able to rigorously track the persistence of lipid compounds in silty and sandy switchgrass bioenergy crop soils. Here, we assessedmore » the influence of lipid structure on soil lipid accrual and degradation as moderated by soil texture, since mineral association is presumed to be the primary mechanism for lipid persistence. After rapid incorporation of 13C glucose into microbial biomass, we found 13C label was retained broadly across chemically diverse lipid classes, even after one year. 13C-labeled lipid profiles varied significantly with soil texture; however, we found no difference between sandy and silty soils in lipid retention, suggesting soil texture may only play a minor role in modulating lipid persistence. Only two lipid subclasses were found to be persistent (i.e., retention of 13C label without significant degradation or production): phosphatidylinositol lipids and hydroxyceramide lipids, both of which are negatively charged, possibly facilitating stabilization by mineral complexation. However, several other subclasses displayed substantial ongoing production. In particular, the accumulation of triacylglycerol lipids across soil textures suggests that storage lipids may be an important component of SOC, highlighting a potential target for management strategies to promote C retention by lipid accrual. Overall, the retention for over a year of 13C label in microbial intact lipid biomarkers reveals the importance of efficient biomass production and turnover when considering microbial C contributions to SOM.« less

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

    Barnett, Samuel E. ; Egan, Rob ; Foster, Brian ; ... - mBio (Online)
    Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations.

  3. The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest

    Roy Chowdhury, Priyanka ; Golas, Stefan M. ; Alteio, Lauren V. ; ... - Frontiers in Microbiology
    Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment,more » we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.« less

  4. An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates

    Hunt, Kristopher A. ; Forbes, Jonathan ; Taub, Fred ; ... - Journal of Microbiological Methods
    Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, here we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data inmore » real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen.« less

  5. Climate warming threatens the persistence of a community of disturbance-adapted native annual plants

    Reed, Paul B. ; Bridgham, Scott D. ; Pfeifer‐Meister, Laurel E. ; ... - Ecology
    With ongoing climate change, populations are expected to exhibit shifts in demographic performance that will alter where a species can persist. This presents unique challenges for managing plant populations and may require ongoing interventions, including in situ management or introduction into new locations. However, few studies have examined how climate change may affect plant demographic performance for a suite of species, or how effective management actions could be in mitigating climate change effects. Over the course of two experiments spanning 6 yr and four sites across a latitudinal gradient in the Pacific Northwest, United States, here we manipulated temperature, precipitation, andmore » disturbance intensity, and quantified effects on the demography of eight native annual prairie species. Each year we planted seeds and monitored germination, survival, and reproduction. We found that disturbance strongly influenced demographic performance and that seven of the eight species had increasingly poor performance with warmer conditions. Across species and sites, we observed 11% recruitment (the proportion of seeds planted that survived to reproduction) following high disturbance, but just 3.9% and 2.3% under intermediate and low disturbance, respectively. Moreover, mean seed production following high disturbance was often more than tenfold greater than under intermediate and low disturbance. Importantly, most species exhibited precipitous declines in their population growth rates (λ) under warmer-than-ambient experimental conditions and may require more frequent disturbance intervention to sustain populations. Aristida oligantha, a C4 grass, was the only species to have λ increase with warmer conditions. These results suggest that rising temperatures may cause many native annual plant species to decline, highlighting the urgency for adaptive management practices that facilitate their restoration or introduction to newly suitable locations. Frequent and intense disturbances are critical to reduce competitors and promote native annuals’ persistence, but even such efforts may prove futile under future climate regimes.« less

  6. Representing the function and sensitivity of coastal interfaces in Earth system models

    Ward, Nicholas D. ; Megonigal, J. Patrick ; Bond-Lamberty, Ben ; ... - Nature Communications

  7. Editorial: The Role of Priming in Terrestrial and Aquatic Ecosystems

    Bianchi, Thomas S. ; Ward, Nicholas D. - Frontiers in Earth Science
    Carbon-containing organic matter (OM) is constantly synthesized from atmospheric carbon dioxide (CO2) by primary producing flora in Earth’s biosphere. The fate of this OM—i.e., how long it persists in the environment before being recycled back to atmospheric CO2 by heterotrophic microbes and fauna—is highly variable, and largely dependent on the diversity of environmental conditions it is exposed to both at its origin and during transport to distant locations. This dynamic cycling of carbon, energy, and matter between the atmosphere and biosphere occurs within and across all types of terrestrial, aquatic, and marine ecosystems. While the underlying biological functions and chemicalmore » reactions related to carbon fixation and decomposition are generally common across ecosystems, the disciplines of terrestrial and aquatic biogeochemistry have historically pursued this topic along separate paths with differing strengths and weaknesses. Although this continues today, several focus areas have recently brought more cross-fertilization between these disciplines. One such focus area where terrestrial and aquatic communities have begun converging is the study of interactive effects on OM decomposition that occur when OM of different origins and reactivities mix. This line of research has embraced the necessity to consider reactivity within the context of the past history and present state of OM in all of its highly diverse forms. Interactive effects on OM cycling were first explored about 100 years ago in the context of soil humus mineralization and have since been termed priming effects. Priming can be defined as the enhancement of recalcitrant (stable) OM breakdown via microbial decay with the addition of a more labile (less-stable) OM source. Priming can involve dissolved and/or particulate OM, in some cases accompanied by nutrients, and results in more efficient decay/consumption of stable OM material than would have occurred otherwise in the absence of the less-stable OM. While much of the work on this topic began in terrestrial systems, aquatic researchers have followed suit and gained momentum in the last decade. Observations of priming in aquatic environments are becoming more widespread, but little consensus has been reached on their role, perhaps because we lack the mechanistic understanding to accurately predict when and where priming effects should occur. The motivation for the collection of studies summarized below is to progress towards a common language, set of experimental approaches, and perspective on the role of priming effects in both terrestrial and aquatic ecosystems.« less

  8. Ecological contingency in species shifts: downslope shifts of woody species under warming climate and land-use change

    Zhang, Xianwu ; Zhang, Bo ; Feeley, Kenneth J. ; ... - Environmental Research Letters
    A predicted impact of a warming climate is an upslope shift of montane plant species. These upslope shifts may be amplified by land-use changes or attenuated by forest recoveries at low elevations where historical disturbances were ceased allowing for plant regrowth. Consequently, species may shift downslope back to low elevations where they had been previously harvested. The cessation-driven downslope shifts are hypothesized to dampen or even reverse climate-driven upslope shifts. We tested this hypothesis by a 20 year (1989–2009) forest inventory dataset from five mountainous areas in eastern China. In our study region, intense deforestation occurred mostly at low elevationsmore » until 1970, but was then ceased to facilitate natural forest recovery. Based on the analyses of 30 216 woody plants in 609 plots, we found that: (1) forest recovery occurred over the 20 year survey period, and increment rates of both recruitment and basal area increased up to 2004. However, in the last period (2004–2009), increment rates of basal area leveled off and recruitment was close to zero; (2) forest recovery was faster at lower elevations, as indicated by the higher increment rates there; (3) despite rising regional temperatures, the mean elevations of study species showed a downslope shift over the 20 years; and (4) the contribution of forest recovery to elevational shifts was supported by the fact that the species shifts were positively related to elevational changes in the recruitment increment, e.g. the negative (or downslope) shifts occurred in association with higher increments at lower elevations. These results suggest that, the cessation of disturbances and consequent lowland forest recovery had greater effects on the species distributions than did warming climate. In mountain systems that are being allowed to recover from historical disturbances, the effects of forest recovery on species distributions should be explicitly accounted for when assessing and predicting climate change impacts.« less

  9. Enhanced aquatic respiration associated with mixing of clearwater tributary and turbid Amazon River waters

    Ward, Nicholas D. ; Sawakuchi, Henrique O. ; Richey, Jeffrey E. ; ... - Frontiers in Earth Science
    When water bodies with unique biogeochemical constituents mix together there is potential for diverse responses by aquatic microbial communities and associated ecosystem functions. Here we evaluate bulk respiration rates under varying mixtures of turbid Amazon River water and two lowland tributaries—the Tapajós and Xingu rivers—based on O2 drawdown in dark rotating incubation chambers. Preliminary experiments containing 50% Tapajós River and 50% Amazon River water were performed during falling water. More detailed experiments containing 5%, 17%, 33%, and 50% tributary water were performed for both the Tapajós and Xingu rivers at 3 different rotation velocities (0, 0.22, and 0.66 m s-1)more » during the falling water period. Respiration rates were higher in the mixtures compared to both river endmembers in most experiments. For both the Xingu and Tapajós rivers a 17% mixture yielded maximal respiration rates that were 1.6 to 2.8 times faster than each tributary, respectively. The 50% mixtures, on the other hand, only yielded 1.4 to 1.9 times amplified respiration rates for the Tapajós and Xingu rivers, respectively, and in one case was respiration was 2.8 times lower in the 50% mixture compared to the tributary. We hypothesize that these enhanced respiration rates are driven, in part, by microbial priming effects that have been previously identified on a molecular level for these rivers. The results of this study suggest that there may be a “sweet spot” for priming effects to occur in terms of the relative abundance of “priming” and “primed” substrates.« less

  10. Marine microbial community responses related to wetland carbon mobilization in the coastal zone

    Ward, Nicholas D. ; Morrison, Elise S. ; Liu, Yina ; ... - Limnology and Oceanography Letters
    Abstract Here, we examine how marine microbial communities respond when dissolved organic matter (DOM) is mobilized from coastal wetlands. Biological transformations of this DOM may increase in the presence of reactive substrates, such as algal‐derived DOM (ADOM) in the coastal zone—a process known as priming. We performed laboratory experiments examining transformations of DOM derived from coastal wetland peat (PDOM) with and without the presence ADOM. Associated shifts in microbial community composition and functional gene abundance were measured to evaluate mechanisms of priming effects. ADOM presence stimulated CO 2 production when compared to the seawater control, which was further enhanced inmore » the copresence of PDOM. DOM characterization showed a substantial difference in features present at the end of the incubation when PDOM was present with and without ADOM, while metagenomic sequencing indicated shifts in microbial community composition and identified 23 unique functional genes associated with pathways for the breakdown of aromatic compounds.« less
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