skip to main content

Search for: All records

Creators/Authors contains: "Silver, Whendee L."

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Abstract

    As climate change increases fire frequency in Mediterranean‐type shrublands, it is essential to understand the links between common postfire plant assemblages and soil nitrogen (N) and carbon (C) cycling during succession. In California chaparral, periodic fire removes shrub cover, deposits ammonium (NH4+‐N) on soils, and allows herbaceous assemblages to dominate for 3–5 years. Herbs influence soil biogeochemistry through several mechanisms, including nutrient uptake, litter decomposition, and rhizodeposition. Controlled experimental removal of select plant groups from wild assemblages can demonstrate interactions between plant groups and how plant traits influence belowground processes. In a two‐year herb‐removal experiment, we investigated the impact of N‐fixing and non‐N‐fixing herbs on soil N and C cycling. Treatments were (1) all herbs, (2) only non‐N‐fixing species, (3) only N‐fixing species, and (4) no herbs. In high‐N environments, N‐fixers were predicted to compete poorly against non‐N‐fixing neighbors. N‐fixers doubled in abundance when non‐N‐fixers were removed, but non‐N‐fixers were unaffected by N‐fixer removal. Two years after fire, no‐herbs plots had the lowest soil microbial respiration rates, and total accumulated C and N were lower than all‐herb plots. Two treatments, no‐herb and N‐fixer plots, had elevated mineral N concentrations, net N mineralization, and net nitrification in the second year of the experiment. Our findings underscore the importance of fire‐following herbs for postfire N retention and organic matter accumulation. A combination of both N‐fixing and non‐N‐fixing herbs maximized total soil C and N, although the accumulation of TC and TN in all‐herb plots was not significantly higher than in non‐N‐fixer plots. Results demonstrated the key role of non‐N‐fixing herbs in accumulating soil C and herbaceous communities for retaining N. Elevated soil nutrient availability two years postfire may contribute to the long‐term recovery of shrubs, even after herbs are no longer dominant. Future investigations should also consider the magnitude of soil microbial N retention in plots with different herb functional groups, along with the species‐specific contribution of non‐N‐fixing herbs to postfire C and N cycling.

    more » « less
  2. Soil nitrous oxide (N 2 O) emissions are an important driver of climate change and are a major mechanism of labile nitrogen (N) loss from terrestrial ecosystems. Evidence increasingly suggests that locations on the landscape that experience biogeochemical fluxes disproportionate to the surrounding matrix (hot spots) and time periods that show disproportionately high fluxes relative to the background (hot moments) strongly influence landscape-scale soil N 2 O emissions. However, substantial uncertainties remain regarding how to measure and model where and when these extreme soil N 2 O fluxes occur. High-frequency datasets of soil N 2 O fluxes are newly possible due to advancements in field-ready instrumentation that uses cavity ring-down spectroscopy (CRDS). Here, we outline the opportunities and challenges that are provided by the deployment of this field-based instrumentation and the collection of high-frequency soil N 2 O flux datasets. While there are substantial challenges associated with automated CRDS systems, there are also opportunities to utilize these near-continuous data to constrain our understanding of dynamics of the terrestrial N cycle across space and time. Finally, we propose future research directions exploring the influence of hot moments of N 2 O emissions on the N cycle, particularly considering the gaps surrounding how global change forces are likely to alter N dynamics in the future. 
    more » « less
  3. null (Ed.)
  4. null (Ed.)
    Abstract. The strong phosphorus (P) sorption capacity of iron (Fe)and aluminum (Al) minerals in highly weathered, acidic soils of humidtropical forests is generally assumed to be an important driver of Plimitation to plants and microbial activity in these ecosystems. Humidtropical forest soils often experience fluctuating redox conditions thatreduce Fe and raise pH. It is commonly thought that Fe reduction generallydecreases the capacity and strength of P sorption. Here we examined theeffects of 14 d oxic and anoxic incubations on soil P sorption dynamics inhumid tropical forest soils from Puerto Rico. Contrary to the conventionalbelief, soil P sorption capacity did not decrease under anoxic conditions,suggesting that soil minerals remain strong P sinks even under reducingconditions. Sorption of P occurred very rapidly in these soils, with atleast 60 % of the added P disappearing from the solution within 6 h.Estimated P sorption capacities were much higher, often by an order ofmagnitude, than the soil total P contents. However, the strength of Psorption under reducing conditions was weaker, as indicated by the increasedsolubility of sorbed P in NaHCO3 solution. Our results show that highlyweathered soil minerals can retain P even under anoxic conditions, where itmight otherwise be susceptible to leaching. Anoxic events can alsopotentially increase P bioavailability by decreasing the strength, ratherthan the capacity, of P sorption. These results improve our understanding ofthe redox effects on biogeochemical cycling in tropical forests. 
    more » « less
  5. Abstract. Tropical ecosystems contribute significantly to global emissionsof methane (CH4), and landscape topography influences the rate ofCH4 emissions from wet tropical forest soils. However, extreme eventssuch as drought can alter normal topographic patterns of emissions. Here weexplain the dynamics of CH4 emissions during normal and droughtconditions across a catena in the Luquillo Experimental Forest, Puerto Rico.Valley soils served as the major source of CH4 emissions in a normalprecipitation year (2016), but drought recovery in 2015 resulted in dramaticpulses in CH4 emissions from all topographic positions. Geochemicalparameters including (i) dissolved organic carbon (C), acetate, and soil pH and (ii) hydrological parameters like soil moisture and oxygen (O2)concentrations varied across the catena. During the drought, soil moisturedecreased in the slope and ridge, and O2 concentrations increased in thevalley. We simulated the dynamics of CH4 emissions with theMicrobial Model for Methane Dynamics-Dual Arrhenius and Michaelis–Menten (M3D-DAMM), which couples a microbialfunctional group CH4 model with a diffusivity module for solute and gastransport within soil microsites. Contrasting patterns of soil moisture,O2, acetate, and associated changes in soil pH with topographyregulated simulated CH4 emissions, but emissions were also altered byrate-limited diffusion in soil microsites. Changes in simulated availablesubstrate for CH4 production (acetate, CO2, and H2) andoxidation (O2 and CH4) increased the predicted biomass ofmethanotrophs during the drought event and methanogens during droughtrecovery, which in turn affected net emissions of CH4. A variance-basedsensitivity analysis suggested that parameters related to aceticlasticmethanogenesis and methanotrophy were most critical to simulate net CH4emissions. This study enhanced the predictive capability for CH4emissions associated with complex topography and drought in wet tropicalforest soils. 
    more » « less
  6. null (Ed.)
    Abstract. Data collected from research networks presentopportunities to test theories and develop models about factors responsiblefor the long-term persistence and vulnerability of soil organic matter(SOM). Synthesizing datasets collected by different research networkspresents opportunities to expand the ecological gradients and scientificbreadth of information available for inquiry. Synthesizing these data ischallenging, especially considering the legacy of soil data that havealready been collected and an expansion of new network science initiatives.To facilitate this effort, here we present the SOils DAta Harmonizationdatabase (SoDaH;, last access: 22 December 2020), a flexible database designed to harmonize diverse SOM datasets frommultiple research networks. SoDaH is built on several network scienceefforts in the United States, but the tools built for SoDaH aim to providean open-access resource to facilitate synthesis of soil carbon data.Moreover, SoDaH allows for individual locations to contribute results fromexperimental manipulations, repeated measurements from long-term studies,and local- to regional-scale gradients across ecosystems or landscapes.Finally, we also provide data visualization and analysis tools that can beused to query and analyze the aggregated database. The SoDaH v1.0 dataset isarchived and availableat (Wieder et al., 2020). 
    more » « less
  7. ABSTRACT While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi , Nitrospirae , Euryarchaeota , and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments. IMPORTANCE 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 studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions. 
    more » « less