utilizing-soil-density-fractionation-to-separate-distinct-soil-carbon

Utilizing Soil Density Fractionation to Separate Distinct Soil Carbon Pools

Soil organic matter (SOM) is a complicated mixture of different compounds that span the range from free, partially degraded plant components to more ...

Oregon State University

One explanation given for the high microbial diversity found in soils is that they contain a large inactive biomass that is able to persist in soils for long periods of time. This persistent microbial fraction may help to buffer the functionality of the soil community during times of low nutrients by providing a reservoir of specialized functions that can be reactivated when conditions improve. A study was designed to test the hypothesis: in soils lacking fresh root or detrital inputs, microbial community composition may persist relatively unchanged. Upon addition of new inputs, this community will be stimulated to grow and break down litter similarly to control soils. Soils from two of the Detrital Input and Removal Treatments (DIRT) at the H. J. Andrews Experimental Forest, the no-input and control treatment plots, were used in a microcosm experiment where Douglas-fir needles were added to soils. After 3 and 151 days of incubation, soil microbial DNA and RNA was extracted and characterized using quantitative PCR (qPCR) and 454 pyrosequencing. The abundance of 16S and 28S gene copies and RNA copies did not vary with soil type or amendment; however, treatment differences were observed in the abundance of archaeal ammonia-oxidizing amoA gene abundance. Analysis of ∼110,000 bacterial sequences showed a significant change in the active (RNA-based) community between day 3 and day 151, but microbial composition was similar between soil types. These results show that even after 12 years of plant litter exclusion, the legacy of community composition was well buffered against a dramatic disturbance.

Soil microbe active community composition and capability of responding to litter addition after 12 years of no inputs.

The goal of this research was to develop modified analytical method for the quantitative analysis of ergosterol, which is highly effective marker for fungal biomass. We suggest that our optimized method for the determination of ergosterol is an effective way to monitor changes in fungal biomass under different environmental conditions.

An optimized HPLC method for soil fungal biomass determination and its application to a detritus manipulation study.

Forest vegetation and soils have been suggested as potentially important sinks for carbon (C) with appropriate management and thus are implicated as effective tools in stabilizing climate even with increasing anthropogenic release of CO . Drought, however, which is often predicted to increase in models of future climate change, may limit net primary productio (NPP) of dry forest types, with unknown effects on soil C storage. We studied C dynamics of a deciduous temperate forest of Hungary that has been subject to significant decreases in precipitation and increases in temperature in recent decades. We resampled plots that were established in 1972 and repeated the full C inventory by analyzing more than 4 decades of data on the number of living trees, biomass of trees and shrubs, and soil C content. Our analyses show that the decline in number and biomass of oaks started around the end of the 1970s with a 71% reduction in the number of sessile oak stems by 2014. Projected growth in this forest, based on the yield table's data for Hungary, was 4.6 kg C/m . Although new species emerged, this new growth and small increases in oak biomass resulted in only 1.9 kg C/m increase over 41 years. The death of oaks increased inputs of coarse woody debris to the surface of the soil, much of which is still identifiable, and caused an increase of 15.5%, or 2.6 kg C/m , in the top 1 m of soil. Stability of this fresh organic matter input to surface soil is unknown, but is likely to be low based on the results of a colocated woody litter decomposition study. The effects of a warmer and drier climate on the C balance of forests in this region will be felt for decades to come as woody litter inputs decay, and forest growth remains impeded.

Long-term effects of climate change on carbon storage and tree species composition in a dry deciduous forest.

Ergosterol is a sterol found ubiquitously in cell membranes of filamentous fungi. Although concentrations in different fungal species span the range of 2.6 to 42μg/mL of dry mass, many studies have shown a strong correlation between soil ergosterol content and fungal biomass. The analysis of ergosterol in soil therefore could be an effective tool for monitoring changes in fungal biomass under different environmental conditions. Stir Bar Sorptive Extraction (SBSE) is a new sample preparation method to extract and concentrate organic analytes from liquid samples. SBSE was here demonstrated to be a simple, fast, and cost effective method for the quantitative analysis of ergosterol from field-collected soils. Using this method we observed that soil ergosterol as a measure of fungal biomass proved to be a sensitive indicator of soil microbial dynamics that were altered by changes in plant detrital inputs to soils in a long-term field experiment.

Application of a Stir Bar Sorptive Extraction sample preparation method with HPLC for soil fungal biomass determination in soils from a detrital manipulation study.

Understanding soil organic matter (OM) biogeochemistry at the molecular-level is essential for assessing potential impacts from management practices and climate change on shifts in soil carbon storage. Biomarker analyses and nuclear magnetic resonance (NMR) spectroscopy were used in an ongoing detrital input and removal treatment experiment in a temperate deciduous forest in Pennsylvania, USA, to examine how above- and below-ground plant inputs control soil OM quantity and quality at the molecular-level. From plant material to surface soils, the free acyclic lipids and cutin, suberin, and lignin biomarkers were preferentially retained over free sugars and free cyclic lipids. After 20years of above-ground litter addition (Double Litter) or exclusion (No Litter) treatments, soil OM composition was relatively more degraded, as revealed by solid-state C NMR spectroscopy. Under Doubled Litter inputs, soil carbon and phospholipid fatty acid (PLFA) concentrations were unchanged, suggesting that the current OM degradation status is a reflection of microbial-mediated degradation that occurred prior to the 20-year sampling campaign. Soil OM degradation was higher in the No Litter treatments, likely due to the decline in fresh, above-ground litter inputs over time. Furthermore, root and root and litter exclusion treatments (No Roots and No Inputs, respectively) both significantly reduced free sugars and PLFAs and increased preservation of suberin-derived compounds. PLFA stress ratios and the low N-acetyl resonances from diffusion edited H NMR also indicate substrate limitations and reduced microbial biomass with these treatments. Overall, we highlight that storage of soil carbon and its biochemical composition do not linearly increase with plant inputs because the microbial processing of soil OM is also likely altered in the studied forest.

Long-term litter manipulation alters soil organic matter turnover in a temperate deciduous forest.

The complexity of processes and interactions that drive soil C dynamics necessitate the use of proxy variables to represent soil characteristics that cannot be directly measured (correlative proxies), or that aggregate information about multiple soil characteristics into one variable (integrative proxies). These proxies have proven useful for understanding the soil C cycle, which is highly variable in both space and time, and are now being used to make predictions of the fate and persistence of C under future climate scenarios. However, the C pools and processes that proxies represent must be thoughtfully considered in order to minimize uncertainties in empirical understanding. This is necessary to capture the full value of a proxy in model parameters and in model outcomes. Here, we provide specific examples of proxy variables that could improve decision-making, and modeling skill, while also encouraging continued work on their mechanistic underpinnings. We explore the use of three common soil proxies used to study soil C cycling: metabolic quotient, clay content, and physical fractionation. We also consider how emerging data types, such as genome-sequence data, can serve as proxies for microbial community activities. By examining some broad assumptions in soil C cycling with the proxies already in use, we can develop new hypotheses and specify criteria for new and needed proxies.

Soil carbon cycling proxies: Understanding their critical role in predicting climate change feedbacks.

Ecological research networks functioning across climatic and edaphic gradients are critical for improving predictive understanding of biogeochemical cycles at local through global scales. One international network, the Detrital Input and Removal Treatment (DIRT) Project, was established to assess how rates and sources of plant litter inputs influence accumulations or losses of organic matter in forest soils. DIRT employs chronic additions and exclusions of aboveground litter inputs and exclusion of root ingrowth to permanent plots at eight forested and two shrub/grass sites to investigate how soil organic matter (SOM) dynamics are influenced by plant detrital inputs across ecosystem and soil types. Across the DIRT network described here, SOM pools responded only slightly, or not at all, to chronic doubling of aboveground litter inputs. Explanations for the slow or even negative response of SOM to litter additions include increased decomposition of new inputs and priming of old SOM. Evidence of priming includes increased soil respiration in litter addition plots, decreased dissolved organic carbon (DOC) output from increased microbial activity, and biochemical markers in soil indicating enhanced SOM degradation. SOM pools decreased in response to chronic exclusion of aboveground litter, which had a greater effect on soil C than did excluding roots, providing evidence that root-derived C is not more critical than aboveground litter C to soil C sequestration. Partitioning of belowground contributions to total soil respiration were predictable based on site-level soil C and N as estimates of site fertility; contributions to soil respiration from root respiration were negatively related to soil fertility and inversely, contributions from decomposing aboveground litter in soil were positively related to site fertility. The commonality of approaches and manipulations across the DIRT network has provided greater insights into soil C cycling than could have been revealed at a single site.

The detrital input and removal treatment (DIRT) network: Insights into soil carbon stabilization.

In 1975, Vitousek and Reiners proposed a conceptual model relating the net retention of a limiting nutrient to the net biomass accumulation in terrestrial ecosystems, whereby terrestrial systems should be highly conservative of nutrients during ecosystem succession when plants are actively accumulating biomass, but should be relatively leakier in older stands, when net plant biomass accumulation nears zero. The model was based on measurements in the White Mountains of New Hampshire. However, recent data showing that nitrate output in streams is declining across this region even as forests are aging seem to be inconsistent with this theory. Because the more recent data do not match the predictions of the Vitousek and Reiners model, either new hypotheses, or modifications of the original hypothesis, need to be considered. I suggest that the original model can be amended by accounting for increased woody debris; an accumulation of both above and belowground high C:N coarse woody debris from tree mortality in these regenerating forests can lead to high microbial immobilization of N and can explain the recent patterns of declining stream nitrate. Few studies or models have attempted to calculate the impacts of coarse woody debris (CWD) decomposition products to the retention of C and N in forested ecosystems and their receiving streams, but evidence suggests that CWD can significantly affect stream N exports and should be considered in future models of ecosystem biogeochemical cycles.

Nutrient retention and loss during ecosystem succession: revisiting a classic model.

Terrestrial dissolved organic matter (DOM) in forested watersheds is a known precursor of disinfection byproducts (DBPs) in drinking water. Although the characteristics of terrestrial DOM may change with increasing nitrogen (N) deposition in forests, how these changes alter formation potential and toxicity of DBPs remains unexplored. We analyzed the speciation and toxicity of DBPs from chlorination of DOM derived from soils (O, A, and B horizons) in an experimental temperate forest with 22 years of N addition. With long-term N addition, the DOM reactivity toward the formation of trihalomethanes (from 27.7-51.8 to 22.8-31.1 µg/mg-dissolved organic carbon (DOC)) and chloral hydrate (from 1.25-1.63 to 1.14-1.36 µg/mg-DOC) decreased, but that toward the formation of haloketones increased (from 0.23-0.26 to 0.26-0.33 µg/mg-DOC). The DOM reactivity toward the formation of haloacetonitriles was increased in the deeper soil but reduced in the surface soil. The DBP formation potential of DOM draining from a certain area of forest soils (in µg-DBP/m-soil) was estimated to be reduced by 20.3% for trihalomethanes and increased by 37.5% for haloketones and have minor changes for haloacetonitriles and chloral hydrate (both <7%). Furthermore, the DBPs from chlorination of the soil-derived DOM showed lowered microtoxicity with N addition possibly due to reduced brominated DBP formation. Overall, this study highlights that N deposition may not increase drinking water toxicity through altering terrestrial DOM characteristics.

Chlorination of soil-derived dissolved organic matter: Long term nitrogen deposition does not increase terrestrial precursors of toxic disinfection byproducts.

Fungi and bacteria are the two principal microbial groups in soil, responsible for the breakdown of organic matter (OM). The relative contribution of fungi and bacteria to decomposition is thought to impact biogeochemical cycling at the ecosystem scale, whereby bacterially dominated decomposition supports the fast turnover of easily available substrates, whereas fungal-dominated decomposition leads to the slower turnover of more complex OM. However, empirical support for this is lacking. We used soils from a detritus input and removal treatment experiment in an old-growth coniferous forest, where above- and belowground litter inputs have been manipulated for 20 yr. These manipulations have generated variation in OM quality, as defined by energetic content and proxied as respiration per g soil organic matter (SOM) and the δ C signature in respired CO and microbial PLFAs. Respiration per g SOM reflects the availability and lability of C substrate to microorganisms, and the δ C signature indicates whether the C used by microorganisms is plant derived and higher quality (more δ C depleted) or more microbially processed and lower quality (more δ C enriched). Surprisingly, higher quality C did not disproportionately benefit bacterial decomposers. Both fungal and bacterial growth increased with C quality, with no systematic change in the fungal-to-bacterial growth ratio, reflecting the relative contribution of fungi and bacteria to decomposition. There was also no difference in the quality of C targeted by bacterial and fungal decomposers either for catabolism or anabolism. Interestingly, respired CO was more δ C enriched than soil C, suggesting preferential use of more microbially processed C, despite its lower quality. Gross N mineralization and consumption were also unaffected by differences in the ratio of fungal-to-bacterial growth. However, the ratio of C to gross N mineralization was lower than the average C/N of SOM, meaning that microorganisms specifically targeted N-rich components of OM, indicative of selective microbial N-mining. Consistent with the δ C data, this reinforces evidence for the use of more microbially processed OM with a lower C/N ratio, rather than plant-derived OM. These results challenge the widely held assumption that microorganisms favor high-quality C sources and suggest that there is a trade-off in OM use that may be related to the growth-limiting factor for microorganisms in the ecosystem.

Nutrient limitation may induce microbial mining for resources from persistent soil organic matter.

Grazing cattle, well-managed or not, is unlikely to increase soil carbon sequestration.

Forest ecosystems are important global soil carbon (C) reservoirs, but their capacity to sequester C is susceptible to climate change factors that alter the quantity and quality of C inputs. To better understand forest soil C responses to altered C inputs, we integrated three molecular composition published data sets of soil organic matter (SOM) and soil microbial communities for mineral soils after 20 years of detrital input and removal treatments in two deciduous forests: Bousson Forest (BF), Harvard Forest (HF), and a coniferous forest: H.J. Andrews Forest (HJA). Soil C turnover times were estimated from radiocarbon measurements and compared with the molecular-level data (based on nuclear magnetic resonance and specific analysis of plant- and microbial-derived compounds) to better understand how ecosystem properties control soil C biogeochemistry and dynamics. Doubled aboveground litter additions did not increase soil C for any of the forests studied likely due to long-term soil priming. The degree of SOM decomposition was higher for bacteria-dominated sites with higher nitrogen (N) availability while lower for the N-poor coniferous forest. Litter exclusions significantly decreased soil C, increased SOM decomposition state, and led to the adaptation of the microbial communities to changes in available substrates. Finally, although aboveground litter determined soil C dynamics and its molecular composition in the coniferous forest (HJA), belowground litter appeared to be more influential in broadleaf deciduous forests (BH and HF). This synthesis demonstrates that inherent ecosystem properties regulate how soil C dynamics change with litter manipulations at the molecular-level. Across the forests studied, 20 years of litter additions did not enhance soil C content, whereas litter reductions negatively impacted soil C concentrations. These results indicate that soil C biogeochemistry at these temperate forests is highly sensitive to changes in litter deposition, which are a product of environmental change drivers.

Article	Year
Soil microbe active community composition and capability of responding to litter addition after 12 years of no inputs. Applied and environmental microbiology\| PubMed ID: 23263952	2013
An optimized HPLC method for soil fungal biomass determination and its application to a detritus manipulation study. Journal of microbiological methods\| PubMed ID: 24918988	2014
Long-term effects of climate change on carbon storage and tree species composition in a dry deciduous forest. Global change biology\| PubMed ID: 28222248	2017
Application of a Stir Bar Sorptive Extraction sample preparation method with HPLC for soil fungal biomass determination in soils from a detrital manipulation study. Journal of microbiological methods\| PubMed ID: 28238755	2017
Long-term litter manipulation alters soil organic matter turnover in a temperate deciduous forest. The Science of the total environment\| PubMed ID: 28711848	2017
Soil carbon cycling proxies: Understanding their critical role in predicting climate change feedbacks. Global change biology\| PubMed ID: 28991399	2018
The detrital input and removal treatment (DIRT) network: Insights into soil carbon stabilization. The Science of the total environment\| PubMed ID: 30021276	2018
Nutrient retention and loss during ecosystem succession: revisiting a classic model. Ecology\| PubMed ID: 31529704	2020
Chlorination of soil-derived dissolved organic matter: Long term nitrogen deposition does not increase terrestrial precursors of toxic disinfection byproducts. Water research\| PubMed ID: 32784033	2020
Nutrient limitation may induce microbial mining for resources from persistent soil organic matter. Ecology\| PubMed ID: 33705567	2021
Grazing cattle, well-managed or not, is unlikely to increase soil carbon sequestration. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 35858462	2022
Soil organic matter molecular composition with long-term detrital alterations is controlled by site-specific forest properties. Global change biology\| PubMed ID: 36169977	2023

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