Geology topics

M. P. Waldrop

Publications and source records attributed to M. P. Waldrop.

12 recordsLinked to original sources

USGS2013

Expert assessment of vulnerability of permafrost carbon to climate change

Approximately 1700 Pg of soil carbon (C) are stored in the northern circumpolar permafrost zone, more than twice as much C than in the atmosphere. The overall amount, rate, and form of C released to the atmosphere in a warmer world will influence the strength of the permafrost C feedback to climate change. We used a survey to quantify variability in the perception of the vulnerability of permafrost C to climate change. Experts were asked to provide quantitative estimates of permafrost change in response to four scenarios of warming. For the highest warming scenario (RCP 8.5), experts hypothesized that C release from permafrost zone soils could be 19–45 Pg C by 2040, 162–288 Pg C by 2100, and 381–616 Pg C by 2300 in CO 2 equivalent using 100-year CH 4 global warming potential (GWP). These values become 50 % larger using 20-year CH 4 GWP, with a third to a half of expected climate forcing coming from CH 4 even though CH 4 was only 2.3 % of the expected C release. Experts projected that two-thirds of this release could be avoided under the lowest warming scenario (RCP 2.6). These results highlight the potential risk from permafrost thaw and serve to frame a hypothesis about the magnitude of this feedback to climate change. However, the level of emissions proposed here are unlikely to overshadow the impact of fossil fuel burning, which will continue to be the main source of C emissions and climate forcing.

Climatic Change↗

USGS2012

Bacterial and enchytraeid abundance accelerate soil carbon turnover along a lowland vegetation gradient in interior Alaska

Boreal wetlands are characterized by a mosaic of plant communities, including forests, shrublands, grasslands, and fens, which are structured largely by changes in topography and water table position. The soil associated with these plant communities contain quantitatively and qualitatively different forms of soil organic matter (SOM) and nutrient availability that drive changes in biogeochemical cycling rates. Therefore different boreal plant communities likely contain different soil biotic communities which in turn affect rates of organic matter decomposition. We examined relationships between plant communities, microbial communities, enchytraeids, and soil C turnover in near-surface soils along a shallow topographic soil moisture and vegetation gradient in interior Alaska. We tested the hypothesis that as soil moisture increases along the gradient, surface soils would become increasingly dominated by bacteria and mesofauna and have more rapid rates of C turnover. We utilized bomb radiocarbon techniques to infer rates of C turnover and the 13C isotopic composition of SOM and respired CO 2 to infer the degree of soil humification. Soil phenol oxidase and peroxidase enzyme activities were generally higher in the rich fen compared with the forest and bog birch sites. Results indicated greater C fluxes and more rapid C turnover in the surface soils of the fen sites compared to the wetland forest and shrub sites. Quantitative PCR analyses of soil bacteria and archaea, combined with enchytraeid counts, indicated that surface soils from the lowland fen ecosystems had higher abundances of these microbial and mesofaunal groups. Fungal abundance was highly variable and not significantly different among sites. Microbial data was utilized in a food web model that confirmed that rapidly cycling systems are dominated by bacterial activity and enchytraeid grazing. However, our results also suggest that oxidative enzymes play an important role in the C mineralization process in saturated systems, which has been often ignored.

Soil Biology and Biochemistry↗

USGS2011

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere1,2,3. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw2. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions4,5. Despite recent advances in the use of molecular tools to study permafrost microbial communities6,7,8,9, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.

Nature↗

USGS2010

Molecular investigations into a globally important carbon pool: Permafrost-protected carbon in Alaskan soils

The fate of carbon (C) contained within permafrost in boreal forest environments is an important consideration for the current and future carbon cycle as soils warm in northern latitudes. Currently, little is known about the microbiology or chemistry of permafrost soils that may affect its decomposition once soils thaw. We tested the hypothesis that low microbial abundances and activities in permafrost soils limit decomposition rates compared with active layer soils. We examined active layer and permafrost soils near Fairbanks, AK, the Yukon River, and the Arctic Circle. Soils were incubated in the lab under aerobic and anaerobic conditions. Gas fluxes at -5 and 5 ??C were measured to calculate temperature response quotients (Q10). The Q10 was lower in permafrost soils (average 2.7) compared with active layer soils (average 7.5). Soil nutrients, leachable dissolved organic C (DOC) quality and quantity, and nuclear magnetic resonance spectroscopy of the soils revealed that the organic matter within permafrost soils is as labile, or even more so, than surface soils. Microbial abundances (fungi, bacteria, and subgroups: methanogens and Basidiomycetes) and exoenzyme activities involved in decomposition were lower in permafrost soils compared with active layer soils, which, together with the chemical data, supports the reduced Q10 values. CH4 fluxes were correlated with methanogen abundance and the highest CH4 production came from active layer soils. These results suggest that permafrost soils have high inherent decomposability, but low microbial abundances and activities reduce the temperature sensitivity of C fluxes. Despite these inherent limitations, however, respiration per unit soil C was higher in permafrost soils compared with active layer soils, suggesting that decomposition and heterotrophic respiration may contribute to a positive feedback to warming of this eco region. Published 2010. This article is a US Government work and is in the public domain in the USA.

Global Change Biology↗

USGS2008

Interactive effects of wildfire and permafrost on microbial communities and soil processes in an Alaskan black spruce forest

Boreal forests contain significant quantities of soil carbon that may be oxidized to CO2 given future increases in climate warming and wildfire behavior. At the ecosystem scale, decomposition and heterotrophic respiration are strongly controlled by temperature and moisture, but we questioned whether changes in microbial biomass, activity, or community structure induced by fire might also affect these processes. We particularly wanted to understand whether postfire reductions in microbial biomass could affect rates of decomposition. Additionally, we compared the short-term effects of wildfire to the long-term effects of climate warming and permafrost decline. We compared soil microbial communities between control and recently burned soils that were located in areas with and without permafrost near Delta Junction, AK. In addition to soil physical variables, we quantified changes in microbial biomass, fungal biomass, fungal community composition, and C cycling processes (phenol oxidase enzyme activity, lignin decomposition, and microbial respiration). Five years following fire, organic surface horizons had lower microbial biomass, fungal biomass, and dissolved organic carbon (DOC) concentrations compared with control soils. Reductions in soil fungi were associated with reductions in phenol oxidase activity and lignin decomposition. Effects of wildfire on microbial biomass and activity in the mineral soil were minor. Microbial community composition was affected by wildfire, but the effect was greater in nonpermafrost soils. Although the presence of permafrost increased soil moisture contents, effects on microbial biomass and activity were limited to mineral soils that showed lower fungal biomass but higher activity compared with soils without permafrost. Fungal abundance and moisture were strong predictors of phenol oxidase enzyme activity in soil. Phenol oxidase enzyme activity, in turn, was linearly related to both 13C lignin decomposition and microbial respiration in incubation studies. Taken together, these results indicate that reductions in fungal biomass in postfire soils and lower soil moisture in nonpermafrost soils reduced the potential of soil heterotrophs to decompose soil carbon. Although in the field increased rates of microbial respiration can be observed in postfire soils due to warmer soil conditions, reductions in fungal biomass and activity may limit rates of decomposition. ?? 2008 The Authors Journal compilation ?? 2008 Blackwell Publishing.

Global Change Biology↗

USGS2008

Short-term response of methane fluxes and methanogen activity to water table and soil warming manipulations in an Alaskan peatland

Growing season CH 4 fluxes were monitored over a two year period following the start of ecosystem-scale manipulations of water table position and surface soil temperatures in a moderate rich fen in interior Alaska. The largest CH 4 fluxes occurred in plots that received both flooding (raised water table position) and soil warming, while the lowest fluxes occurred in unwarmed plots in the lowered water table treatment. A combination of treatment and soil hydroclimate variables explained more than 70% of the variation in ln-transformed CH 4 fluxes, with mean daily water table position representing the strongest predictor. We used quantitative PCR of the α -subunit of mcr operon to explore the influence of soil climate manipulations on methanogen abundances. Methanogen abundances were greatest in warmed plots, and showed a positive relationship with mean daily CH 4 fluxes. Our results show that water table manipulations that led to soil inundation (flooding) had a stronger effect on CH 4 fluxes than water table drawdown. Seasonal CH 4 fluxes increased by 80–300% under the combined wetter and warmer soil climate treatments. Thus, while warming is expected to increase CH 4 emissions from Alaskan wetlands, higher water table positions caused by increases in precipitation or disturbances such as permafrost thaw that lead to thermokarst and flooding in wetlands will stimulate CH 4 emissions beyond the effects of soil warming alone. Consequently, we argue that modeling the effects of climate change on Alaskan wetland CH 4 emissions needs to consider the interactive effects of soil warming and water table position on CH 4 production and transport.

Alaska↗

USGS2007

Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition

The fungal community of the forest floor was examined as the cause of previously reported increases in soil organic matter due to experimental N deposition in ecosystems producing predominantly high-lignin litter, and the opposite response in ecosystems producing low-lignin litter. The mechanism proposed to explain this phenomenon was that white-rot basidiomycetes are more important in the degradation of high-lignin litter than of low-lignin litter, and that their activity is suppressed by N deposition. We found that forest floor mass in the low-lignin sugar-maple dominated system decreased in October due to experimental N deposition, whereas forest floor mass of high-lignin oak-dominated ecosystems was unaffected by N deposition. Increased relative abundance of basidiomycetes in high-lignin forest floor was confirmed by denaturing gradient gel electrophoresis (DGGE) and sequencing. Abundance of basidiomycete laccase genes, encoding an enzyme used by white-rot basidiomycetes in the degradation of lignin, was 5-10 times greater in high-lignin forest floor than in low-lignin forest floor. While the differences between the fungal communities in different ecosystems were consistent with the proposed mechanism, no significant effects of N deposition were detected on DGGE profiles, laccase gene abundance, laccase length heterogeneity profiles, or phenol oxidase activity. Our observations indicate that the previously detected accumulation of soil organic matter in the high-lignin system may be driven by effects of N deposition on organisms in the mineral soil, rather than on organisms residing in the forest floor. However, studies of in situ gene expression and temporal and spatial variability within forest floor communities will be necessary to further relate the ecosystem dynamics of organic carbon to microbial communities and atmospheric N deposition. ?? 2007 The Authors; Journal compilation ?? 2007 Society for Applied Microbiology and Blackwell Publishing Ltd.

Environmental Microbiology↗

USGS2006

Response of microbial community composition and function to soil climate change

Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

Microbial Ecology↗

USGS2006

Response of oxidative enzyme activities to nitrogen deposition affects soil concentrations of dissolved organic carbon

Recent evidence suggests that atmospheric nitrate (NO3- ) deposition can alter soil carbon (C) storage by directly affecting the activity of lignin-degrading soil fungi. In a laboratory experiment, we studied the direct influence of increasing soil NO 3- concentration on microbial C cycling in three different ecosystems: black oak-white oak (BOWO), sugar maple-red oak (SMRO), and sugar maple-basswood (SMBW). These ecosystems span a broad range of litter biochemistry and recalcitrance; the BOWO ecosystem contains the highest litter lignin content, SMRO had intermediate lignin content, and SMBW leaf litter has the lowest lignin content. We hypothesized that increasing soil solution NO 3- would reduce lignolytic activity in the BOWO ecosystem, due to a high abundance of white-rot fungi and lignin-rich leaf litter. Due to the low lignin content of litter in the SMBW, we further reasoned that the NO3- repression of lignolytic activity would be less dramatic due to a lower relative abundance of white-rot basidiomycetes; the response in the SMRO ecosystem should be intermediate. We increased soil solution NO3- concentrations in a 73-day laboratory incubation and measured microbial respiration and soil solution dissolved organic carbon (DOC) and phenolics concentrations. At the end of the incubation, we measured the activity of ??-glucosidase, N-acetyl-glucosaminidase, phenol oxidase, and peroxidase, which are extracellular enzymes involved with cellulose and lignin degradation. We quantified the fungal biomass, and we also used fungal ribosomal intergenic spacer analysis (RISA) to gain insight into fungal community composition. In the BOWO ecosystem, increasing NO 3- significantly decreased oxidative enzyme activities (-30% to -54%) and increased DOC (+32% upper limit) and phenolic (+77% upper limit) concentrations. In the SMRO ecosystem, we observed a significant decrease in phenol oxidase activity (-73% lower limit) and an increase in soluble phenolic concentrations (+57% upper limit) in response to increasing NO 3- in soil solution, but there was no significant change in DOC concentration. In contrast to these patterns, increasing soil solution NO3- in the SMBW soil resulted in significantly greater phenol oxidase activity (+700% upper limit) and a trend toward lower DOC production (-52% lower limit). Nitrate concentration had no effect on microbial respiration or ??-glucosidase or N-acetyl-glucosaminidase activities. Fungal abundance and basidiomycete diversity tended to be highest in the BOWO soil and lowest in the SMBW, but neither displayed a consistent response to NO 3- additions. Taken together, our results demonstrate that oxidative enzyme production by microbial communities responds directly to NO3- deposition, controlling extracellular enzyme activity and DOC flux. The regulation of oxidative enzymes by different microbial communities in response to NO3- deposition highlights the fact that the composition and function of soil microbial communities directly control ecosystem-level responses to environmental change. ?? 2006 Springer Science+Business Media, Inc.

Ecosystems↗

USGS2006

Resource availability controls fungal diversity across a plant diversity gradient

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales. ?? 2006 Blackwell Publishing Ltd/CNRS.

Ecology Letters↗

USGS2006

Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling microbial community composition and function. ?? 2006 Springer Science+Business Media, Inc.

Microbial Ecology↗

USGS2006

A molecular dawn for biogeochemistry

Biogeochemistry is at the dawn of an era in which molecular advances enable the discovery of novel microorganisms having unforeseen metabolic capabilities, revealing new insight into the underlying processes regulating elemental cycles at local to global scales. Traditionally, biogeochemical inquiry began by studying a process of interest, and then focusing downward to uncover the microorganisms and metabolic pathways mediating that process. With the ability to sequence functional genes from the environment, molecular approaches now enable the flow of inquiry in the opposite direction. Here, we argue that a focus on functional genes, the microorganisms in which they reside, and the interaction of those organisms with the broader microbial community could transform our understanding of many globally important biogeochemical processes. ?? 2006 Elsevier Ltd. All rights reserved.

Trends in Ecology and Evolution↗