Mark P. Waldrop

Stoichiometry of soil enzyme activity at global scale

Extracellular enzymes are the proximate agents of organic matter decomposition and measures of these activities can be used as indicators of microbial nutrient demand. We conducted a global-scale meta-analysis of the seven-most widely measured soil enzyme activities, using data from 40 ecosystems. The activities of beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-N-acetylglucosaminidase and phosphatase g(-1) soil increased with organic matter concentration; leucine aminopeptidase, phenol oxidase and peroxidase activities showed no relationship. All activities were significantly related to soil pH. Specific activities, i.e. activity g(-1) soil organic matter, also varied in relation to soil pH for all enzymes. Relationships with mean annual temperature (MAT) and precipitation (MAP) were generally weak. For hydrolases, ratios of specific C, N and P acquisition activities converged on 1 : 1 : 1 but across ecosystems, the ratio of C : P acquisition was inversely related to MAP and MAT while the ratio of C : N acquisition increased with MAP. Oxidative activities were more variable than hydrolytic activities and increased with soil pH. Our analyses indicate that the enzymatic potential for hydrolyzing the labile components of soil organic matter is tied to substrate availability, soil pH and the stoichiometry of microbial nutrient demand. The enzymatic potential for oxidizing the recalcitrant fractions of soil organic material, which is a proximate control on soil organic matter accumulation, is most strongly related to soil pH. These trends provide insight into the biogeochemical processes that create global patterns in ecological stoichiometry and organic matter storage.

Linking microbial community composition to function in a tropical soil.

Abstract If changes in the composition of the soil microbial community alter the physiological capacity of the community then such changes may have ecosystem consequences. We examined the relationships among community composition (PLFA), microbial biomass (CFDE), substrate utilization profiles (BIOLOG), lignocellulose degrading enzyme activities (β-glucosidase, cellobiohydrolase, β-xylosidase, phenol oxidase, peroxidase), and nutrient releasing enzyme activities (phosphatase, sulphatase) in a Tropeptic Haplustol soil. The soils supported a tropical forest and pineapple plantations of varying ages that were at different stages within the management cycle. Conversion from forest to agriculture significantly decreased %C and %N of the soil by 50–55%, microbial biomass by 75%, β-glucosidase by 54%, sulphatase activity by 85%, decreased Ca, Mg, and Mn availability, and produced compositionally and functionally distinct microbial communities. Total enzyme activities were generally correlated with %C, %N, microbial biomass and, occasionally with community composition. We calculated the specific activities of the enzymes assayed (enzyme activity per unit microbial biomass C) in order to normalize activity to the size of the microbial community. Values for enzyme specific activities were more highly correlated with community composition than were total enzyme activities. In addition, BIOLOG was not correlated with community composition or enzyme activities. Enzyme activities and specific activities may provide a useful linkage between microbial community composition and carbon processing.

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 atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, 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.

Vulnerability of high‐latitude soil organic carbon in North America to disturbance

[1] This synthesis addresses the vulnerability of the North American high‐latitude soil organic carbon (SOC) pool to climate change. Disturbances caused by climate warming in arctic, subarctic, and boreal environments can result in significant redistribution of C among major reservoirs with potential global impacts. We divide the current northern high‐latitude SOC pools into (1) near‐surface soils where SOC is affected by seasonal freeze‐thaw processes and changes in moisture status, and (2) deeper permafrost and peatland strata down to several tens of meters depth where SOC is usually not affected by short‐term changes. We address key factors (permafrost, vegetation, hydrology, paleoenvironmental history) and processes (C input, storage, decomposition, and output) responsible for the formation of the large high‐latitude SOC pool in North America and highlight how climate‐related disturbances could alter this pool’s character and size. Press disturbances of relatively slow but persistent nature such as top‐down thawing of permafrost, and changes in hydrology, microbiological communities, pedological processes, and vegetation types, as well as pulse disturbances of relatively rapid and local nature such as wildfires and thermokarst, could substantially impact SOC stocks. Ongoing climate warming in the North American high‐latitude region could result in crossing environmental thresholds, thereby accelerating press disturbances and increasingly triggering pulse disturbances and eventually affecting the C source/sink net character of northern high‐latitude soils. Finally, we assess postdisturbance feedbacks, models, and predictions for the northern high‐latitude SOC pool, and discuss data and research gaps to be addressed by future research.

Nitrogen Deposition Modifies Soil Carbon Storage Through Changes In Microbial Enzymatic Activity

Atmospheric nitrogen (N) deposition derived from fossil-fuel combustion, land clearing, and biomass burning is occurring over large geographical regions on nearly every continent. Greater ecosystem N availability can result in greater aboveground carbon (C) sequestration, but little is understood as to how soil C storage could be altered by N deposition. High concentrations of inorganic N accelerate the degradation of easily decom- posable litter and slow the decomposition of recalcitrant litter containing large amounts of lignin. This pattern has been attributed to stimulation or repression of different sets of microbial extracellular enzymes. We hypothesized that soil C cycling in forest ecosystems with markedly different litter chemistry and decomposition rates would respond to anthro- pogenic N deposition in a manner consistent with the biochemical composition of the dominant vegetation. Specifically, oak-dominated ecosystems with low litter quality should gain soil C, and sugar maple ecosystems with high litter quality should lose soil C in response to high levels of N deposition (80 kg N-ha-1-yr-1). Consistent with this hypothesis, we observed over a three-year period a significant loss of soil C (20%) from a sugar maple- dominated ecosystem and a significant gain (10%) in soil C in an oak-dominated ecosystem, a result that appears to be mediated by the regulation of the microbial extracellular enzyme phenol oxidase. Elevated N deposition resulted in changes in soil carbon that were ecosystem specific and resulted from the divergent regulatory control of microbial extracellular en- zymes by soil N availability.

Microbial community utilization of recalcitrant and simple carbon compounds: impact of oak-woodland plant communities

Little is known about how the structure of microbial communities impacts carbon cycling or how soil microbial community composition mediates plant effects on C-decomposition processes. We examined the degradation of four 13C-labeled compounds (starch, xylose, vanillin, and pine litter), quantified rates of associated enzyme activities, and identified microbial groups utilizing the 13C-labeled substrates in soils under oaks and in adjacent open grasslands. By quantifying increases in non-13C-labeled carbon in microbial biomarkers, we were also able to identify functional groups responsible for the metabolism of indigenous soil organic matter. Although microbial community composition differed between oak and grassland soils, the microbial groups responsible for starch, xylose, and vanillin degradation, as defined by 13C-PLFA, did not differ significantly between oak and grassland soils. Microbial groups responsible for pine litter and SOM-C degradation did differ between the two soils. Enhanced degradation of SOM resulting from substrate addition (priming) was greater in grassland soils, particularly in response to pine litter addition; under these conditions, fungal and Gram + biomarkers showed more incorporation of SOM-C than did Gram – biomarkers. In contrast, the oak soil microbial community primarily incorporated C from the added substrates. More 13C (from both simple and recalcitrant sources) was incorporated into the Gram – biomarkers than Gram + biomarkers despite the fact that the Gram + group generally comprised a greater portion of the bacterial biomass than did markers for the Gram – group. These experiments begin to identify components of the soil microbial community responsible for decomposition of different types of C-substrates. The results demonstrate that the presence of distinctly different plant communities did not alter the microbial community profile responsible for decomposition of relatively labile C-substrates but did alter the profiles of microbial communities responsible for decomposition of the more recalcitrant substrates, pine litter and indigenous soil organic matter.

Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska

Nitrification and denitrification processes are crucial to plant nutrient availability, eutrophication and greenhouse gas production both locally and globally. Unravelling the major environmental predictors for nitrification and denitrification is thus pivotal in order to understand and model environmental nitrogen (N) cycling. Here, we sampled five plant community types characteristic of interior Alaska, including black spruce, bog birch, tussock grass and two fens. We assessed abundance of functional genes affiliated with nitrification (bacterial and archaeal amoA) and denitrification (nirK/S and nosZ) using qPCR, soil characteristics, potential nitrification and denitrification rates (PNR and PDR) and gross mineralization rates. The main chemical and biological predictors for PNR and PDR were assigned through path analysis. The potential N cycling rates varied dramatically between sites, from some of the highest (in fens) to some of the lowest (in black spruce) measured globally. Based on path analysis, functional gene abundances were the most important variables to predict potential rates. PNR was best explained by bacterial amoA gene abundance followed by ammonium content, whereas PDR was best explained directly by nosZ gene abundance and indirectly by nirK/S gene abundance and nitrate. Hence, functional gene abundance is a valuable index that integrates recent environmental history and recent process activity, and therefore is a good predictor of potential rates. The results of this study contribute to our understanding of the relative importance of different biological and chemical factors in driving the potential for nitrification and denitrification across terrestrial ecosystems.

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 NO3− 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 NO3− 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 β-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 NO3− 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 NO3− 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 β-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 NO3− 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.

Integrating microbial ecology into ecosystem models: challenges and priorities

Microbial communities can potentially mediate feedbacks between global change and ecosystem function, owing to their sensitivity to environmental change and their control over critical biogeochemical processes. Numerous ecosystem models have been developed to predict global change effects, but most do not consider microbial mechanisms in detail. In this idea paper, we examine the extent to which incorporation of microbial ecology into ecosystem models improves predictions of carbon (C) dynamics under warming, changes in precipitation regime, and anthropogenic nitrogen (N) enrichment. We focus on three cases in which this approach might be especially valuable: temporal dynamics in microbial responses to environmental change, variation in ecological function within microbial communities, and N effects on microbial activity. Four microbially-based models have addressed these scenarios. In each case, predictions of the microbial-based models differ—sometimes substantially—from comparable conventional models. However, validation and parameterization of model performance is challenging. We recommend that the development of microbial-based models must occur in conjunction with the development of theoretical frameworks that predict the temporal responses of microbial communities, the phylogenetic distribution of microbial functions, and the response of microbes to N enrichment.

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

Over 20% of Earth’s terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular ‘omics’ approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.