Tropical Soil

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Mary K. Firestone - One of the best experts on this subject based on the ideXlab platform.

  • Influence of oxic/anoxic fluctuations on ammonia oxidizers and nitrification potential in a wet Tropical Soil
    FEMS microbiology ecology, 2013
    Co-Authors: Jennifer Pett-ridge, Dorthe Groth Petersen, Erin E. Nuccio, Mary K. Firestone
    Abstract:

    Ammonia oxidation is a key process in the global nitrogen cycle. However, in Tropical Soils, little is known about ammonia-oxidizing microorganisms and how characteristically variable oxygen regimes affect their activity. We investigated the influence of brief anaerobic periods on ammonia oxidation along an elevation, moisture, and oxygen availability gradient in wet Tropical Soils. Soils from three forest types were incubated for up to 36 weeks in lab microcosms under three regimes: (1) static aerobic; (2) static anaerobic; and (3) fluctuating (aerobic/anaerobic). Nitrification potential was measured in field-fresh Soils and incubated Soils. The native ammonia-oxidizing community was also characterized, based on diversity assessments (clone libraries) and quantification of the ammonia monooxygenase α–subunit ( amoA ) gene. These relatively low pH Soils appear to be dominated by ammonia-oxidizing archaea (AOA), and AOA communities in the three Soil types differed significantly in their ability to oxidize ammonia. Soils from an intermediate elevation, and those incubated with fluctuating redox conditions, tended to have the highest nitrification potential following an influx of oxygen, although all Soils retained the capacity to nitrify even after long anoxic periods. Together, these results suggest that wet Tropical Soil AOA are tolerant of extended periods of anoxia.

  • redox fluctuation structures microbial communities in a wet Tropical Soil
    Applied and Environmental Microbiology, 2005
    Co-Authors: Jennifer Pettridge, Mary K. Firestone
    Abstract:

    Frequent high-amplitude redox fluctuation may be a strong selective force on the phylogenetic and physiological composition of Soil bacterial communities and may promote metabolic plasticity or redox tolerance mechanisms. To determine effects of fluctuating oxygen regimens, we incubated Tropical Soils under four treatments: aerobic, anaerobic, 12-h oxic/anoxic fluctuation, and 4-day oxic/anoxic fluctuation. Changes in Soil bacterial community structure and diversity were monitored with terminal restriction fragment length polymorphism (T-RFLP) fingerprints. These profiles were correlated with gross N cycling rates, and a Web-based phylogenetic assignment tool was used to infer putative community composition from multiple fragment patterns. T-RFLP ordinations indicated that bacterial communities from 4-day oxic/anoxic incubations were most similar to field communities, whereas those incubated under consistently aerobic or anaerobic regimens developed distinctly different molecular profiles. Terminal fragments found in field Soils persisted either in 4-day fluctuation/aerobic conditions or in anaerobic/12-h treatments but rarely in both. Only 3 of 179 total fragments were ubiquitous in all Soils. Soil bacterial communities inferred from in silico phylogenetic assignment appeared to be dominated by Actinobacteria (especially Micrococcus and Streptomycetes), "Bacilli," "Clostridia," and Burkholderia and lost significant diversity under consistently or frequently anoxic incubations. Community patterns correlated well with redox-sensitive processes such as nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification but did not predict patterns of more general functions such as N mineralization and consumption. The results suggest that this Soil's indigenous bacteria are highly adapted to fluctuating redox regimens and generally possess physiological tolerance mechanisms which allow them to withstand unfavorable redox periods.

  • linking microbial community composition to function in a Tropical Soil
    Soil Biology & Biochemistry, 2000
    Co-Authors: Mark P Waldrop, Teri C Balser, Mary K. Firestone
    Abstract:

    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.

Kokgan Chan - One of the best experts on this subject based on the ideXlab platform.

Jian-woon Chen - One of the best experts on this subject based on the ideXlab platform.

Benjamin L. Turner - One of the best experts on this subject based on the ideXlab platform.

  • Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in Tropical Soil
    Nature Ecology & Evolution, 2018
    Co-Authors: Qiuming Yao, Benjamin L. Turner, Terry C. Hazen, Yang Song, S. Joseph Wright, Xuan Guo, Susannah G. Tringe, Malak M. Tfaily, Ljiljana Paša-tolić, Melanie A. Mayes
    Abstract:

    Phosphorus is a scarce nutrient in many Tropical ecosystems, yet how Soil microbial communities cope with growth-limiting phosphorus deficiency at the gene and protein levels remains unknown. Here, we report a metagenomic and metaproteomic comparison of microbial communities in phosphorus-deficient and phosphorus-rich Soils in a 17-year fertilization experiment in a Tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex Soil communities. A greater than fourfold increase in the gene abundance of 3-phytase was the strongest response of Soil communities to phosphorus deficiency. Phytase catalyses the release of phosphate from phytate, the most recalcitrant phosphorus-containing compound in Soil organic matter. Genes and proteins for the degradation of phosphorus-containing nucleic acids and phospholipids, as well as the decomposition of labile carbon and nitrogen, were also enhanced in the phosphorus-deficient Soils. In contrast, microbial communities in the phosphorus-rich Soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, transformation of nitrogenous compounds and assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in Soil microbial communities in response to shifting nutrient constraints. Metagenomic and metaproteomic analysis of Soil from a 17-year Tropical forest fertilization experiment supports the hypothesis that microbial communities respond to nutrient deficiency by enhancing the extraction of phosphorus from recalcitrant substrates.

  • Soil carbon stocks across Tropical forests of panama regulated by base cation effects on fine roots
    Biogeochemistry, 2018
    Co-Authors: Daniela F. Cusack, Richard Condit, Lars Markesteijn, Owen T Lewis, Benjamin L. Turner
    Abstract:

    Tropical forests are the most carbon (C)-rich ecosystems on Earth, containing 25–40% of global terrestrial C stocks. While large-scale quantification of aboveground biomass in Tropical forests has improved recently, Soil C dynamics remain one of the largest sources of uncertainty in Earth system models, which inhibits our ability to predict future climate. Globally, Soil texture and climate predict ≤ 30% of the variation in Soil C stocks, so ecosystem models often predict Soil C using measures of aboveground plant growth. However, this approach can underestimate Tropical Soil C stocks, and has proven inaccurate when compared with data for Soil C in data-rich northern ecosystems. By quantifying Soil organic C stocks to 1 m depth for 48 humid Tropical forest plots across gradients of rainfall and Soil fertility in Panama, we show that Soil C does not correlate with common predictors used in models, such as plant biomass or litter production. Instead, a structural equation model including base cations, Soil clay content, and rainfall as exogenous factors and root biomass as an endogenous factor predicted nearly 50% of the variation in Tropical Soil C stocks, indicating a strong indirect effect of base cation availability on Tropical Soil C storage. Including Soil base cations in C cycle models, and thus emphasizing mechanistic links among nutrients, root biomass, and Soil C stocks, will improve prediction of climate-Soil feedbacks in Tropical forests.

  • variation in wood nutrients along a Tropical Soil fertility gradient
    New Phytologist, 2016
    Co-Authors: Katherine D Heineman, Benjamin L. Turner, James W. Dalling
    Abstract:

    Wood contains the majority of the nutrients in Tropical trees, yet controls over wood nutrient concentrations and their function are poorly understood. We measured wood nutrient concentrations in 106 tree species in 10 forest plots spanning a regional fertility gradient in Panama. For a subset of species, we quantified foliar nutrients and wood density to test whether wood nutrients scale with foliar nutrients at the species level, or wood nutrient storage increases with wood density as predicted by the wood economics spectrum. Wood nutrient concentrations varied enormously among species from fourfold in nitrogen (N) to > 30-fold in calcium (Ca), potassium (K), magnesium (Mg) and phosphorus (P). Community-weighted mean wood nutrient concentrations correlated positively with Soil Ca, K, Mg and P concentrations. Wood nutrients scaled positively with leaf nutrients, supporting the hypothesis that nutrient allocation is conserved across plant organs. Wood P was most sensitive to variation in Soil nutrient availability, and significant radial declines in wood P indicated that Tropical trees retranslocate P as sapwood transitions to heartwood. Wood P decreased with increasing wood density, suggesting that low wood P and dense wood are traits associated with tree species persistence on low fertility Soils. Substantial variation among species and communities in wood nutrient concentrations suggests that allocation of nutrients to wood, especially P, influences species distributions and nutrient dynamics in Tropical forests.

Richard Condit - One of the best experts on this subject based on the ideXlab platform.

  • Soil carbon stocks across Tropical forests of panama regulated by base cation effects on fine roots
    Biogeochemistry, 2018
    Co-Authors: Daniela F. Cusack, Richard Condit, Lars Markesteijn, Owen T Lewis, Benjamin L. Turner
    Abstract:

    Tropical forests are the most carbon (C)-rich ecosystems on Earth, containing 25–40% of global terrestrial C stocks. While large-scale quantification of aboveground biomass in Tropical forests has improved recently, Soil C dynamics remain one of the largest sources of uncertainty in Earth system models, which inhibits our ability to predict future climate. Globally, Soil texture and climate predict ≤ 30% of the variation in Soil C stocks, so ecosystem models often predict Soil C using measures of aboveground plant growth. However, this approach can underestimate Tropical Soil C stocks, and has proven inaccurate when compared with data for Soil C in data-rich northern ecosystems. By quantifying Soil organic C stocks to 1 m depth for 48 humid Tropical forest plots across gradients of rainfall and Soil fertility in Panama, we show that Soil C does not correlate with common predictors used in models, such as plant biomass or litter production. Instead, a structural equation model including base cations, Soil clay content, and rainfall as exogenous factors and root biomass as an endogenous factor predicted nearly 50% of the variation in Tropical Soil C stocks, indicating a strong indirect effect of base cation availability on Tropical Soil C storage. Including Soil base cations in C cycle models, and thus emphasizing mechanistic links among nutrients, root biomass, and Soil C stocks, will improve prediction of climate-Soil feedbacks in Tropical forests.

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