Physical disturbance to ecological niches created by soil structure alters community composition of methanotrophs.

PubMed

Kumaresan, Deepak; Stralis-Pavese, Nancy; Abell, Guy C J; Bodrossy, Levente; Murrell, J Colin

2011-10-01

Aggregates of different sizes and stability in soil create a composite of ecological niches differing in terms of physico-chemical and structural characteristics. The aim of this study was to identify, using DNA-SIP and mRNA-based microarray analysis, whether shifts in activity and community composition of methanotrophs occur when ecological niches created by soil structure are physically perturbed. Landfill cover soil was subject to three treatments termed: 'control' (minimal structural disruption), 'sieved' (sieved soil using 2 mm mesh) and 'ground' (grinding using mortar and pestle). 'Sieved' and 'ground' soil treatments exhibited higher methane oxidation potentials compared with the 'control' soil treatment. Analysis of the active community composition revealed an effect of physical disruption on active methanotrophs. Type I methanotrophs were the most active methanotrophs in 'sieved' and 'ground' soil treatments, whereas both Type I and Type II methanotrophs were active in the 'control' soil treatment. The result emphasize that changes to a particular ecological niche may not result in an immediate change to the active bacterial composition and change in composition will depend on the ability of the bacterial communities to respond to the perturbation. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Elemental Analysis of Soils by Laser Induced Breakdown Spectroscopy

NASA Astrophysics Data System (ADS)

Gondal, Mohammed Ashraf; Dastageer, Mohamed A.

The chemical and elemental composition of soil is very complex as it contains many constituents like minerals, organic matters, living organisms, fossils, air and water. Considering the diversity of soil contents, quality and usability, a systematic scientific study on the elemental and chemical composition of soil is very important. In order to study the chemical composition of soil, Laser induced breakdown spectroscopy (LIBS) has been applied recently. The important features of LIBS system and its applications for the measurement of nutrients in green house soil, on-line monitoring of remediation process of chromium polluted soil, determination of trace elements in volcanic erupted soil samples collected from ancient cenozoic lava eruption sites and detection of toxic metals in Gulf war oil spill contaminated soil using LIBS are described in this chapter.

Herbivore species identity and composition affect soil enzymatic activity through altered plant composition in a coastal tallgrass prairie

USDA-ARS?s Scientific Manuscript database

Although single species of herbivores are known to affect soil microbial communities, the effects of herbivore species identity and functional composition on soil microbes is unknown. We tested the effects of single species of orthopterans and multiple species combinations on soil enzymatic activity...

Research on the reasonable pile spacing of micro pile composite soil nailing

NASA Astrophysics Data System (ADS)

Liu, Jun yan; Liu, Yan; Song, Xiang hua

2017-08-01

Through the numerical simulation software FLAC3D, study on the synergetic effect of micro pile composite soil nailing will be studied. By adjusting the micro pile spacing and analysing the displacement field and stress field of soil, we can find that supporting effect of the soil nail hasn’t work yet when the micro pile spacing is 2D. The soil arching between piles has been formed in the pile spacing 4D ∼ 6D. The composite effect of micro pile and soil nailing will be the best and the soil arch behind piles will be firstly formed in 6D, the horizontal saddle soil arch will be formed between the nails. The nail head coincidence pressure area and micro pile pressure area are overlapping to maintain stability in the soil between piles. When the micro pile spacing is 9D, the arch behind piles will be failure, the soil flows around, but the saddle arch between the nails into circular arch, the supporting effect of the soil nailing is enhanced. When the micro pile spacing is 12D, the arch of the nails becomes smaller, sliding surface appears primitively. Based on the conclusions above, it is suggested that the micro pile spacing between 2D ∼ 6D is suitable for the micro pile and soil nailing composite support. The conclusion can provide theoretical basis for the design and construction of micro pile composite soil nailing.

Earthworms are associated with subpopulations of Gammaproteobacteria irrespective of the total soil microbiota composition and stability.

PubMed

Fjøsne, Trine; Myromslien, Frøydis D; Wilson, Robert C; Rudi, Knut

2018-05-01

Soil represents one of the most complex microbial ecosystems on earth. It is well-known that invertebrates such as earthworms have a major impact on transformations of organic material in soil, while their effect on the soil microbiota remains largely unknown. The aim of our work was therefore to investigate the association of earthworms with temporal stability, composition and diversity in two soil microbiota experimental series. We found that earthworms were consistently associated with an increase in subgroups of Gammaproteobacteria, despite major differences in microbiota composition and temporal stability across the experimental series. Our results therefore suggest that earthworms can affect subpopulation dynamics in the soil microbiota, irrespective of the total microbiota composition. If the soil microbiota is comprised of independent microbiota components, this can contribute to our general understanding of the complexity of the soil microbiota.

Deconvoluting effects of vine and soil properties on grape berry composition.

PubMed

Zerihun, Ayalsew; McClymont, Lexie; Lanyon, Dean; Goodwin, Ian; Gibberd, Mark

2015-01-01

Grape berry composition is influenced by several factors including grapevine and soil properties and their interactions. Understanding how these factors interact to determine berry composition is integral to producing berries with desired composition. Here we used extensive spatio-temporal data to identify significant vine and soil features that influence Shiraz berry composition. The concentrations of berry flavonoids (anthocyanins, tannin and total phenolics), total soluble solids and pH were typically negatively associated with canopy, crop and berry size factors whereas titratable acidity was positively associated. The strengths of the associations, however, were generally greater with the crop and berry size factors than with the canopy size factor. The analyses also resolved separate influences of berry and crop size on berry composition. Soil properties had significant influences on berry composition; however, when influences of soil factors on vine-attributes were accounted for, the apparent effects of soil factors on berry composition were largely non-existent. At each site, variations in berry composition were more strongly associated with crop and berry size than with canopy size factors. Apparent influences of soil properties on berry composition are indirect, being mediated via their effects on vine attributes (canopy, crop and berry sizes). © 2014 Society of Chemical Industry.

Dust Composition in Climate Models: Current Status and Prospects

NASA Astrophysics Data System (ADS)

Pérez García-Pando, C.; Miller, R. L.; Perlwitz, J. P.; Kok, J. F.; Scanza, R.; Mahowald, N. M.

2015-12-01

Mineral dust created by wind erosion of soil particles is the dominant aerosol by mass in the atmosphere. It exerts significant effects on radiative fluxes, clouds, ocean biogeochemistry, and human health. Models that predict the lifecycle of mineral dust aerosols generally assume a globally uniform mineral composition. However, this simplification limits our understanding of the role of dust in the Earth system, since the effects of dust strongly depend on the particles' physical and chemical properties, which vary with their mineral composition. Hence, not only a detailed understanding of the processes determining the dust emission flux is needed, but also information about its size dependent mineral composition. Determining the mineral composition of dust aerosols is complicated. The largest uncertainty derives from the current atlases of soil mineral composition. These atlases provide global estimates of soil mineral fractions, but they are based upon massive extrapolation of a limited number of soil samples assuming that mineral composition is related to soil type. This disregards the potentially large variability of soil properties within each defined soil type. In addition, the analysis of these soil samples is based on wet sieving, a technique that breaks the aggregates found in the undisturbed parent soil. During wind erosion, these aggregates are subject to partial fragmentation, which generates differences on the size distribution and composition between the undisturbed parent soil and the emitted dust aerosols. We review recent progress on the representation of the mineral and chemical composition of dust in climate models. We discuss extensions of brittle fragmentation theory to prescribe the emitted size-resolved dust composition, and we identify key processes and uncertainties based upon model simulations and an unprecedented compilation of observations.

About the possibility of obtaining cementitious soil composites of high strength on the basis of belozems of carbonate composition

NASA Astrophysics Data System (ADS)

Karapetyan, K. A.; Hayroyan, S. G.; Manukyan, E. S.

2018-04-01

The problem of manufacturing high strength cementitious soils based on belozems of carbonate composition, which experience compression (no less than 10 MPa), without application of surface active substances is considered. The portland cement of type 400 was used as a binding agent to develop compositions of cementitious soil composites, and the ordinary pipe water was used to obtain solutions of cementitious soils. The chemical and mineralogical composition of the initial ingredients and the granulometric composition of belozems were determined. The measurements showed that the upper and lower plasticity limits, the optimum moisture content, and the maximal density of the skeleton of belozems, as well as the considered compositions of cementitious soils, are insignificant, while the plasticity index of cementitious soils is less than one for belozems. It is experimentally proved that an increase in the portland cement amount lead to an increase in the compressive strength of cementitious soils with a decreasing speed. But for the same amount of portland cement used in the cementitious soil compositions, the values of the strength ratio of the pieces tested at the age of 60 and 28 days remain the same and are approximately equal to 1.2. A comparison of experimental data showed that it seems to be real to manufacture a cementitious soil on the basis of belozems of carbonate composition, which contain 10% of cement of the weight of dry mixture and have strength more than 10 MPa, without adding any surfactants to the material composition.

Investigating the Relationship Between Soil Water Mobility and Stable Isotope Composition with Implications for the Ecohydrologic Separation Hypothesis

NASA Astrophysics Data System (ADS)

Shuler, J.; McNamara, J. P.; Benner, S. G.; Kohn, M. J.; Evans, S.

2017-12-01

The ecohydrologic separation (ES) hypothesis states that streams and plants return different soil water compartments to the atmosphere and that these compartments bear distinct isotopic compositions that can be used to infer soil water mobility. Recent studies have found isotopic evidence for ES in a variety of ecosystems, though interpretations of these data vary. ES investigations frequently suffer from low sampling frequencies as well as incomplete or missing soil moisture and matric potential data to support assumptions of soil water mobility. We sampled bulk soil water every 2-3 weeks in the upper 1 m of a hillslope profile from May 2016 to July 2017 in a semi-arid watershed outside Boise, ID. Twig samples of three plant species were also collected concurrently. Plant and soil water samples extracted via cryogenic vacuum distillation were analyzed for δ2H and δ18O composition. Soil moisture and soil matric potential sensors were installed at five and four depths in the profile, respectively. Shallow bulk soil water was progressively enriched in both isotopes over the growing season and plotted along a soil evaporation line in a plot of δ2H versus δ18O. Plant water during the growing season plotted below both the Local Meteoric Water Line and soil evaporation line. Plant water isotopic composition could not be traced to any source sampled in this study. Additionally, soil moisture and matric potential data revealed that soils were well-drained and that mobile soil water was unavailable throughout most of the growing season at the depths sampled. Soil water isotopic composition alone failed to predict mobility as observed in soil moisture and matric potential data. These results underscore the need for standard hydrologic definitions for the mobile and immobile compartments of soil water in future studies of the ES hypothesis and ecohydrologic processes in general.

Agglutinates as recorders of fossil soil compositions. [of Apollo 17 lunar probes

NASA Technical Reports Server (NTRS)

Taylor, G. J.; Wentworth, S.; Warner, R. D.; Keil, K.

1978-01-01

The composition of agglutinates in polished sections of the Apollo 17 drill core was studied in an attempt to deduce the nature of the Taurus-Littrow valley regolith prior to the formation of the Camelot and Central Cluster craters. The agglutinate compositions in the soils differed from the host soil compositions except for samples from the North Massif. Local materials from the valley floor and the massifs appear to form the pre-Central Cluster regolith. It is also shown that chemical mixing models for bulk soil compositions can be misleading unless the petrologic characteristics of each soil are taken into account.

Influence of Soil Properties on Soldierless Termite Distribution.

PubMed

Bourguignon, Thomas; Drouet, Thomas; Šobotník, Jan; Hanus, Robert; Roisin, Yves

2015-01-01

In tropical rainforests, termites constitute an important part of the soil fauna biomass, and as for other soil arthropods, variations in soil composition create opportunities for niche partitioning. The aim of this study was twofold: first, we tested whether soil-feeding termite species differ in the foraging substrate; second, we investigated whether soil-feeding termites select their foraging sites to enhance nutrients intake. To do so, we collected termites and analysed the composition and structure of their feeding substrates. Although Anoplotermes-group members are all considered soil-feeders, our results show that some species specifically feed on abandoned termite nests and very rotten wood, and that this substrate selection is correlated with previous stable isotope analyses, suggesting that one component of niche differentiation among species is substrate selection. Our results show that the composition and structure of bare soils on which different termite species foraged do not differ, suggesting that there is no species specialization for a particular type of bare soil. Finally, the bare soil on which termites forage does not differ from random soil samples. Overall, our results suggest that few species of the Anoplotermes-group are specialized toward substrates rich in organic matter, but that the vast majority forage on soil independently of its structural and chemical composition, being ecologically equivalent for this factor.

Methane Emissions from Natural Gas Vehicles in Beijing, Baoding, and Shijiazhuang, China during CAREBEIJING Field Campaign

NASA Astrophysics Data System (ADS)

Pérez García-Pando, C.; Miller, R. L.; Perlwitz, J. P.; Kok, J. F.; Scanza, R.; Mahowald, N. M.

2014-12-01

Mineral dust created by wind erosion of soil particles is the dominant aerosol by mass in the atmosphere. It exerts significant effects on radiative fluxes, clouds, ocean biogeochemistry, and human health. Models that predict the lifecycle of mineral dust aerosols generally assume a globally uniform mineral composition. However, this simplification limits our understanding of the role of dust in the Earth system, since the effects of dust strongly depend on the particles' physical and chemical properties, which vary with their mineral composition. Hence, not only a detailed understanding of the processes determining the dust emission flux is needed, but also information about its size dependent mineral composition. Determining the mineral composition of dust aerosols is complicated. The largest uncertainty derives from the current atlases of soil mineral composition. These atlases provide global estimates of soil mineral fractions, but they are based upon massive extrapolation of a limited number of soil samples assuming that mineral composition is related to soil type. This disregards the potentially large variability of soil properties within each defined soil type. In addition, the analysis of these soil samples is based on wet sieving, a technique that breaks the aggregates found in the undisturbed parent soil. During wind erosion, these aggregates are subject to partial fragmentation, which generates differences on the size distribution and composition between the undisturbed parent soil and the emitted dust aerosols. We review recent progress on the representation of the mineral and chemical composition of dust in climate models. We discuss extensions of brittle fragmentation theory to prescribe the emitted size-resolved dust composition, and we identify key processes and uncertainties based upon model simulations and an unprecedented compilation of observations.

Chemical composition and Zn bioavailability of the soil solution extracted from Zn amended variable charge soils.

PubMed

Zampella, Mariavittoria; Adamo, Paola

2010-01-01

A study on variable charge soils (volcanic Italian and podzolic Scottish soils) was performed to investigate the influence of soil properties on the chemical composition of soil solution. Zinc speciation, bioavailability and toxicity in the soil solution were examined. The soils were spiked with increasing amounts of Zn (0, 100, 200, 400 and 1000 mg/kg) and the soil solutions were extracted using rhizon soil moisture samplers. The pH, total organic carbon (TOC), base cations, anions, total Zn and free Zn2+ in soil solution were analysed. A rapid bioassay with the luminescent bacterium Escherichia coli HB101 pUCD607 was performed to assess Zn toxicity. The influence of soil type and Zn treatments on the chemical composition of soil solution and on Zn toxicity was considered and discussed. Different trends of total and free Zn concentrations, base cations desorption and luminescence of E. coli HB101 pUCD607 were observed. The soil solution extracted from the volcanic soils had very low total and free Zn concentrations and showed specific Zn2+/Ca2+ exchange. The soil solution from the podzolic soil had much higher total and free Zn concentrations and showed no evidence of specific Zn2+/Ca2+ exchange. In comparison with the subalkaline volcanic soils, the acidic podzol showed enhanced levels of toxic free Zn2+ and consequently stronger effects on E. coli viability.

Soil amino acid composition across a boreal forest successional sequence

Treesearch

Nancy R. Werdin-Pfisterer; Knut Kielland; Richard D. Boone

2009-01-01

Soil amino acids are important sources of organic nitrogen for plant nutrition, yet few studies have examined which amino acids are most prevalent in the soil. In this study, we examined the composition, concentration, and seasonal patterns of soil amino acids across a primary successional sequence encompassing a natural gradient of plant productivity and soil...

The sources and composition of humus in some soils of West Antarctica

NASA Astrophysics Data System (ADS)

Abakumov, E. V.

2010-05-01

Original data on humus-forming substances and their elemental and biochemical compositions in Antarctic soils are discussed. Mosses, lichens, algae, remains of higher vascular plants, and penguin guano of two types differ considerably in their chemical compositions. This leads to significant differences in the formation of humic substances in plant materials themselves in the course of their transformation. However, no significant differences in the composition of humus in the fine earth of soils developing under different humus-forming materials have been revealed, which may be related to the extremely low rates of humification. Significant differences between the soils of Antarctic landscapes proper and the soils of the Subantarctic King George Island are only observed in the humus enrichment with nitrogen. The soils of Antarctica are low-humus soils with the humate-fulvate or fulvate types of humus.

Soil ecosystem functioning under climate change: plant species and community effects.

PubMed

Kardol, Paul; Cregger, Melissa A; Campany, Courtney E; Classen, Aimee T

2010-03-01

Feedbacks of terrestrial ecosystems to atmospheric and climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering the soil communities that depend on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and precipitation in Tennessee (USA). Specifically, we collected soils at the plot level (plant community soils) and beneath dominant plant species (plant-specific soils). We used microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: (1) Overall, while there were some interactions, water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activity, and soil nematodes. Multiple climate-change factors can interact to shape ecosystems, but in our study, those interactions were largely driven by changes in water. (2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning, and this impact was not obvious when looking at plant community soils. Climate-change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. These results indicate that accurate assessments of climate-change impacts on soil ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate-change-induced shifts in plant community composition will likely modify or counteract the direct impact of atmospheric and climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting the manner in which global change will alter ecosystem functioning.

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

DOE PAGES

Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.

2015-09-04

Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing ofmore » ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha –1 yr –1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. As a result, given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.« less

Temporal dynamics of the compositions and activities of soil microbial communities post-application of the insecticide chlorantraniliprole in paddy soils.

PubMed

Wu, Meng; Liu, Jia; Li, Weitao; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

2017-10-01

Chlorantraniliprole (CAP) is a newly developed insecticide widely used in rice fields in China. There has been few studies evaluating the toxicological effects of CAP on soil-associated microbes. An 85-day microcosm experiment was performed to reveal the dissipation dynamics of CAP in three types of paddy soils in subtropical China. The effects of CAP on microbial activities (microbial biomass carbon-MBC, basal soil respiration-BSR, microbial metabolic quotient-qCO 2 , acid phosphatase and sucrose invertase activities) in the soils were periodically evaluated. Microbial phospholipid fatty acid (PLFA) analysis was used to evaluate the change of soil microbial community composition on day 14 and 50 of the experiment. CAP residues were extracted using the quick, easy, cheap, effective, rugged, and safe (QuChERS) method and quantification was measured by high performance liquid chromatography (HPLC). The half-lives (DT 50 ) of CAP were in the range of 41.0-53.0 days in the three soils. The results showed that CAP did not impart negative effects on MBC during the incubation. CAP inhibited BSR, qCO 2 , acid phosphatase and sucrose invertase activities in the first 14 days of incubation in all the soils. After day 14, the soil microbial parameters of CAP-treated soils became statistically at par with their controls. Principal component analysis (PCA) determining abundance of biomarker PLFAs indicated that the application of CAP significantly changed the compositions of microbial communities in all three paddy soils on day 14 but the compositions of soil microbial communities recovered by day 50. This study indicates that CAP does not ultimately impair microbial activities and microbial compositions of these three paddy soil types. Copyright © 2017 Elsevier Inc. All rights reserved.

Soil bacterial and fungal community responses to nitrogen addition across soil depth and microhabitat in an arid shrubland

USGS Publications Warehouse

Mueller, Rebecca C.; Belnap, Jayne; Kuske, Cheryl R.

2015-01-01

Arid shrublands are stressful environments, typified by alkaline soils low in organic matter, with biologically-limiting extremes in water availability, temperature, and UV radiation. The widely-spaced plants and interspace biological soil crusts in these regions provide soil nutrients in a localized fashion, creating a mosaic pattern of plant- or crust-associated microhabitats with distinct nutrient composition. With sporadic and limited rainfall, nutrients are primarily retained in the shallow surface soil, patterning biological activity. We examined soil bacterial and fungal community responses to simulated nitrogen (N) deposition in an arid Larrea tridentata-Ambrosia dumosa field experiment in southern Nevada, USA, using high-throughput sequencing of ribosomal RNA genes. To examine potential interactions among the N application, microhabitat and soil depth, we sampled soils associated with shrub canopies and interspace biological crusts at two soil depths (0–0.5 or 0–10 cm) across the N-amendment gradient (0, 7, and 15 kg ha−1 yr−1). We hypothesized that localized compositional differences in soil microbiota would constrain the impacts of N addition to a microhabitat distribution that would reflect highly localized geochemical conditions and microbial community composition. The richness and community composition of both bacterial and fungal communities differed significantly by microhabitat and with soil depth in each microhabitat. Only bacterial communities exhibited significant responses to the N addition. Community composition correlated with microhabitat and depth differences in soil geochemical features. Given the distinct roles of soil bacteria and fungi in major nutrient cycles, the resilience of fungi and sensitivity of bacteria to N amendments suggests that increased N input predicted for many arid ecosystems could shift nutrient cycling toward pathways driven primarily by fungal communities.

Soil mineral composition matters: response of microbial communities to phenanthrene and plant litter addition in long-term matured artificial soils.

PubMed

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications.

Soil Mineral Composition Matters: Response of Microbial Communities to Phenanthrene and Plant Litter Addition in Long-Term Matured Artificial Soils

PubMed Central

Babin, Doreen; Vogel, Cordula; Zühlke, Sebastian; Schloter, Michael; Pronk, Geertje Johanna; Heister, Katja; Spiteller, Michael; Kögel-Knabner, Ingrid; Smalla, Kornelia

2014-01-01

The fate of polycyclic aromatic hydrocarbons (PAHs) in soil is determined by a suite of biotic and abiotic factors, and disentangling their role in the complex soil interaction network remains challenging. Here, we investigate the influence of soil composition on the microbial community structure and its response to the spiked model PAH compound phenanthrene and plant litter. We used long-term matured artificial soils differing in type of clay mineral (illite, montmorillonite) and presence of charcoal or ferrihydrite. The soils received an identical soil microbial fraction and were incubated for more than two years with two sterile manure additions. The matured artificial soils and a natural soil were subjected to the following spiking treatments: (I) phenanthrene, (II) litter, (III) litter + phenanthrene, (IV) unspiked control. Total community DNA was extracted from soil sampled on the day of spiking, 7, 21, and 63 days after spiking. Bacterial 16S rRNA gene and fungal internal transcribed spacer amplicons were quantified by qPCR and subjected to denaturing gradient gel electrophoresis (DGGE). DGGE analysis revealed that the bacterial community composition, which was strongly shaped by clay minerals after more than two years of incubation, changed in response to spiked phenanthrene and added litter. DGGE and qPCR showed that soil composition significantly influenced the microbial response to spiking. While fungal communities responded only in presence of litter to phenanthrene spiking, the response of the bacterial communities to phenanthrene was less pronounced when litter was present. Interestingly, microbial communities in all artificial soils were more strongly affected by spiking than in the natural soil, which might indicate the importance of higher microbial diversity to compensate perturbations. This study showed the influence of soil composition on the microbiota and their response to phenanthrene and litter, which may increase our understanding of complex interactions in soils for bioremediation applications. PMID:25222697

Seasonal Variation in Soil Microbial Biomass, Bacterial Community Composition and Extracellular Enzyme Activity in Relation to Soil Respiration in a Northern Great Plains Grassland

NASA Astrophysics Data System (ADS)

Wilton, E.; Flanagan, L. B.

2014-12-01

Soil respiration rate is affected by seasonal changes in temperature and moisture, but is this a direct effect on soil metabolism or an indirect effect caused by changes in microbial biomass, bacterial community composition and substrate availability? In order to address this question, we compared continuous measurements of soil and plant CO2 exchange made with an automatic chamber system to analyses conducted on replicate soil samples collected on four dates during June-August. Microbial biomass was estimated from substrate-induced respiration rate, bacterial community composition was determined by 16S rRNA amplicon pyrosequencing, and β-1,4-N-acetylglucosaminidase (NAGase) and phenol oxidase enzyme activities were assayed fluorometrically or by absorbance measurements, respectively. Soil microbial biomass declined from June to August in strong correlation with a progressive decline in soil moisture during this time period. Soil bacterial species richness and alpha diversity showed no significant seasonal change. However, bacterial community composition showed a progressive shift over time as measured by Bray-Curtis dissimilarity. In particular, the change in community composition was associated with increasing relative abundance in the alpha and delta classes, and declining abundance of the beta and gamma classes of the Proteobacteria phylum during June-August. NAGase showed a progressive seasonal decline in potential activity that was correlated with microbial biomass and seasonal changes in soil moisture. In contrast, phenol oxidase showed highest potential activity in mid-July near the time of peak soil respiration and ecosystem photosynthesis, which may represent a time of high input of carbon exudates into the soil from plant roots. This input of exudates may stimulate the activity of phenol oxidase, a lignolytic enzyme involved in the breakdown of soil organic matter. These analyses indicated that seasonal change in soil respiration is a complex interaction between temporal changes in soil environmental factors and biological changes in the plant and microbial community that affect soil respiratory metabolism.

Influences of space, soil, nematodes and plants on microbial community composition of chalk grassland soils.

PubMed

Yergeau, Etienne; Bezemer, T Martijn; Hedlund, Katarina; Mortimer, Simon R; Kowalchuk, George A; Van Der Putten, Wim H

2010-08-01

Microbial communities respond to a variety of environmental factors related to resources (e.g. plant and soil organic matter), habitat (e.g. soil characteristics) and predation (e.g. nematodes, protozoa and viruses). However, the relative contribution of these factors on microbial community composition is poorly understood. Here, we sampled soils from 30 chalk grassland fields located in three different chalk hill ridges of Southern England, using a spatially explicit sampling scheme. We assessed microbial communities via phospholipid fatty acid (PLFA) analyses and PCR-denaturing gradient gel electrophoresis (DGGE) and measured soil characteristics, as well as nematode and plant community composition. The relative influences of space, soil, vegetation and nematodes on soil microorganisms were contrasted using variation partitioning and path analysis. Results indicate that soil characteristics and plant community composition, representing habitat and resources, shape soil microbial community composition, whereas the influence of nematodes, a potential predation factor, appears to be relatively small. Spatial variation in microbial community structure was detected at broad (between fields) and fine (within fields) scales, suggesting that microbial communities exhibit biogeographic patterns at different scales. Although our analysis included several relevant explanatory data sets, a large part of the variation in microbial communities remained unexplained (up to 92% in some analyses). However, in several analyses, significant parts of the variation in microbial community structure could be explained. The results of this study contribute to our understanding of the relative importance of different environmental and spatial factors in driving the composition of soil-borne microbial communities. © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Soil ecosystem functioning under climate change: plant species and community effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kardol, Paul; Cregger, Melissa; Campany, Courtney E

2010-01-01

Feedbacks of terrestrial ecosystems to climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering the microbial communities that feed on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and water availability. Specifically, we collected soils at the plot level (plant community soils), and beneathmore » dominant plant species (plant-specific soils). We used microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: 1) Overall, while there were some interactions, water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activities, and soil nematodes. Multiple climate change factors can interact to shape ecosystems, but in this case, those interactions were largely driven by changes in water availability. 2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning and this impact was not obvious when looking at plant community soils. Climate change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. In sum, these results indicate that accurate assessments of climate change impacts on soil ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate change-induced shifts in plant community composition will likely modify or counteract the direct impact of climate change on soil ecosystem functioning, and hence, these indirect effects should be taken into account when predicting how climate change will alter ecosystem functioning.« less

[Analysis of XRD spectral characteristics of soil clay mineral in two typical cultivated soils].

PubMed

Zhang, Zhi-Dan; Luo, Xiang-Li; Jiang, Hai-Chao; Li, Qiao; Shen, Cong-Ying; Liu, Hang; Zhou, Ya-Juan; Zhao, Lan-Po; Wang, Ji-Hong

2014-07-01

The present paper took black soil and chernozem, the typical cultivated soil in major grain producing area of Northeast, as the study object, and determinated the soil particle composition characteristics of two cultivated soils under the same climate and location. Then XRD was used to study the composition and difference of clay mineral in two kinds of soil and the evolutionary mechanism was explored. The results showed that the two kinds of soil particles were composed mainly of the sand, followed by clay and silt. When the particle accumulation rate reached 50%, the central particle size was in the 15-130 microm interval. Except for black soil profile of Shengli Xiang, the content of clay showed converse sequence to the central particle in two soils. Clay accumulated under upper layer (18.82%) in black soil profile while under caliche layer (17.41%) in chernozem profile. Clay content was the least in parent material horizon except in black profile of Quanyanling. Analysis of clay XRD atlas showed that the difference lied in not only the strength of diffraction peak, but also in the mineral composition. The main contents of black soil and chernozem were both 2 : 1 clay, the composition of black soil was smectite/illite mixed layer-illite-vermiculite and that of chernozem was S/I mixture-illite-montmorillonite, and both of them contained little kaolinite, chlorite, quartz and other primary mineral. This paper used XRD to determine the characteristics of clay minerals comprehensively, and analyzed two kinds of typical cultivated soil comparatively, and it was a new perspective of soil minerals study.

Understory growth and composition resulting from soil disturbances on the long-term soil productivity study sites in Mississippi

Treesearch

R.H. Stagg; D. Andrew Scott

2006-01-01

The response of understory plant communities to forest management can have important impacts on crop tree production, biodiversity, wildlife habitat, and water and nutrient cycling. Soil disturbance caused by harvesting and site preparation can alter soil fertility and porosity and may change understory species composition. At the Long-Term Soil Productivity study in...

Influence of Effluent Irrigation on Community Composition and Function of Ammonia-Oxidizing Bacteria in Soil

PubMed Central

Oved, Tamar; Shaviv, Avi; Goldrath, Tal; Mandelbaum, Raphi T.; Minz, Dror

2001-01-01

The effect of effluent irrigation on community composition and function of ammonia-oxidizing bacteria (AOB) in soil was evaluated, using techniques of molecular biology and analytical soil chemistry. Analyses were conducted on soil sampled from lysimeters and from a grapefruit orchard which had been irrigated with wastewater effluent or fertilizer-amended water (FAW). Specifically, comparisons of AOB community composition were conducted using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified fragments of the gene encoding the α-subunit of the ammonia monooxygenase gene (amoA) recovered from soil samples and subsequent sequencing of relevant bands. A significant and consistent shift in the population composition of AOB was detected in soil irrigated with effluent. This shift was absent in soils irrigated with FAW, despite the fact that the ammonium concentration in the FAW was similar. At the end of the irrigation period, Nitrosospira-like populations were dominant in soils irrigated with FAW, while Nitrosomonas-like populations were dominant in effluent-irrigated soils. Furthermore, DGGE analysis of the amoA gene proved to be a powerful tool in evaluating the soil AOB community population and population shifts therein. PMID:11472914

Apollo 15 clastic materials and their relationship to local geologic features

NASA Technical Reports Server (NTRS)

Fruchter, J. S.; Stoeser, J. W.; Lindstrom, M. M.; Goles, G. G.

1973-01-01

Ninety sub-samples of Apollo 15 materials have been analyzed by instrumental neutron activation analysis techniques for as many as 21 elements. Soil and soil breccia compositions show considerable variation from station to station although at any given station the soils and soil breccias were compositionally very similar to one another. Mixing model calculations show that the station-to-station variations can be related to important local geologic features. These features include the Apennine Front, Hadley Rille and the ray from the craters Aristillus or Autolycus. Compositional similarities between soils and soil breccias at the Apollo 15 site indicate that the breccias and soils are related in some fundamental way, although the exact nature of this relationship is not yet fully understood.

Alkanes as Components of Soil Hydrocarbon Status: Behavior and Indication Significance

NASA Astrophysics Data System (ADS)

Gennadiev, A. N.; Zavgorodnyaya, Yu. A.; Pikovskii, Yu. I.; Smirnova, M. A.

2018-01-01

Studies of soils on three key plots with different climatic conditions and technogenic impacts in Volgograd, Moscow, and Arkhangelsk oblasts have showed that alkanes in the soil exchange complex have some indication potential for the identification of soil processes. The following combinations of soil-forming factors and processes have been studied: (a) self-purification of soil after oil pollution; (b) accumulation of hydrocarbons coming from the atmosphere to soils of different land use patterns; and (c) changes in the soil hydrocarbon complex beyond the zone of technogenic impact due to the input of free hydrocarbon-containing gases. At the injection input of hydrocarbon pollutants, changes in the composition and proportions of alkanes allow tracing the degradation trend of pollutants in the soil from their initial content to the final stage of soil self-purification, when the background concentrations of hydrocarbons are reached. Upon atmospheric deposition of hydrocarbons onto the soil, from the composition and mass distribution of alkanes, conclusions can be drawn about the effect of toxicants on biogeochemical processes in the soil, including their manifestation under different land uses. Composition analysis of soil alkanes in natural landscapes can reveal signs of hydrocarbon emanation fluxes in soils. The indication potentials of alkanes in combination with polycyclic aromatic hydrocarbons and other components of soil hydrocarbon complex can also be used for the solution of other soil-geochemical problems.

[Composition and stability of soil aggregates in hedgerow-crop slope land].

PubMed

Pu, Yu-Lin; Lin, Chao-Wen; Xie, De-Ti; Wei, Chao-Fu; Ni, Jiu-Pai

2013-01-01

Based on a long-term experiment of using hedgerow to control soil and water loss, this paper studied the composition and stability of soil aggregates in a hedgerow-crop slope land. Compared with those under routine contour cropping, the contents of > 0.25 mm soil mechanical-stable and water-stable aggregates under the complex mode hedgerow-crop increased significantly by 13.3%-16.1% and 37.8% -55.6%, respectively. Under the complex mode, the contents of > 0.25 mm soil water-stable aggregates on each slope position increased obviously, and the status of > 0.25 mm soil water-stable aggregates being relatively rich at low slope and poor at top slope was improved. Planting hedgerow could significantly increase the mean mass diameter and geometric mean diameter of soil aggregates, decrease the fractal dimension of soil aggregates and the destruction rate of > 0.25 mm soil aggregates, and thus, increase the stability and erosion-resistance of soil aggregates in slope cropland. No significant effects of slope and hedgerow types were observed on the composition, stability and distribution of soil aggregates.

The soil microbial community composition and soil microbial carbon uptake are more affected by soil type than by different vegetation types (C3 and C4 plants) and seasonal changes

NASA Astrophysics Data System (ADS)

Griselle Mellado Vazquez, Perla; Lange, Markus; Gleixner, Gerd

2016-04-01

This study investigates the influence of different vegetation types (C3 and C4 plants), soil type and seasonal changes on the soil microbial biomass, soil microbial community composition and soil microbial carbon (C) uptake. We collected soil samples in winter (non-growing season) and summer (growing season) in 2012 from an experimental site cropping C3 and C4 plants for 6 years on two different soil types (sandy and clayey). The amount of phospholipid fatty acids (PLFAs) and their compound-specific δ13C values were used to determined microbial biomass and the flow of C from plants to soil microorganisms, respectively. Higher microbial biomass was found in the growing season. The microbial community composition was mainly explained by soil type. Higher amounts of SOC were driving the predominance of G+ bacteria, actinobacteria and cyclic G- bacteria in sandy soils, whereas root biomass was significantly related to the increased proportions of G- bacteria in clayey soils. Plant-derived C in G- bacteria increased significantly in clayey soils in the growing season. This increase was positively and significantly driven by root biomass. Moreover, changes in plant-derived C among microbial groups pointed to specific capabilities of different microbial groups to decompose distinct sources of C. We concluded that soil texture and favorable growth conditions driven by rhizosphere interactions are the most important factors controlling the soil microbial community. Our results demonstrate that a change of C3 plants vs. C4 plants has only a minor effect on the soil microbial community. Thus, such experiments are well suited to investigate soil organic matter dynamics as they allow to trace the C flow from plants into the soil microbial community without changing the community abundance and composition.

Essentials of Chemical Fertilizer Use in PRC.

DTIC Science & Technology

1978-09-06

fertilizer contains even more effective nutrient. So proper amounts of chemical fertilizer in each mou in addition to farmyard manure, according to soil ...learn about soil composition and characteristics and their effect on fertilizing power. Composition and Function of Soil The soil is composed of matter...fertilizing effect is still good. Sandy soil has low water-retaining capability, so nutrients are easily leached. When easily-soluble fast- release

Effects of heavy metals on soil microbial community

NASA Astrophysics Data System (ADS)

Chu, Dian

2018-02-01

Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

Soil Fauna Alter the Effects of Litter Composition on Nitrogen Cycling in a Mineral Soil

EPA Science Inventory

Plant chemical composition and the soil community are known to influence litter and soil organic matter decomposition. Although these two factors are likely to interact, their mechanisms and outcomes of interaction are not well understood. Studies of their interactive effects are...

Soil moisture effects on the carbon isotopic composition of soil respiration

EPA Science Inventory

The carbon isotopic composition ( 13C) of recently assimilated plant carbon is known to depend on water-stress, caused either by low soil moisture or by low atmospheric humidity. Air humidity has also been shown to correlate with the 13C of soil respiration, which suggests indir...

Soil bacterial community response to vegetation succession after fencing in the grassland of China.

PubMed

Zeng, Quanchao; An, Shaoshan; Liu, Yang

2017-12-31

Natural succession is an important process in terrestrial system, playing an important role in enhancing soil quality and plant diversity. Soil bacteria is the linkage between soil and plant, has an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems, driving the decomposition of soil organic matter and plant litter. However, the role of soil bacteria in the secondary succession has not been well understood, particularly in the degraded soil of Loess Plateau. In this study, we investigated soil nutrients and soil bacterial community during the secondary succession after a long-term fencing in the grassland, in the Yuwu Mountain, northwest China. The chronosequence included 1year, 12years, 20years and 30years. The soil bacterial community composition was determined by the Illumina HiSeq sequencing method. The data showed that soil bacterial diversity had no significant changes along the chronosequence, but soil bacterial community compositions significantly changed. Proteobacteria, Acidobacteria and Actinobacteria were the main phyla in all the samples across succession. With the accumulation of soil organic matter and nutrients, the relative abundance of Actinobacteria decreased, whereas Proteobacteria increased. These shifts may be caused by the increase of the available nutrients across the secondary succession. In the younger sites, soils were dominated by oligotrophic groups, whereas soil in the late-succession site were dominated by copiotrophic groups, indicating the dependence of soil bacterial community composition on the contents of soil available nutrients. Copyright © 2017 Elsevier B.V. All rights reserved.

Long-term variation in above and belowground plant inputs alters soil organic matter biogeochemistry at the molecular-level

NASA Astrophysics Data System (ADS)

Simpson, M. J.; Pisani, O.; Lin, L.; Lun, O.; Simpson, A.; Lajtha, K.; Nadelhoffer, K. J.

2015-12-01

The long-term fate of soil carbon reserves with global environmental change remains uncertain. Shifts in moisture, altered nutrient cycles, species composition, or rising temperatures may alter the proportions of above and belowground biomass entering soil. However, it is unclear how long-term changes in plant inputs may alter the composition of soil organic matter (SOM) and soil carbon storage. Advanced molecular techniques were used to assess SOM composition in mineral soil horizons (0-10 cm) after 20 years of Detrital Input and Removal Treatment (DIRT) at the Harvard Forest. SOM biomarkers (solvent extraction, base hydrolysis and cupric (II) oxide oxidation) and both solid-state and solution-state nuclear magnetic resonance (NMR) spectroscopy were used to identify changes in SOM composition and stage of degradation. Microbial activity and community composition were assessed using phospholipid fatty acid (PLFA) analysis. Doubling aboveground litter inputs decreased soil carbon content, increased the degradation of labile SOM and enhanced the sequestration of aliphatic compounds in soil. The exclusion of belowground inputs (No roots and No inputs) resulted in a decrease in root-derived components and enhanced the degradation of leaf-derived aliphatic structures (cutin). Cutin-derived SOM has been hypothesized to be recalcitrant but our results show that even this complex biopolymer is susceptible to degradation when inputs entering soil are altered. The PLFA data indicate that changes in soil microbial community structure favored the accelerated processing of specific SOM components with littler manipulation. These results collectively reveal that the quantity and quality of plant litter inputs alters the molecular-level composition of SOM and in some cases, enhances the degradation of recalcitrant SOM. Our study also suggests that increased litterfall is unlikely to enhance soil carbon storage over the long-term in temperate forests.

Correspondence and Least Squares Analyses of Soil and Rock Compositions for the Viking Lander 1 and Pathfinder Sites

NASA Technical Reports Server (NTRS)

Larsen, K. W.; Arvidson, R. E.; Jolliff, B. L.; Clark, B. C.

2000-01-01

Correspondence and Least Squares Mixing Analysis techniques are applied to the chemical composition of Viking 1 soils and Pathfinder rocks and soils. Implications for the parent composition of local and global materials are discussed.

Partitioning the relative contributions of inorganic plant composition and soil characteristics to the quality of Helichrysum italicum subsp. italicum (Roth) G. Don fil. essential oil.

PubMed

Bianchini, Ange; Santoni, François; Paolini, Julien; Bernardini, Antoine-François; Mouillot, David; Costa, Jean

2009-07-01

Composition of Helichrysum italicum subsp. italicum essential oil showed chemical variability according to vegetation cycle, environment, and geographic origins. In the present work, 48 individuals of this plant at different development stages and the corresponding root soils were sampled: i) 28 volatile components were identified and measured in essential oil by using GC and GC/MS; ii) ten elements from plants and soils have been estimated using colorimetry in continuous flux, flame atomic absorption spectrometry, or emission spectrometry (FAAS/FAES); iii) texture and acidity (real and potential) of soil samples were also reported. Relationships between the essential-oil composition, the inorganic plant composition, and the soil characteristics (inorganic composition, texture, and acidity) have been established using multivariate analysis such as Principal Component Analysis (PCA) and partial Redundancy Analysis (RDA). This study demonstrates a high level of intraspecific differences in oil composition due to environmental factors and, more particularly, soil characteristics.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing.

PubMed

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-09

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing's built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

NASA Astrophysics Data System (ADS)

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-01

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Community composition of ammonia-oxidizing bacteria and archaea in rice field soil as affected by nitrogen fertilization.

PubMed

Wang, Yanan; Ke, Xiubin; Wu, Liqin; Lu, Yahai

2009-02-01

Little information is available on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in flooded rice soils. Consequently, a microcosm experiment was conducted to determine the effect of nitrogen fertilizer on the composition of AOB and AOA communities in rice soil by using molecular analyses of ammonia monooxygenase gene (amoA) fragments. Experimental treatments included three levels of N (urea) fertilizer, i.e. 50, 100 and 150 mgNkg(-1) soil. Soil samples were operationally divided into four fractions: surface soil, bulk soil deep layer, rhizosphere and washed root material. NH(4)(+)-N was the dominant form of N in soil porewater and increased with N fertilization. Cloning and sequencing of amoA gene fragments showed that the AOB community in the rice soil consisted of three major groups, i.e. Nitrosomonas communis cluster, Nitrosospira cluster 3a and cluster 3b. The sequences related to Nitrosomonas were predominant. There was a clear effect of N fertilizer and soil depth on AOB community composition based on terminal restriction fragment length polymorphism fingerprinting. Nitrosomonas appeared to be more abundant in the potentially oxic or micro-oxic fractions, including surface soil, rhizosphere and washed root material, than the deep layer of anoxic bulk soil. Furthermore, Nitrosomonas increased relatively in the partially oxic fractions and that of Nitrosospira decreased with the increasing application of N fertilizer. However, AOA community composition remained unchanged according to the denaturing gradient gel electrophoresis analyses.

Sources and Practices Contributing to Soil Contamination

Treesearch

A.S. Knox; A.P. Gamerdinger; D.C. Adriano; R.K. Kolka; D.I. Kaplan

1999-01-01

The term soil contamination can have different connotations because anthropogehic sources of contaminants have affected virtually every natural ecosystem in the world; a commonly held view is that contamination occurs when the soil composition deiiates from the normal composition (Adriano et al., 1997). Other specialists have defined soil pollution as the presence of...

Rapid recovery of soil bacterial communities after wildfire in a Chinese boreal forest

PubMed Central

Xiang, Xingjia; Shi, Yu; Yang, Jian; Kong, Jianjian; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Chu, Haiyan

2014-01-01

Fires affect hundreds of millions of hectares annually. Above-ground community composition and diversity after fire have been studied extensively, but effects of fire on soil bacterial communities remain largely unexamined despite the central role of bacteria in ecosystem recovery and functioning. We investigated responses of bacterial community to forest fire in the Greater Khingan Mountains, China, using tagged pyrosequencing. Fire altered soil bacterial community composition substantially and high-intensity fire significantly decreased bacterial diversity 1-year-after-burn site. Bacterial community composition and diversity returned to similar levels as observed in controls (no fire) after 11 years. The understory vegetation community typically takes 20–100 years to reach pre-fire states in boreal forest, so our results suggest that soil bacteria could recover much faster than plant communities. Finally, soil bacterial community composition significantly co-varied with soil pH, moisture content, NH4+ content and carbon/nitrogen ratio (P < 0.05 in all cases) in wildfire-perturbed soils, suggesting that fire could indirectly affect bacterial communities by altering soil edaphic properties. PMID:24452061

Effect of Metal Oxide Nanoparticles on Microbial Community Structure and Function in Two Different Soil Types

PubMed Central

Frenk, Sammy; Ben-Moshe, Tal; Dror, Ishai; Berkowitz, Brian; Minz, Dror

2013-01-01

Increased availability of nanoparticle-based products will, inevitably, expose the environment to these materials. Engineered nanoparticles (ENPs) may thus find their way into the soil environment via wastewater, dumpsters and other anthropogenic sources; metallic oxide nanoparticles comprise one group of ENPs that could potentially be hazardous for the environment. Because the soil bacterial community is a major service provider for the ecosystem and humankind, it is critical to study the effects of ENP exposure on soil bacteria. These effects were evaluated by measuring bacterial community activity, composition and size following exposure to copper oxide (CuO) and magnetite (Fe3O4) nanosized (<50 nm) particles. Two different soil types were examined: a sandy loam (Bet-Dagan) and a sandy clay loam (Yatir), under two ENP concentrations (1%, 0.1%). Results indicate that the bacterial community in Bet-Dagan soil was more susceptible to change due to exposure to these ENPs, relative to Yatir soil. More specifically, CuO had a strong effect on bacterial hydrolytic activity, oxidative potential, community composition and size in Bet-Dagan soil. Few effects were noted in the Yatir soil, although 1% CuO exposure did cause a significant decreased oxidative potential and changes to community composition. Fe3O4 changed the hydrolytic activity and bacterial community composition in Bet-Dagan soil but did not affect the Yatir soil bacterial community. Furthermore, in Bet-Dagan soil, abundance of bacteria annotated to OTUs from the Bacilli class decreased after addition of 0.1% CuO but increased with 1% CuO, while in Yatir soil their abundance was reduced with 1% CuO. Other important soil bacterial groups, including Rhizobiales and Sphingobacteriaceae, were negatively affected by CuO addition to soil. These results indicate that both ENPs are potentially harmful to soil environments. Furthermore, it is suggested that the clay fraction and organic matter in different soils interact with the ENPs and reduce their toxicity. PMID:24349575

Application of DRIFTS, 13 C NMR, and py-MBMS to Characterize the Effects of Soil Science Oxidation Assays on Soil Organic Matter Composition in a Mollic Xerofluvent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Margenot, Andrew J.; Calderón, Francisco J.; Magrini, Kimberly A.

Chemical oxidations are routinely employed in soil science to study soil organic matter (SOM), and their interpretation could be improved by characterizing oxidation effects on SOM composition with spectroscopy. We investigated the effects of routinely employed oxidants on SOM composition in a Mollic Xerofluvent representative of intensively managed agricultural soils in the California Central Valley. Soil samples were subjected to oxidation by potassium permanganate (KMnO4), sodium hypochlorite (NaOCl), and hydrogen peroxide (H2O2). Additionally, non-oxidized and oxidized soils were treated with hydrofluoric acid (HF) to evaluate reduction of the mineral component to improve spectroscopy of oxidation effects. Oxidized non-HF and HF-treatedmore » soils were characterized by diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), 13C cross polarization magic angle spinning (CP-MAS) nuclear magnetic resonance (NMR) spectroscopy, and pyrolysis molecular beam mass spectrometry (py-MBMS), and for particle size distribution (PSD) using laser diffractometry (LD). Across the range of soil organic carbon (OC) removed by oxidations (14-72%), aliphatic C-H stretch at 3000-2800 cm-1 (DRIFTS) decreased with OC removal, and this trend was enhanced by HF treatment due to significant demineralization in this soil (70%). Analysis by NMR spectroscopy was feasible only after HF treatment, and did not reveal trends between OC removal and C functional groups. Pyrolysis-MBMS did not detect differences among oxidations, even after HF treatment of soils. Hydrofluoric acid entailed OC loss (13-39%), and for H2O2 oxidized soils increased C:N and substantially decreased mean particle size. This study demonstrates the feasibility of using HF to improve characterizations of SOM composition following oxidations as practiced in soil science, in particular for DRIFTS. Since OC removal by oxidants, mineral removal by HF, and the interaction of oxidants and HF observed for this soil may differ for soils with different mineralogies, future work should examine additional soil and land use types to optimize characterizations of oxidation effects on SOM composition.« less

Relative Roles of Soil Moisture, Nutrient Supply, Depth, and Mechanical Impedance in Determining Composition and Structure of Wisconsin Prairies

PubMed Central

Wernerehl, Robert W.; Givnish, Thomas J.

2015-01-01

Ecologists have long classified Midwestern prairies based on compositional variation assumed to reflect local gradients in moisture availability. The best known classification is based on Curtis’ continuum index (CI), calculated using the presence of indicator species thought centered on different portions of an underlying moisture gradient. Direct evidence of the extent to which CI reflects differences in moisture availability has been lacking, however. Many factors that increase moisture availability (e.g., soil depth, silt content) also increase nutrient supply and decrease soil mechanical impedance; the ecological effects of the last have rarely been considered in any ecosystem. Decreased soil mechanical impedance should increase the availability of soil moisture and nutrients by reducing the root costs of retrieving both. Here we assess the relative importance of soil moisture, nutrient supply, and mechanical impedance in determining prairie composition and structure. We used leaf δ13C of C3 plants as a measure of growing-season moisture availability, cation exchange capacity (CEC) x soil depth as a measure of mineral nutrient availability, and penetrometer data as a measure of soil mechanical impedance. Community composition and structure were assessed in 17 remnant prairies in Wisconsin which vary little in annual precipitation. Ordination and regression analyses showed that δ13C increased with CI toward “drier” sites, and decreased with soil depth and % silt content. Variation in δ13C among remnants was 2.0‰, comparable to that along continental gradients from ca. 500–1500 mm annual rainfall. As predicted, LAI and average leaf height increased significantly toward “wetter” sites. CI accounted for 54% of compositional variance but δ13C accounted for only 6.2%, despite the strong relationships of δ13C to CI and CI to composition. Compositional variation reflects soil fertility and mechanical impedance more than moisture availability. This study is the first to quantify the effects of soil mechanical impedance on community ecology. PMID:26368936

Relative Roles of Soil Moisture, Nutrient Supply, Depth, and Mechanical Impedance in Determining Composition and Structure of Wisconsin Prairies.

PubMed

Wernerehl, Robert W; Givnish, Thomas J

2015-01-01

Ecologists have long classified Midwestern prairies based on compositional variation assumed to reflect local gradients in moisture availability. The best known classification is based on Curtis' continuum index (CI), calculated using the presence of indicator species thought centered on different portions of an underlying moisture gradient. Direct evidence of the extent to which CI reflects differences in moisture availability has been lacking, however. Many factors that increase moisture availability (e.g., soil depth, silt content) also increase nutrient supply and decrease soil mechanical impedance; the ecological effects of the last have rarely been considered in any ecosystem. Decreased soil mechanical impedance should increase the availability of soil moisture and nutrients by reducing the root costs of retrieving both. Here we assess the relative importance of soil moisture, nutrient supply, and mechanical impedance in determining prairie composition and structure. We used leaf δ13C of C3 plants as a measure of growing-season moisture availability, cation exchange capacity (CEC) x soil depth as a measure of mineral nutrient availability, and penetrometer data as a measure of soil mechanical impedance. Community composition and structure were assessed in 17 remnant prairies in Wisconsin which vary little in annual precipitation. Ordination and regression analyses showed that δ13C increased with CI toward "drier" sites, and decreased with soil depth and % silt content. Variation in δ13C among remnants was 2.0‰, comparable to that along continental gradients from ca. 500-1500 mm annual rainfall. As predicted, LAI and average leaf height increased significantly toward "wetter" sites. CI accounted for 54% of compositional variance but δ13C accounted for only 6.2%, despite the strong relationships of δ13C to CI and CI to composition. Compositional variation reflects soil fertility and mechanical impedance more than moisture availability. This study is the first to quantify the effects of soil mechanical impedance on community ecology.

Alterations in soil microbial community composition and biomass following agricultural land use change.

PubMed

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-04

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Alterations in soil microbial community composition and biomass following agricultural land use change

NASA Astrophysics Data System (ADS)

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-01

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

PubMed Central

Turner, Stephanie; Mikutta, Robert; Meyer-Stüve, Sandra; Guggenberger, Georg; Schaarschmidt, Frank; Lazar, Cassandre S.; Dohrmann, Reiner; Schippers, Axel

2017-01-01

Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR) and community composition (pyrosequencing) as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand). Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate), O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR) and community patterns (T-RFLP) were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to subsoil conditions, especially in nutrient-depleted old soils. PMID:28579976

Roles of Arbuscular Mycorrhizal Fungi and Soil Abiotic Conditions in the Establishment of a Dry Grassland Community.

PubMed

Knappová, Jana; Pánková, Hana; Münzbergová, Zuzana

2016-01-01

The importance of soil biota in the composition of mature plant communities is commonly acknowledged. In contrast, the role of soil biota in the early establishment of new plant communities and their relative importance for soil abiotic conditions are still poorly understood. The aim of this study was to understand the effects of soil origin and soil fungal communities on the composition of a newly established dry grassland plant community. We used soil from two different origins (dry grassland and abandoned field) with different pH and nutrient and mineral content. Grassland microcosms were established by sowing seeds of 54 species of dry grassland plants into the studied soils. To suppress soil fungi, half of the pots were regularly treated with fungicide. In this way, we studied the independent and combined effects of soil origin and soil community on the establishment of dry grassland communities. The effect of suppressing the soil fungal community on the richness and composition of the plant communities was much stronger than the effect of soil origin. Contrary to our expectations, the effects of these two factors were largely additive, indicating the same degree of importance of soil fungal communities in the establishment of species-rich plant communities in the soils from both origins. The negative effect of suppressing soil fungi on species richness, however, occurred later in the soil from the abandoned field than in the soil from the grassland. This result likely occurred because the negative effects of the suppression of fungi in the field soil were caused mainly by changes in plant community composition and increased competition. In contrast, in the grassland soil, the absence of soil fungi was limiting for plants already at the early stages of their establishment, i.e., in the phases of germination and early recruitment. While fungicide affects not only arbuscular mycorrhizal fungi but also other biota, our data indicate that changes in the AMF communities are the most likely drivers of the observed changes. The effects of other soil biota, however, cannot be fully excluded. These results suggest that the availability of soil fungi may not be the most important limiting factor for the establishment of grassland species in abandoned fields if we manage to reduce the intensity of competition at these sites e.g., by mowing or grazing.

Soil moisture effects on the carbon isotope composition of soil respiration

Treesearch

Claire L. Phillips; Nick Nickerson; David Risk; Zachary E. Kayler; Chris Andersen; Alan Mix; Barbara J. Bond

2010-01-01

The carbon isotopic composition (δ13C) of recently assimilated plant carbon is known to depend on water-stress, caused either by low soil moisture or by low atmospheric humidity. Air humidity has also been shown to correlate with the δ13C of soil respiration, which suggests indirectly that recently fixed photosynthates...

Fungal community composition and diversity vary with soil depths and landscape position in a no-till wheat cropping system.

USDA-ARS?s Scientific Manuscript database

Fungal communities in soil are critical to plant health and ecosystem processes in agricultural systems. Although the composition of fungal communities is often related to soil edaphic characteristic and host plant identity, there is a paucity of information on how communities vary with soil depth a...

Soil macrofauna webmasters of ecosystem

NASA Astrophysics Data System (ADS)

Frouz, Jan

2015-04-01

The role of plant roots and microflora in shaping many ecosystem processes is generally appreciated in the contrary rho role of soil mcrofauna in this context is assumed to be negligible and rather anecdotic. But more than half of the litter fall is consumed by soil fauna and soil fauna can also consume and or translocation substantial amount of soil. Here we demonstrate on example of post mining chronosequences how site colonization by soil fauna affect composition of whole soil biota community, plant succession and soil formation. Filed and laboratory experiments show that decomposition of fauna feces may be sped up compare to litter at the very beginning but in long term fauna feces decompose slower than litter. This is also supported by micro morphological observation which shows that fauna feces form substantial part of soil. Fauna feces also induce lover or even negative priming effect when introduced in soil in comparison with litter that triggers positive priming effect. Laboratory experiment show that fauna effect is context sensitive and is more pronounced in systems already affected by soil fauna. Soil mixing by soil fauna consequently affect environmental conditions in soils such as water holding capacity or nutrient availability, it also affect composition of decomposer food web including microbial community (fungal bacterial ratio) which feed back in alternation of plant community composition during succession This fauna activity is not constant everywhere the higher effect of fauna activity on litter layer was observed in temperate soils of deciduous forests and with litter having CN between 20-30. In conclusion soil fauna use directly only small proportion of energy in the litter but can substantially affect soil carbon turnover, soil formation, decomposer food web and plant community.

Impact of biological soil crusts and desert plants on soil microfaunal community composition

USGS Publications Warehouse

Darby, B.J.; Neher, D.A.; Belnap, J.

2010-01-01

Carbon and nitrogen are supplied by a variety of sources in the desert food web; both vascular and non-vascular plants and cyanobacteria supply carbon, and cyanobacteria and plant-associated rhizosphere bacteria are sources of biological nitrogen fixation. The objective of this study was to compare the relative influence of vascular plants and biological soil crusts on desert soil nematode and protozoan abundance and community composition. In the first experiment, biological soil crusts were removed by physical trampling. Treatments with crust removed had fewer nematodes and a greater relative ratio of bacterivores to microphytophages than treatments with intact crust. However, protozoa composition was similar with or without the presence of crusts. In a second experiment, nematode community composition was characterized along a spatial gradient away from stems of grasses or shrubs. Although nematodes generally occurred in increasing abundance nearer to plant stems, some genera (such as the enrichment-type Panagrolaimus) increased disproportionately more than others (such as the stress-tolerant Acromoldavicus). We propose that the impact of biological soil crusts and desert plants on soil microfauna, as reflected in the community composition of microbivorous nematodes, is a combination of carbon input, microclimate amelioration, and altered soil hydrology. ?? Springer Science + Business Media B.V. 2009.

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

PubMed

Barberán, Albert; McGuire, Krista L; Wolf, Jeffrey A; Jones, F Andrew; Wright, Stuart Joseph; Turner, Benjamin L; Essene, Adam; Hubbell, Stephen P; Faircloth, Brant C; Fierer, Noah

2015-12-01

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. © 2015 John Wiley & Sons Ltd/CNRS.

Composite Behavior of Geosynthetic Reinforced Soil Mass

DOT National Transportation Integrated Search

2013-07-01

This study investigated the composite behavior of a geosynthetic reinforced soil (GRS) mass. Many studies have been conducted on the behavior of GRS structures; however, the interactive behavior between the soil and geosynthetic reinforcement in a GR...

Identification of Cellulose-Responsive Bacterial and Fungal Communities in Geographically and Edaphically Different Soils by Using Stable Isotope Probing

PubMed Central

Eichorst, Stephanie A.

2012-01-01

Many bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [13C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the 13C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or 12C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of the Burkholderiales, Caulobacteriales, Rhizobiales, Sphingobacteriales, Xanthomonadales, and the subdivision 1 Acidobacteria were prevalent in the 13C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of the Trichocladium, Chaetomium, Dactylaria, and Arthrobotrys genera, along with two novel Ascomycota clusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community. PMID:22287013

Divergent composition but similar function of soil food webs of individual plants: plant species and community effects.

PubMed

Bezemer, T M; Fountain, M T; Barea, J M; Christensen, S; Dekker, S C; Duyts, H; van Hal, R; Harvey, J A; Hedlund, K; Maraun, M; Mikola, J; Mladenov, A G; Robin, C; de Ruiter, P C; Scheu, S; Setälä, H; Smilauer, P; van der Putten, W H

2010-10-01

Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon mineralization or food web stability. Hence, the composition and structure of entire soil food webs vary at the scale of individual plants and are strongly influenced by the species identity of the plant. However, the ecosystem functions these food webs provide are determined by the identity of the entire plant community.

Plant-soil-microbe interactions regulating soil C storage

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.

2016-12-01

Integration across disciplines is required to identify the emergent microbial scale properties that regulate the release or occlusion of plant inputs in soil organic matter. To investigate how micro-scale processes influence soil carbon cycling, we measured microbial community composition and activity within soil aggregates monthly over two growing seasons of a long-term bioenergy field experiment. Using a biologically sensitive sieving technique, soil aggregates were isolated and microbial community activity and composition were measured. This aggregate approach revealed biogeochemical processes regulating C cycling that are not detected using whole soil approaches. Soil aggregation influenced microbe-substrate interactions, where diversified perennial grassland systems supported greater aggregation and reduced severity of aggregate turnover compared to corn systems. Aggregate turnover and concurrent increases in activity resulted in greater microbial biomass and physical protection of soil organic matter in prairie systems, especially fertilized prairies. Fertilized prairie enhanced microbial biomass, enzyme activity, and soil aggregation despite greater root biomass in unfertilized prairie. Independent of ecosystem or sampling date, N-acetyl-glucosaminidase activity and Nitrospirae abundance was greatest in large macroaggregates (>2000 µm), which harbored the highest C:N; cellobiohydrolase activity and Acidobacteria abundance was greatest in microaggregates (<250 µm) which had the lowest C:N. Aggregate fractions differed in microbial community composition (bacteria, archaea, and fungi) and potential enzyme activity, independent of cropping system. Microaggregates harbored significantly greater microbial diversity and richness across all bioenergy cropping systems. Together these results suggest that by mediating access to substrates, soil structure (aggregates) can influence the microbial community composition and extracellular enzyme activity to regulate ecosystem scale decomposition of soil organic matter.

Predator community composition is linked to soil carbon retention across a human land use gradient.

PubMed

Schmitz, Oswald J; Buchkowski, Robert W; Smith, Jeffrey R; Telthorst, Mark; Rosenblatt, Adam E

2017-05-01

Soil carbon (C) storage is a major component of the carbon cycle. Consensus holds that soil C uptake and storage is regulated by plant-microbe-soil interactions. However, the contribution of animals in aboveground food webs to this process has been overlooked. Using insights from prior long-term experimentation in an old-field ecosystem and mathematical modeling, we predicted that the amount of soil C retention within a field should increase with the proportion of active hunting predators comprising the aboveground community of active hunting and sit-and-wait predators. This comes about because predators with different hunting modes have different cascading effects on plants. Our test of the prediction revealed that the composition of the arthropod predator community and associated cascading effects on the plant community explained 41% of variation in soil C retention among 15 old fields across a human land use gradient. We also evaluated the potential for several other candidate factors to explain variation in soil C retention among fields, independent of among-field variation in the predator community. These included live plant biomass, insect herbivore community composition, soil arthropod decomposer community composition, degree of land use development around the fields, field age, and soil texture. None of these candidate variables significantly explained soil C retention among the fields. The study offers a generalizable understanding of the pathways through which arthropod predator community composition can contribute to old-field ecosystem carbon storage. This insight helps support ongoing efforts to understand and manage the effects of anthropogenic land use change on soil C storage. © 2017 by the Ecological Society of America.

Effects of 10-year management regimes on the soil seed bank in saline-alkaline grassland.

PubMed

Ma, Hongyuan; Yang, Haoyu; Liang, Zhengwei; Ooi, Mark K J

2015-01-01

Management regimes for vegetation restoration of degraded grasslands can significantly affect the process of ecological succession. However, few studies have focused on variation in the soil seed bank during vegetation restoration under different management regimes, especially in saline-alkaline grassland habitats. Our aim was to provide insights into the ecological effects of grassland management regimes on soil seed bank composition and vegetation establishment in mown, fenced, transplanted and natural grassland sites, all dominated by the perennial rhizomatous grass Leymus chinensis. We studied species composition and diversity in both the soil seed bank and aboveground vegetation in differently managed grasslands in Northeast China. An NMDS (nonmetric multidimensional scaling) was used to evaluate the relationship between species composition, soil seed banks, aboveground vegetation and soil properties. Fenced and mown grassland sites had high density and species richness in both the soil seed bank and aboveground vegetation. The Transplanted treatment exhibited the highest vegetation growth and seed production of the target species L. chinensis. Seeds of L. chinensis in the soil occurred only in transplanted and natural grassland. Based on the NMDS analysis, the number of species in both the soil seed bank and aboveground vegetation were significantly related to soil Na+, Cl-, RSC (residual sodium carbonate), alkalinity, ESP (exchangeable sodium percentage) and AP (available phosphorus). Soil seed bank composition and diversity in the saline-alkaline grassland were significantly affected by the management regimes implemented, and were also significantly related to the aboveground vegetation and several soil properties. Based on vegetative growth, reproductive output and maintenance of soil seed bank, the transplanting was identified as the most effective method for relatively rapid restoration of the target species L. chinensis. This approach could be beneficial for the restoration of dominant species in a wide range of degraded grassland ecosystems.

Changes in ectomycorrhizal fungal community composition and declining diversity along a 2-million-year soil chronosequence.

PubMed

Albornoz, Felipe E; Teste, François P; Lambers, Hans; Bunce, Michael; Murray, Dáithí C; White, Nicole E; Laliberté, Etienne

2016-10-01

Ectomycorrhizal (ECM) fungal communities covary with host plant communities along soil fertility gradients, yet it is unclear whether this reflects changes in host composition, fungal edaphic specialization or priority effects during fungal community establishment. We grew two co-occurring ECM plant species (to control for host identity) in soils collected along a 2-million-year chronosequence representing a strong soil fertility gradient and used soil manipulations to disentangle the effects of edaphic properties from those due to fungal inoculum. Ectomycorrhizal fungal community composition changed and richness declined with increasing soil age; these changes were linked to pedogenesis-driven shifts in edaphic properties, particularly pH and resin-exchangeable and organic phosphorus. However, when differences in inoculum potential or soil abiotic properties among soil ages were removed while host identity was held constant, differences in ECM fungal communities and richness among chronosequence stages disappeared. Our results show that ECM fungal communities strongly vary during long-term ecosystem development, even within the same hosts. However, these changes could not be attributed to short-term fungal edaphic specialization or differences in fungal inoculum (i.e. density and composition) alone. Rather, they must reflect longer-term ecosystem-level feedback between soil, vegetation and ECM fungi during pedogenesis. © 2016 John Wiley & Sons Ltd.

Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China

NASA Astrophysics Data System (ADS)

Ren, Chengjie; Sun, Pingsheng; Kang, Di; Zhao, Fazhu; Feng, Yongzhong; Ren, Guangxin; Han, Xinhui; Yang, Gaihe

2016-06-01

In the present paper, we investigated the effects of afforestation on nitrogen fractions and microbial communities. A total of 24 soil samples were collected from farmland (FL) and three afforested lands, namely Robinia pseudoacacia L (RP), Caragana korshinskii Kom (CK), and abandoned land (AL), which have been arable for the past 40 years. Quantitative PCR and Illumina sequencing of 16S rRNA genes were used to analyze soil bacterial abundance, diversity, and composition. Additionally, soil nitrogen (N) stocks and fractions were estimated. The results showed that soil N stock, N fractions, and bacterial abundance and diversity increased following afforestation. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant phyla of soil bacterial compositions. Overall, soil bacterial compositions generally changed from Actinobacteria (Acidobacteria)-dominant to Proteobacteria-dominant following afforestation. Soil N fractions, especially for dissolved organic nitrogen (DON), were significantly correlated with most bacterial groups and bacterial diversity, while potential competitive interactions between Proteobacteria (order Rhizobiales) and Cyanobacteria were suggested. In contrast, nitrate nitrogen (NO3--N) influenced soil bacterial compositions less than other N fractions. Therefore, the present study demonstrated that bacterial diversity and specific species respond to farmland-to-forest conversion and hence have the potential to affect N dynamic processes in the Loess Plateau.

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity.

PubMed

Sun, Bingjie; Jia, Shuxia; Zhang, Shixiu; McLaughlin, Neil B; Liang, Aizhen; Chen, Xuewen; Liu, Siyi; Zhang, Xiaoping

2016-04-01

Soil microbial community can vary with different agricultural managements, which in turn can affect soil quality. The objective of this work was to evaluate the effects of long-term tillage practice (no tillage (NT) and conventional tillage (CT)) and crop rotation (maize-soybean (MS) rotation and monoculture maize (MM)) on soil microbial community composition and metabolic capacity in different soil layers. Long-term NT increased the soil organic carbon (SOC) and total nitrogen (TN) mainly at the 0-5 cm depth which was accompanied with a greater microbial abundance. The greater fungi-to-bacteria (F/B) ratio was found in NTMS at the 0-5 cm depth. Both tillage and crop rotation had a significant effect on the metabolic activity, with the greatest average well color development (AWCD) value in NTMS soil at all three soil depths. Redundancy analysis (RDA) showed that the shift in microbial community composition was accompanied with the changes in capacity of utilizing different carbon substrates. Therefore, no tillage combined with crop rotation could improve soil biological quality and make agricultural systems more sustainable.

[Humus composition and stable carbon isotope natural abundance in paddy soil under long-term fertilization].

PubMed

Ma, Li; Yang, Lin-Zhang; Ci, En; Wang, Yan; Yin, Shi-Xue; Shen, Ming-Xing

2008-09-01

Soil samples were collected from an experimental paddy field with long-term (26 years) fertilization in Taihu Lake region of Jiangsu Province to study the effects of different fertilization on the organic carbon distribution and stable carbon isotope natural abundance (delta 13C) in the soil profile, and on the humus composition. The results showed that long-term fertilization increased the organic carbon content in top soil significantly, and there was a significantly negative exponential correlation between soil organic carbon content and soil depth (P < 0.01). The organic carbon content in 10-30 cm soil layer under chemical fertilizations and in 20-40 cm soil layer under organic fertilizations was relatively stable. Soil delta 13C increased gradually with soil depth, its variation range being from -24% per thousand to -28 per thousand, and had a significantly negative linear correlation with soil organic carbon content (P < 0.05). In 0-20 cm soil layer, the delta 13C in treatments organic manure (M), M + NP, M + NPK, M + straw (R) + N, and R + N decreased significantly; while in 30-50 cm soil layer, the delta 13C in all organic fertilization treatments except R + N increased significantly. Tightly combined humus (humin) was the main humus composition in the soil, occupying 50% or more, and the rest were loosely and stably combined humus. Long-term fertilization increased the content of loosely combined humus and the ratio of humic acid (HA) to fulvic acid (FA).

Change of physical and chemical composition of soil washing out during vegetation season from differently used fields

NASA Astrophysics Data System (ADS)

Baryła, A.; Pierzgalski, E.; Karczmarczyk, A.

2009-04-01

oil losses due to water erosion not only decrease of soil fertility but also influence on pollution of water bodies. One of the method for limitation of water erosion process is protected soil management and choose suitable plants which requires knowledge about effect and mechanism of erosion under different environmental conditions. The results of measurements of quantity and quality of soil losses from three experimental plots are given in the article. Plots were located in Experimental Agricultural Station Puczniew in central part of Poland. Surface soil layer on the plots had mechanical composition of medium loam soil. On two plots grass and barley were planted. Third plot was used as fallow and tilled land. Measurements were carried out four times in the period May-October 2007. Physical and chemical composition of washed soil material was analyzed.

Plant community composition as a predictor of regional soil carbon storage in Alaskan boreal black spruce ecosystems

Treesearch

T.N. Hollingsworth; E.A.G. Schuur; F.S. III Chapin; M.D. Walker

2008-01-01

The boreal forest is the largest terrestrial biome in North America and holds a large portion of the world's reactive soil carbon. Therefore, understanding soil carbon accumulation on a landscape or regional scale across the boreal forest is useful for predicting future soil carbon storage. Here, we examined the relationship between floristic composition and...

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization

DOE PAGES

Oates, Lawrence G.; Duncan, David S.; Sanford, Gregg R.; ...

2016-10-03

The choice of crops and their management can strongly influence soil microbial communities and their processes. Here, we used lipid biomarker profiling to characterize how soil microbial composition of five potential bioenergy cropping systems diverged from a common baseline five years after they were established. The cropping systems we studied included an annual system (continuous no-till corn) and four perennial crops (switchgrass, miscanthus, hybrid poplar, and restored prairie). Partial- and no-stover removal were compared for the corn system, while N-additions were compared to unfertilized plots for the perennial cropping systems. Arbuscular mycorrhizal fungi (AMF) and Gram-negative biomass was higher inmore » unfertilized perennial grass systems, especially in switchgrass and prairie. Gram-positive bacterial biomass decreased in all systems relative to baseline values in surface soils (0–10 cm), but not subsurface soils (10–25 cm). Overall microbial composition was similar between the two soil depths. Our findings demonstrate the capacity of unfertilized perennial cropping systems to recreate microbial composition found in undisturbed soil environments and indicate how strongly agroecosystem management decisions such as N addition and plant community composition can influence soil microbial assemblages.« less

Bioenergy cropping systems that incorporate native grasses stimulate growth of plant-associated soil microbes in the absence of nitrogen fertilization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oates, Lawrence G.; Duncan, David S.; Sanford, Gregg R.

The choice of crops and their management can strongly influence soil microbial communities and their processes. Here, we used lipid biomarker profiling to characterize how soil microbial composition of five potential bioenergy cropping systems diverged from a common baseline five years after they were established. The cropping systems we studied included an annual system (continuous no-till corn) and four perennial crops (switchgrass, miscanthus, hybrid poplar, and restored prairie). Partial- and no-stover removal were compared for the corn system, while N-additions were compared to unfertilized plots for the perennial cropping systems. Arbuscular mycorrhizal fungi (AMF) and Gram-negative biomass was higher inmore » unfertilized perennial grass systems, especially in switchgrass and prairie. Gram-positive bacterial biomass decreased in all systems relative to baseline values in surface soils (0–10 cm), but not subsurface soils (10–25 cm). Overall microbial composition was similar between the two soil depths. Our findings demonstrate the capacity of unfertilized perennial cropping systems to recreate microbial composition found in undisturbed soil environments and indicate how strongly agroecosystem management decisions such as N addition and plant community composition can influence soil microbial assemblages.« less

Metatranscriptomic census of active protists in soils.

PubMed

Geisen, Stefan; Tveit, Alexander T; Clark, Ian M; Richter, Andreas; Svenning, Mette M; Bonkowski, Michael; Urich, Tim

2015-10-01

The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system.

Metatranscriptomic census of active protists in soils

PubMed Central

Geisen, Stefan; Tveit, Alexander T; Clark, Ian M; Richter, Andreas; Svenning, Mette M; Bonkowski, Michael; Urich, Tim

2015-01-01

The high numbers and diversity of protists in soil systems have long been presumed, but their true diversity and community composition have remained largely concealed. Traditional cultivation-based methods miss a majority of taxa, whereas molecular barcoding approaches employing PCR introduce significant biases in reported community composition of soil protists. Here, we applied a metatranscriptomic approach to assess the protist community in 12 mineral and organic soil samples from different vegetation types and climatic zones using small subunit ribosomal RNA transcripts as marker. We detected a broad diversity of soil protists spanning across all known eukaryotic supergroups and revealed a strikingly different community composition than shown before. Protist communities differed strongly between sites, with Rhizaria and Amoebozoa dominating in forest and grassland soils, while Alveolata were most abundant in peat soils. The Amoebozoa were comprised of Tubulinea, followed with decreasing abundance by Discosea, Variosea and Mycetozoa. Transcripts of Oomycetes, Apicomplexa and Ichthyosporea suggest soil as reservoir of parasitic protist taxa. Further, Foraminifera and Choanoflagellida were ubiquitously detected, showing that these typically marine and freshwater protists are autochthonous members of the soil microbiota. To the best of our knowledge, this metatranscriptomic study provides the most comprehensive picture of active protist communities in soils to date, which is essential to target the ecological roles of protists in the complex soil system. PMID:25822483

Chemistry of rocks and soils at Meridiani Planum from the Alpha Particle X-ray Spectrometer.

PubMed

Rieder, R; Gellert, R; Anderson, R C; Brückner, J; Clark, B C; Dreibus, G; Economou, T; Klingelhöfer, G; Lugmair, G W; Ming, D W; Squyres, S W; d'Uston, C; Wänke, H; Yen, A; Zipfel, J

2004-12-03

The Alpha Particle X-ray Spectrometer on the Opportunity rover determined major and minor elements of soils and rocks in Meridiani Planum. Chemical compositions differentiate between basaltic rocks, evaporite-rich rocks, basaltic soils, and hematite-rich soils. Although soils are compositionally similar to those at previous landing sites, differences in iron and some minor element concentrations signify the addition of local components. Rocky outcrops are rich in sulfur and variably enriched in bromine relative to chlorine. The interaction with water in the past is indicated by the chemical features in rocks and soils at this site.

Contents and composition of organic matter in subsurface soils affected by land use and soil mineralogy

NASA Astrophysics Data System (ADS)

Ellerbrock, Ruth H.; Kaiser, Michael

2010-05-01

Land use and mineralogy affect the ability of surface as well as subsurface soils to sequester organic carbon and their contribution to mitigate the greenhouse effect. This study aimed to investigate the long-term impact of land use (i.e., arable and forest) and soil mineralogy on contents and composition of soil organic matter (SOM) from subsurface soils. Seven soils different in mineralogy (Albic and Haplic Luvisol, Colluvic and Haplic Regosol, Haplic and Vertic Cambisol, Haplic Stagnosol) were selected within Germany. Soil samples were taken from forest and adjacent arable sites. First, particulate and water soluble organic matter were separated from the subsurface soil samples. From the remaining solid residues the OM(PY) fractions were separated, analyzed for its OC content (OCPY) and characterized by FTIR spectroscopy. For the arable subsurface soils multiple regression analyses indicate significant positive relationships between the soil organic carbon contents and the contents of i) exchangeable Ca and oxalate soluble Fe, and Alox contents. Further for the neutral arable subsurface soils the contents OCPY weighted by its C=O contents were found to be related to the contents of Ca indicating interactions between OM(PY) and Ca cations. For the forest subsurface soils (pH <5) the OCPY contents were positively related with the contents of Na-pyrophosphate soluble Fe and Al. For the acidic forest subsurface soils such findings indicate interactions between OM(PY) and Fe3+ and Al3+ cations. The effects of land use and soil mineralogy on contents and composition of SOM and OM(PY) will be discussed.

[Effect of Trichoderma species fungi on soil micromycetes, causing infectious conifer seedling lodging in Siberian tree nurseries].

PubMed

Iakimenko, E E; Grodinitskaia, I D

2000-01-01

Soils in the tree nurseries studied were characterized by a lower species diversity of fungi than adjacent virgin soils. In particular, the relative abundances of representatives of the genera Mucor, Chaetomium, and Trichoderma in the nursery soil were two times lower than in adjacent virgin soils. On the other hand, the nursery soil exhibited greater abundances of fungi of the genus Fusarium, which are causative agents of many diseases of conifer seedlings. To appreciate the efficiency of biocontrol of the infectious diseases of conifer seedlings, we introduced several indigenous Trichoderma strains into the nursery soil and found that this affected the species composition of soil microflora considerably. Changes in the species composition of mycobiota beneficially influenced the phytosanitary state of soils and reduced the infectious lodging of conifer seedlings.

Extractable nitrogen and microbial community structure respond to grassland restoration regardless of historical context and soil composition

PubMed Central

Dickens, Sara Jo M.; Allen, Edith B.; Santiago, Louis S.; Crowley, David

2015-01-01

Grasslands have a long history of invasion by exotic annuals, which may alter microbial communities and nutrient cycling through changes in litter quality and biomass turnover rates. We compared plant community composition, soil chemical and microbial community composition, potential soil respiration and nitrogen (N) turnover rates between invaded and restored plots in inland and coastal grasslands. Restoration increased microbial biomass and fungal : bacterial (F : B) ratios, but sampling season had a greater influence on the F : B ratio than did restoration. Microbial community composition assessed by phospholipid fatty acid was altered by restoration, but also varied by season and by site. Total soil carbon (C) and N and potential soil respiration did not differ between treatments, but N mineralization decreased while extractable nitrate and nitrification and N immobilization rate increased in restored compared with unrestored sites. The differences in soil chemistry and microbial community composition between unrestored and restored sites indicate that these soils are responsive, and therefore not resistant to feedbacks caused by changes in vegetation type. The resilience, or recovery, of these soils is difficult to assess in the absence of uninvaded control grasslands. However, the rapid changes in microbial and N cycling characteristics following removal of invasives in both grassland sites suggest that the soils are resilient to invasion. The lack of change in total C and N pools may provide a buffer that promotes resilience of labile pools and microbial community structure. PMID:25555522

Prediction of the effects of soil-based countermeasures on soil solution chemistry of soils contaminated with radiocesium using the hydrogeochemical code PHREEQC.

PubMed

Hormann, Volker; Kirchner, Gerald

2002-04-22

For agriculturally used areas, which are contaminated by the debris from a nuclear accident, the use of chemical amendmends (e.g. potassium chloride and lime) is among the most common soil-based countermeasures. These countermeasures are intended to reduce the plant uptake of radionuclides (mainly 137Cs and 90Sr) by competitive inhibition by chemically similar ions. So far, the impacts of countermeasures on soil solution composition - and thus, their effectiveness - have almost exclusively been established experimentally, since they depend on mineral composition and chemical characteristics of the soil affected. In this study, which focuses on caesium contamination, the well-established code PHREEQC was used as a geochemical model to calculate the changes in the ionic compositions of soil solutions, which result from the application of potassium or ammonium in batch equilibrium experiments. The simple ion exchange model used by PHREEQC was improved by taking into account selective sorption of Cs+, NH4+ and K+ by clay minerals. Calculations were performed with three different initial soil solution compositions, corresponding to particular soil types (loam, sand, peat). For loamy and sandy soils, our calculational results agree well with experimental data reported by Nisbet (Effectiveness of soil-based countermeasures six months and one year after contamination of five diverse soil types with caesium-134 and strontium-90. Contract Report NRPB-M546, National Radiation Protection Board, Chilton, 1995.). For peat, discrepancies were found indicating that for organic soils a reliable set of exchange constants of the relevant cations still has to be determined experimentally. For cesium, however, these discrepancies almost disappeared if selective sites were assumed to be inaccessible. Additionally, results of sensitivity analyses are presented by which the influence of the main soil parameters on Cs+ concentrations in solution after soil treatment has been systematically studied. It is shown that calculating the impacts of soil-based chemical countermeasures on soil solution chemistry using geochemical codes such as PHREEQC offers an attractive alternative to establishing these impacts by often time-consuming and site-specific experiments.

Microbial community composition affects soil fungistasis.

PubMed

de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J A; Kowalchuk, George A; van Veen, Johannes A

2003-02-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.

The role of topographic structure and soil macrofauna presence at spoil heaps during spontaneous succession.

NASA Astrophysics Data System (ADS)

Walmsley, Alena; Vachová, Pavla; Vach, Marek

2016-04-01

This research was investigating whether topographic features, which determine soil nutrient and moisture distribution, in combination with soil fauna (wireworm and earthworm) presence, affect plant community composition at a spontaneously revegetated post mining area with an undulating surface. Two sites of different age with 3 types of topographic features were selected, soil moisture and nutrient content were measured, plant community composition and soil macrofauna community was sampled at each position. Wireworms were present at all positions and were most abundant at bottoms of waves at the younger site; their presence was correlated with several plant species, but the direction of the interaction isn't clear. Earthworms were only present at the older site and had highest abundance at flat sections. Earthworm presence affected the amount of nitrogen in soil - the most nitrogen content was at the site with highest earthworm density and was followed by higher diversity of plant community. The plant community composition was generally correlated with plant available nutrient content - especially P and N. We infer that topographic features affect nutrient and soil fauna distribution, which consequently influences plant community composition.

[Study on preparation of composite nano-scale Fe3O4 for phosphorus control].

PubMed

Li, Lei; Pan, Gang; Chen, Hao

2010-03-01

Composite nano-scale Fe3O4 particles were prepared in sodium carboxymethyl cellulose (CMC) solution by the oxidation deposition method. The adsorptions of phosphorus by micro-scale Fe3O4 and composite nano-scale Fe3O4 were investigated in water and soil, and the role of cellulase in the adsorption of composite nano-scale Fe3O4 was studied. Kinetic tests indicated that the equilibrium adsorption capacity of phosphorous on the composite nano-scale Fe3O4 (2.1 mg/g) was less than that of micro-scale Fe3O4 (3.2 mg/g). When cellulase was added to the solution of composite nano-scale Fe3O4 to degrade CMC, the removal rate of P by the nanoparticles (86%) was enhanced to the same level as the microparticles (90%). In the column tests, when the composite nano-scale Fe3O4 suspension was introduced in the downflow mode through the soil column, 72% of Fe3O4 penetrated through the soil bed under gravity. In contrast, the micro-scale Fe3O4 failed to pass through the soil column. The retention rate of P was 45% in the soil column when treated by the CMC-stabilized nanoparticles, in comparison with only 30% for the untreated soil column, however it could be improved to 74% in the soil column when treated by both the CMC-stabilized nanoparticles and cellulase, which degraded CMC after the nanoparticles were delivered into the soil.

Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too.

PubMed

Tripathi, Binu M; Kim, Mincheol; Singh, Dharmesh; Lee-Cruz, Larisa; Lai-Hoe, Ang; Ainuddin, A N; Go, Rusea; Rahim, Raha Abdul; Husni, M H A; Chun, Jongsik; Adams, Jonathan M

2012-08-01

The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.

Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

PubMed

Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

2014-03-01

Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p < 0.001). Amplicons of AOA from the Nitrososphaera cluster dominated all four ecosystem soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental warming and antecedent fire alter leaf element composition and increase soil C:N ratio in sub-alpine open heathland.

PubMed

White-Monsant, A C; Clark, G J; Ng Kam Chuen, M A G; Tang, C

2017-10-01

Plant communities in alpine ecosystems worldwide are being altered by climate warming. In the alpine open heathland of the Bogong High Plains, Australia, warming and fire have affected the growth and phenology of plants, and have recently been found to alter soil nutrient availability. We examined the effects of nine years of passive warming by open-top chambers and nine years post-fire on (i) the soluble and extractable nutrients and toxic elements available for plant uptake in the soil and (ii) on the element composition of leaves of seven dominant sub-alpine open heathland plants. Warming increased soil C, soil C:N, and decreased soil δ 13 C, indicating an accumulation of soil organic matter and C sequestration. Warming increased soil δ 15 N, indicating increased N mineralization, which concurred with the increased availability of NH 4 + (measured by ion-exchange membranes). Leaf element composition varied among the plant species in response to changes in soil element availabilities, suggesting the importance of species-specific knowledge. Warming decreased leaf N concentration and increased leaf C:N, generally in the plant community, and specifically in Asterolasia trymalioides, Carex breviculmis, Poa hiemata, and Rytidosperma nudiflorum. Warming increased soil P availability, but did not significantly affect leaf P in any species. Antecedent fire increased soil C:N, and decreased concentrations of Ca and Mg in Celmisia pugioniformis more than in the other species. The results suggest that warming and fire changed the nutrient composition of plants and increased soil C:N, which might lead to progressive N limitation in the alpine ecosystem. Copyright © 2017 Elsevier B.V. All rights reserved.

Context dependency and saturating effects of loss of rare soil microbes on plant productivity.

PubMed

Hol, W H Gera; de Boer, Wietse; de Hollander, Mattias; Kuramae, Eiko E; Meisner, Annelein; van der Putten, Wim H

2015-01-01

Land use intensification is associated with loss of biodiversity and altered ecosystem functioning. Until now most studies on the relationship between biodiversity and ecosystem functioning focused on random loss of species, while loss of rare species that usually are the first to disappear received less attention. Here we test if the effect of rare microbial species loss on plant productivity depends on the origin of the microbial soil community. Soils were sampled from three land use types at two farms. Microbial communities with increasing loss of rare species were created by inoculating sterilized soils with serially diluted soil suspensions. After 8 months of incubation, the effects of the different soil communities on abiotic soil properties, soil processes, microbial community composition, and plant productivity was measured. Dilution treatments resulted in increasing species loss, which was in relation to abundance of bacteria in the original field soil, without affecting most of the other soil parameters and processes. Microbial species loss affected plant biomass positively, negatively or not at all, depending on soil origin, but not on land use history. Even within fields the effects of dilution on plant biomass varied between replicates, suggesting heterogeneity in microbial community composition. The effects of medium and severe species loss on plant biomass were similar, pointing toward a saturating effect of species loss. We conclude that changes in the composition of the soil microbial community, including rare species loss, can affect plant productivity, depending on the composition of the initial microbial community. Future work on the relation between function and species loss effects should address this variation by including multiple sampling origins.

Carbon availability structures microbial community composition and function in soil aggregate fractions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

2014-12-01

Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of microbial communities on terrestrial C and N cycling.

[Identification of using organic carbon isotopic composition of soil pollution process].

PubMed

Guo, Qing-Jun; Chen, Tong-Bin; Yang, Jun; Strauss, Harald; Lei, Mei; Zhu, Guang-Xu; Li, Yan-Mei; Zhou, Xiao-Yong; Li, Xiao-Yan

2011-10-01

This study has taken advantage of the characteristics of concentration of soil organic matter (SOC) and delta13 C(SOC) values to provide proofs for environment quality assessment and to know more about polluted sources, sizes and processes in Beijing steel company area. delta13C values of SOC is good for tracing sources and documenting shifts in community composition and distribution. Two sections (Beijing steel company area and Yongledian, Tongzhou) which belong to two different soil types collected in Beijing, and organic carbon isotopic composition and total soil organic carbon were analyzed. These results shows that SOC of soil samples from Beijing steel company area are quite high, and even 9.7% at the surface sample, however SOC from unpolluted area (Yongledian area) is lower than those of industrial area. delta13 C(SOC) from soils of Beijing steel company area and Yongledian area respectively vary from -24.8 per thousand to -23.1 per thousand and -26.4 per thousand to -20.5 per thousand, the results are quite different. The results reflect that there are different organic carbon sources in different types' soil: Organic carbon from Beijing steel company area has been mainly affected by coal burning, soil organic carbon concentrations are quite high, and pollution can affect on soils 70 cm deep underground; and soils from Yongledian area, have been not polluted, and organic matter is from natural litter (C3 plants). Although there are different soil organic carbon concentrations and isotope compositions, two soil sections have similar variation trends. This study provides proofs for environment quality assessment and know more about polluted and natural sources, sizes in Beijing.

Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity.

PubMed

Dassen, Sigrid; Cortois, Roeland; Martens, Henk; de Hollander, Mattias; Kowalchuk, George A; van der Putten, Wim H; De Deyn, Gerlinde B

2017-08-01

Plants are known to influence belowground microbial community structure along their roots, but the impacts of plant species richness and plant functional group (FG) identity on microbial communities in the bulk soil are still not well understood. Here, we used 454-pyrosequencing to analyse the soil microbial community composition in a long-term biodiversity experiment at Jena, Germany. We examined responses of bacteria, fungi, archaea, and protists to plant species richness (communities varying from 1 to 60 sown species) and plant FG identity (grasses, legumes, small herbs, tall herbs) in bulk soil. We hypothesized that plant species richness and FG identity would alter microbial community composition and have a positive impact on microbial species richness. Plant species richness had a marginal positive effect on the richness of fungi, but we observed no such effect on bacteria, archaea and protists. Plant species richness also did not have a large impact on microbial community composition. Rather, abiotic soil properties partially explained the community composition of bacteria, fungi, arbuscular mycorrhizal fungi (AMF), archaea and protists. Plant FG richness did not impact microbial community composition; however, plant FG identity was more effective. Bacterial richness was highest in legume plots and lowest in small herb plots, and AMF and archaeal community composition in legume plant communities was distinct from that in communities composed of other plant FGs. We conclude that soil microbial community composition in bulk soil is influenced more by changes in plant FG composition and abiotic soil properties, than by changes in plant species richness per se. © 2017 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Effect of long-term fertilization strategies on bacterial community composition in a 35-year field experiment of Chinese Mollisols.

PubMed

Ma, Mingchao; Zhou, Jing; Ongena, Marc; Liu, Wenzheng; Wei, Dan; Zhao, Baisuo; Guan, Dawei; Jiang, Xin; Li, Jun

2018-02-13

Bacteria play vital roles in soil biological fertility; however, it remains poorly understood about their response to long-term fertilization in Chinese Mollisols, especially when organic manure is substituted for inorganic nitrogen (N) fertilizer. To broaden our knowledge, high-throughput pyrosequencing and quantitative PCR were used to explore the impacts of inorganic fertilizer and manure on bacterial community composition in a 35-year field experiment of Chinese Mollisols. Soils were collected from four treatments: no fertilizer (CK), inorganic phosphorus (P) and potassium (K) fertilizer (PK), inorganic P, K, and N fertilizer (NPK), and inorganic P and K fertilizer plus manure (MPK). All fertilization differently changed soil properties. Compared with CK, the PK and NPK treatments acidified soil by significantly decreasing soil pH from 6.48 to 5.53 and 6.16, respectively, while MPK application showed no significant differences of soil pH, indicating alleviation of soil acidification. Moreover, all fertilization significantly increased soil organic matter (OM) and soybean yields, with the highest observed under MPK regime. In addition, the community composition at each taxonomic level varied considerably among the fertilization strategies. Bacterial taxa, associated with plant growth promotion, OM accumulation, disease suppression, and increased soil enzyme activity, were overrepresented in the MPK regime, while they were present at low abundant levels under NPK treatment, i.e. phyla Proteobacteria and Bacteroidetes, class Alphaproteobacteria, and genera Variovorax, Chthoniobacter, Massilia, Lysobacter, Catelliglobosispora and Steroidobacter. The application of MPK shifted soil bacterial community composition towards a better status, and such shifts were primarily derived from changes in soil pH and OM.

Root controls on soil microbial community structure in forest soils.

PubMed

Brant, Justin B; Myrold, David D; Sulzman, Elizabeth W

2006-07-01

We assessed microbial community composition as a function of altered above- and belowground inputs to soil in forest ecosystems of Oregon, Pennsylvania, and Hungary as part of a larger Detritus Input and Removal Treatment (DIRT) experiment. DIRT plots, which include root trenching, aboveground litter exclusion, and doubling of litter inputs, have been established in forested ecosystems in the US and Europe that vary with respect to dominant tree species, soil C content, N deposition rate, and soil type. This study used phospholipid fatty-acid (PLFA) analysis to examine changes in the soil microbial community size and composition in the mineral soil (0-10 cm) as a result of the DIRT treatments. At all sites, the PLFA profiles from the plots without roots were significantly different from all other treatments. PLFA analysis showed that the rootless plots generally contained larger quantities of actinomycete biomarkers and lower amounts of fungal biomarkers. At one of the sites in an old-growth coniferous forest, seasonal changes in PLFA profiles were also examined. Seasonal differences in soil microbial community composition were greater than treatment differences. Throughout the year, treatments without roots continued to have a different microbial community composition than the treatments with roots, although the specific PLFA biomarkers responsible for these differences varied by season. These data provide direct evidence that root C inputs exert a large control on microbial community composition in the three forested ecosystems studied.

Predicting effects of climate change on the composition and function of soil microbial communities

NASA Astrophysics Data System (ADS)

Dubinsky, E.; Brodie, E.; Myint, C.; Ackerly, D.; van Nostrand, J.; Bird, J.; Zhou, J.; Andersen, G.; Firestone, M.

2008-12-01

Complex soil microbial communities regulate critical ecosystem processes that will be altered by climate change. A critical step towards predicting the impacts of climate change on terrestrial ecosystems is to determine the primary controllers of soil microbial community composition and function, and subsequently evaluate climate change scenarios that alter these controllers. We surveyed complex soil bacterial and archaeal communities across a range of climatic and edaphic conditions to identify critical controllers of soil microbial community composition in the field and then tested the resulting predictions using a 2-year manipulation of precipitation and temperature using mesocosms of California annual grasslands. Community DNA extracted from field soils sampled from six different ecosystems was assayed for bacterial and archaeal communities using high-density phylogenetic microarrays as well as functional gene arrays. Correlations among the relative abundances of thousands of microbial taxa and edaphic factors such as soil moisture and nutrient content provided a basis for predicting community responses to changing soil conditions. Communities of soil bacteria and archaea were strongly structured by single environmental predictors, particularly variables related to soil water. Bacteria in the Actinomycetales and Bacilli consistently demonstrated a strong negative response to increasing soil moisture, while taxa in a greater variety of lineages responded positively to increasing soil moisture. In the climate change experiment, overall bacterial community structure was impacted significantly by total precipitation but not by plant species. Changes in soil moisture due to decreased rainfall resulted in significant and predictable alterations in community structure. Over 70% of the bacterial taxa in common with the cross-ecosystem study responded as predicted to altered precipitation, with the most conserved response from Actinobacteria. The functional consequences of these predictable changes in community composition were measured with functional arrays that detect genes involved in the metabolism of carbon, nitrogen and other elements. The response of soil microbial communities to altered precipitation can be predicted from the distribution of microbial taxa across moisture gradients.

Warming-Induced Changes to the Molecular Composition of Soil Organic Matter

NASA Astrophysics Data System (ADS)

Feng, X.; Simpson, M. J.; Simpson, A. J.; Wilson, K. P.; Williams, D.

2007-12-01

Soil organic matter (SOM) contains two times more carbon than the atmosphere and the potential changes to SOM quantity and quality with global warming are a major concern. It is commonly believed that global warming will accelerate the decomposition of labile SOM compounds while refractory SOM constituents will remain stable. However, experimental evidence of molecular-level changes to SOM composition with global warming is currently lacking. Here we employ SOM biomarkers and nuclear magnetic resonance (NMR) spectroscopy to study SOM composition and degradation in a soil warming experiment in southern Ontario, Canada. The soil warming experiment consisted of a control and a treatment plot in a mixed forest that had a temperature difference of about 5 degrees C for 14 months. Before soil warming the control and treatment plots had the same organic carbon (OC) content and SOM composition. Soil warming significantly increased soil OC content and the abundance of cutin-derived carbon originating from leaf tissues and decreased carbohydrates that are regarded as easily degradable. Lignin components, which are believed to be part of the stable and slowly-cycling SOM, were observed to be in an advanced stage of degradation. This observation is corroborated by increases in fungal biomass in the warmed soil because fungi are considered the primary decomposer of lignin in the soil environment. An NMR study of SOM in the warmed and control plots indicates that alkyl carbon, mainly originating from plant cuticles in the soil, increased in the warmed soil while O-alkyl carbon, primarily occurring in carbohydrates, decreased. Aromatic and phenolic carbon regions, which include the main structures found in lignin, decreased in the warmed soil. These data collectively suggest that there is a great potential for lignin degradation with soil warming, and that the refractory (aromatic) soil carbon storage may be reduced as a result of increased fungal growth in a warmer climate.

Structure, composition and metagenomic profile of soil microbiomes associated to agricultural land use and tillage systems in Argentine Pampas.

PubMed

Carbonetto, Belén; Rascovan, Nicolás; Álvarez, Roberto; Mentaberry, Alejandro; Vázquez, Martin P

2014-01-01

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no-tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability.

Structure, Composition and Metagenomic Profile of Soil Microbiomes Associated to Agricultural Land Use and Tillage Systems in Argentine Pampas

PubMed Central

Carbonetto, Belén; Rascovan, Nicolás; Álvarez, Roberto; Mentaberry, Alejandro; Vázquez, Martin P.

2014-01-01

Agriculture is facing a major challenge nowadays: to increase crop production for food and energy while preserving ecosystem functioning and soil quality. Argentine Pampas is one of the main world producers of crops and one of the main adopters of conservation agriculture. Changes in soil chemical and physical properties of Pampas soils due to different tillage systems have been deeply studied. Still, not much evidence has been reported on the effects of agricultural practices on Pampas soil microbiomes. The aim of our study was to investigate the effects of agricultural land use on community structure, composition and metabolic profiles on soil microbiomes of Argentine Pampas. We also compared the effects associated to conventional practices with the effects of no-tillage systems. Our results confirmed the impact on microbiome structure and composition due to agricultural practices. The phyla Verrucomicrobia, Plactomycetes, Actinobacteria, and Chloroflexi were more abundant in non cultivated soils while Gemmatimonadetes, Nitrospirae and WS3 were more abundant in cultivated soils. Effects on metabolic metagenomic profiles were also observed. The relative abundance of genes assigned to transcription, protein modification, nucleotide transport and metabolism, wall and membrane biogenesis and intracellular trafficking and secretion were higher in cultivated fertilized soils than in non cultivated soils. We also observed significant differences in microbiome structure and taxonomic composition between soils under conventional and no- tillage systems. Overall, our results suggest that agronomical land use and the type of tillage system have induced microbiomes to shift their life-history strategies. Microbiomes of cultivated fertilized soils (i.e. higher nutrient amendment) presented tendencies to copiotrophy while microbiomes of non cultivated homogenous soils appeared to have a more oligotrophic life-style. Additionally, we propose that conventional tillage systems may promote copiotrophy more than no-tillage systems by decreasing soil organic matter stability and therefore increasing nutrient availability. PMID:24923965

Organic matter composition of soil macropore surfaces under different agricultural management practices

NASA Astrophysics Data System (ADS)

Glæsner, Nadia; Leue, Marin; Magid, Jacob; Gerke, Horst H.

2016-04-01

Understanding the heterogeneous nature of soil, i.e. properties and processes occurring specifically at local scales is essential for best managing our soil resources for agricultural production. Examination of intact soil structures in order to obtain an increased understanding of how soil systems operate from small to large scale represents a large gap within soil science research. Dissolved chemicals, nutrients and particles are transported through the disturbed plow layer of agricultural soil, where after flow through the lower soil layers occur by preferential flow via macropores. Rapid movement of water through macropores limit the contact between the preferentially moving water and the surrounding soil matrix, therefore contact and exchange of solutes in the water is largely restricted to the surface area of the macropores. Organomineral complex coated surfaces control sorption and exchange properties of solutes, as well as availability of essential nutrients to plant roots and to the preferentially flowing water. DRIFT (Diffuse Reflectance infrared Fourier Transform) Mapping has been developed to examine composition of organic matter coated macropores. In this study macropore surfaces structures will be determined for organic matter composition using DRIFT from a long-term field experiment on waste application to agricultural soil (CRUCIAL, close to Copenhagen, Denmark). Parcels with 5 treatments; accelerated household waste, accelerated sewage sludge, accelerated cattle manure, NPK and unfertilized, will be examined in order to study whether agricultural management have an impact on the organic matter composition of intact structures.

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Mass flow of a volatile organic liquid mixture in soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerstl, Z.; Galin, Ts.; Yaron, B.

1994-05-01

The flow of kerosene, a volatile organic liquid mixture (VOLM), was studied in loam and clay soils and in a medium sand. The kerosene residual capacity and conductivity were determined for all three media at different initial moisture contents and with kerosene of different compositions. The kerosene conductivity of the soil was found to be strongly influenced by the soil texture and initial moisture content as well as by the kerosene composition. The kerosene conductivity of the sand was two orders of magnitude greater than that of the soils and was unaffected by initial moisture contents as high as fieldmore » capacity. The kerosene conductivity of the loam soil was similar in oven dry and air dry soils, but increased significantly in soils at 70% and fun field capacity due to the Yuster effect. In the clay soil the kerosene conductivity of the air dry sod was four times that of the oven dry sod and increased somewhat in the soil at 70% field capacity. No kerosene flow was observed in the oven dry soil at full field capacity. The differences in kerosene conductivity in these soils and the effect of moisture content were attributed to the different pore-sin distributions of the soil& Changes in the composition of the kerosene due to volatilization of the light fractions resulted in increased viscosity of the residual kerosene. This increased viscosity affected the fluid properties of kerosene, which resulted in decreased kerosene conductivity in the sand and the soils. 29 refs., 4 figs., 4 tabs.« less

Response of microbial community composition and function to soil climate change

USGS Publications Warehouse

Waldrop, M.P.; Firestone, M.K.

2006-01-01

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.

Advanced multivariate analysis to assess remediation of hydrocarbons in soils.

PubMed

Lin, Deborah S; Taylor, Peter; Tibbett, Mark

2014-10-01

Accurate monitoring of degradation levels in soils is essential in order to understand and achieve complete degradation of petroleum hydrocarbons in contaminated soils. We aimed to develop the use of multivariate methods for the monitoring of biodegradation of diesel in soils and to determine if diesel contaminated soils could be remediated to a chemical composition similar to that of an uncontaminated soil. An incubation experiment was set up with three contrasting soil types. Each soil was exposed to diesel at varying stages of degradation and then analysed for key hydrocarbons throughout 161 days of incubation. Hydrocarbon distributions were analysed by Principal Coordinate Analysis and similar samples grouped by cluster analysis. Variation and differences between samples were determined using permutational multivariate analysis of variance. It was found that all soils followed trajectories approaching the chemical composition of the unpolluted soil. Some contaminated soils were no longer significantly different to that of uncontaminated soil after 161 days of incubation. The use of cluster analysis allows the assignment of a percentage chemical similarity of a diesel contaminated soil to an uncontaminated soil sample. This will aid in the monitoring of hydrocarbon contaminated sites and the establishment of potential endpoints for successful remediation.

Nature and Properties of Lateritic Soils Derived from Different Parent Materials in Taiwan

PubMed Central

2014-01-01

The objective of this study was to investigate the physical, chemical, and mineralogical composition of lateritic soils in order to use these soils as potential commercial products for industrial application in the future. Five lateritic soils derived from various parent materials in Taiwan, including andesite, diluvium, shale stone, basalt, and Pleistocene deposit, were collected from the Bt1 level of soil samples. Based on the analyses, the Tungwei soil is an alfisol, whereas other lateritic soils are ultisol. Higher pH value of Tungwei is attributed to the large amounts of Ca2+ and Mg2+. Loupi and Pingchen soils would be the older lateritic soils because of the lower active iron ratio. For the iron minerals, the magnetic iron oxides such as major amounts of magnetite and maghemite were found for Tamshui and Tungwei lateritic soils, respectively. Lepidocrocite was only found in Soka soil and intermediate amounts of goethite were detected for Loupi and Pingchen soils. After Mg-saturated and K-saturated processes, major amounts of mixed layer were observed in Loupi and Soka soils, whereas the montmorillonite was only detected in Tungwei soil. The investigation results revealed that the parent materials would play an important role during soil weathering process and physical, chemical, and mineralogy compositions strongly affect the formation of lateritic soils. PMID:24883366

Nature and properties of lateritic soils derived from different parent materials in Taiwan.

PubMed

Ko, Tzu-Hsing

2014-01-01

The objective of this study was to investigate the physical, chemical, and mineralogical composition of lateritic soils in order to use these soils as potential commercial products for industrial application in the future. Five lateritic soils derived from various parent materials in Taiwan, including andesite, diluvium, shale stone, basalt, and Pleistocene deposit, were collected from the Bt1 level of soil samples. Based on the analyses, the Tungwei soil is an alfisol, whereas other lateritic soils are ultisol. Higher pH value of Tungwei is attributed to the large amounts of Ca(2+) and Mg(2+). Loupi and Pingchen soils would be the older lateritic soils because of the lower active iron ratio. For the iron minerals, the magnetic iron oxides such as major amounts of magnetite and maghemite were found for Tamshui and Tungwei lateritic soils, respectively. Lepidocrocite was only found in Soka soil and intermediate amounts of goethite were detected for Loupi and Pingchen soils. After Mg-saturated and K-saturated processes, major amounts of mixed layer were observed in Loupi and Soka soils, whereas the montmorillonite was only detected in Tungwei soil. The investigation results revealed that the parent materials would play an important role during soil weathering process and physical, chemical, and mineralogy compositions strongly affect the formation of lateritic soils.

Soil biochar amendment shapes the composition of N2O-reducing microbial communities.

PubMed

Harter, Johannes; Weigold, Pascal; El-Hadidi, Mohamed; Huson, Daniel H; Kappler, Andreas; Behrens, Sebastian

2016-08-15

Soil biochar amendment has been described as a promising tool to improve soil quality, sequester carbon, and mitigate nitrous oxide (N2O) emissions. N2O is a potent greenhouse gas. The main sources of N2O in soils are microbially-mediated nitrogen transformation processes such as nitrification and denitrification. While previous studies have focused on the link between N2O emission mitigation and the abundance and activity of N2O-reducing microorganisms in biochar-amended soils, the impact of biochar on the taxonomic composition of the nosZ gene carrying soil microbial community has not been subject of systematic study to date. We used 454 pyrosequencing in order to study the microbial diversity in biochar-amended and biochar-free soil microcosms. We sequenced bacterial 16S rRNA gene amplicons as well as fragments of common (typical) nosZ genes and the recently described 'atypical' nosZ genes. The aim was to describe biochar-induced shifts in general bacterial community diversity and taxonomic variations among the nosZ gene containing N2O-reducing microbial communities. While soil biochar amendment significantly altered the 16S rRNA gene-based community composition and structure, it also led to the development of distinct functional traits capable of N2O reduction containing typical and atypical nosZ genes related to nosZ genes found in Pseudomonas stutzeri and Pedobacter saltans, respectively. Our results showed that biochar amendment can affect the relative abundance and taxonomic composition of N2O-reducing functional microbial traits in soil. Thus these findings broaden our knowledge on the impact of biochar on soil microbial community composition and nitrogen cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Role and Variation of the Amount and Composition of Glomalin in Soil Properties in Farmland and Adjacent Plantations with Reference to a Primary Forest in North-Eastern China

PubMed Central

Wang, Qiong; Wang, Wenjie; He, Xingyuan; Zhang, Wentian; Song, Kaishan; Han, Shijie

2015-01-01

The glycoprotein known as glomalin-related soil protein (GRSP) is abundantly produced on the hyphae and spores of arbuscular mycorrhizal fungi (AMF) in soil and roots. Few studies have focused on its amount, composition and associations with soil properties and possible land-use influences, although the data hints at soil rehabilitation. By choosing a primary forest soil as a non-degraded reference, it is possible to explore whether afforestation can improve degraded farmland soil by altering GRSP. In this paper, close correlations were found between various soil properties (soil organic carbon, nitrogen, pH, electrical conductivity (EC), and bulk density) and the GRSP amount, between various soil properties and GRSP composition (main functional groups, fluorescent substances, and elements). Afforestation on farmland decreased the EC and bulk density (p < 0.05). The primary forest had a 2.35–2.56-fold higher GRSP amount than those in the plantation forest and farmland, and GRSP composition (tryptophan-like and fulvic acid-like fluorescence; functional groups of C–H, C–O, and O–H; elements of Al, O, Si, C, Ca, and N) in primary forest differed from those in plantation forest and farmland (p < 0.05). However, no evident differences in GRSP amount and composition were observed between the farmland and the plantation forest. Our finding highlights that 30 years poplar afforestation on degraded farmland is not enough to change GRSP-related properties. A longer period of afforestation with close-to-nature managements may favor the AMF-related underground recovery processes. PMID:26430896

Effects of management, soil attributes and region on soil microbial communities in vineyards (Napa, California, USA)

USDA-ARS?s Scientific Manuscript database

Soil microorganisms play an important role in soil health. However, little is known about the relationship between soil microbial community composition and diversity and commercially significant aspects of soil health. The purpose of this study is to: (1) assess the impact of management practices on...

Variations in bacterial and fungal community composition along the soil depth profiles determined by pyrosequencing

NASA Astrophysics Data System (ADS)

Ko, D.; Yoo, G.; Jun, S. C.; Yun, S. T.; Chung, H.

2015-12-01

Soil microorganisms play key roles in nutrient cycling, and are distributed throughout the soil profile. Currently, there is little information about the characteristics of the microbial communities along the soil depth because most studies focus on microorganisms inhabiting the soil surface. To better understand the functions and composition of microbial communities and the biogeochemical factors that shape them at different soil depth, we analyzed soil microbial activities and bacterial and fungal community composition in a soil profile of a fallow field located in central Korea. Soil samples were taken using 120-cm soil cores. To analyze the composition of bacterial and fungal communities, barcoded pyrosequnecing analysis of 16S rRNA genes (bacteria) and ITS region (fungi) was conducted. Among the bacterial groups, the abundance of Proteobacteria (38.5, 23.2, 23.3, 26.1 and 17.5%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) and Firmicutes (12.8, 11.3, 8.6, 4.3 and 0.4%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively) decreased with soil depth. On the other hand, the abundance of Ascomycota (51.2, 48.6, 65.7, 46.1, and 45.7%, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively), a dominant fungal group at this site, showed no significant difference along the soil profile. To examine the vertical difference of microbial activities, activity of five extracellular enzymes that take part in cycling of C, N, and P in soil ecosystems, beta-1,4-glucosidase, cellobiohydrolase, beta-1,4-xylosidase, beta-1,4-N-acetylglucosaminidase, and acid phosphatase were analyzed. The soil enzyme activity declined with soil depth. For example, acid phosphatase activity was 88.5 (± 14.6 (± 1 SE)), 30.0 (± 5.9), 18.0 (± 3.5), 14.1 (± 3.7), and 10.7 (± 3.8) nmol g-1 hr-1, at 15-, 30-, 60-, 90-, and 120-cm depth, respectively. These metagenomics studies, along with other studies on microbial functions, are expected to enhance our understanding on the complexity of soil microbial communities and their relationship with biogeochemical factors.

Autoclaving as a mean of modifying the soil wettability characteristics

NASA Astrophysics Data System (ADS)

Urbanek, Emilia; Bodi, Merche; Shakesby, Rick; Doerr, Stefan

2010-05-01

Studies of soil water repellency have often attempted to isolate its hydrological impact by comparing responses of wettable and water repellent soils. It is, however, almost impossible to identify natural wettable and water repellent soils that are otherwise fully comparable. Furthermore no established methodology exists that allows changing a soil from wettable to water repellent (or vice versa) without affecting its chemical composition. Approaches used for rendering wettable soil (or sands) water repellent involve coating particles with hydrophobic or commercial water repellent spray. Heating soil to temperatures >300 °C has been used to eliminate existing water repellency from samples, but this can permanently alter the composition of organic matter. Here we report on a new technique for rendering wettable soil water repellent involving autoclaving. Autoclaving is commonly applied in medicine and biology for sterilization. It uses moist heat and pressure to destroy the bacteria, viruses and fungi. The same method has also been used in soil ecology studies for selective removal of certain micro-organisms. In our study, soils at various moisture contents were autoclaved in sealed bags for 1hr at 121°C. The soils became water repellent and the degree of water repellency was found to be dependent on the original soil moisture content and the soil wettability remained unchanged even with further drying of the soil up to 105°C. No changes in soil wettability were found after autoclaving very dry or wet soils. Only at certain intermediate water contents was the soil able to switch to a hydrophobic state. We suspect that the changes occurring during the autoclaving involve molecular orientation of hydrophobic and hydrophilic groups of soil organic matter, and moist heat and pressure cause the hydrophobic groups to be directed towards the outside of the soil particles which consequently repels water. Treatment of soil in this way presents a simple, inexpensive method of making a soil hydrophobic without changing its chemical composition. This has considerable potential for controlled experiments requiring both soils that differ only in terms of their degree of hydrophobicity.

Influence of petroleum hydrocarbon contamination on microalgae and microbial activities in a long-term contaminated soil.

PubMed

Megharaj, M; Singleton, I; McClure, N C; Naidu, R

2000-05-01

Petroleum hydrocarbons are widespread environmental pollutants. Although biodegradation of petroleum hydrocarbons has been the subject of numerous investigations, information on their toxicity to microorganisms in soil is limited, with virtually no work conducted on soil algae. We carried out a screening experiment for total petroleum hydrocarbons (TPH) and their toxicity to soil algal populations, microbial biomass, and soil enzymes (dehydrogenase and urease) in a long-term TPH-polluted site with reference to an adjacent unpolluted site. Microbial biomass, soil enzyme activity, and microalgae declined in medium to high-level (5,200-21,430 mg kg(-1) soil) TPH-polluted soils, whereas low-level (<2,120 mg kg(-1) soil) pollution stimulated the algal populations and showed no effect on microbial biomass and enzymes. However, inhibition of all the tested parameters was more severe in soil considered to have medium-level pollution than in soils that were highly polluted. This result could not be explained by chemical analysis alone. Of particular interest was an observed shift in the species composition of algae in polluted soils with elimination of sensitive species in the medium to high polluted soils. Also, an algal growth inhibition test carried out using aqueous eluates prepared from polluted soils supported these results. Given the sensitivity of algae to synthetic pollutants, alteration in the algal species composition can serve as a useful bioindicator of pollution. The results of this experiment suggest that chemical analysis alone is not adequate for toxicological estimations and should be used in conjunction with bioassays. Furthermore, changes in species composition of algae proved to be more sensitive than microbial biomass and soil enzyme activity measurements.

Alaskan Arctic Soils: Relationship between Microbial Carbon Usage and Soil Composition

NASA Astrophysics Data System (ADS)

Li, H.; Ziolkowski, L. A.

2015-12-01

Carbon stored in Arctic permafrost carbon is sensitive to climate change. Microbes are known to degrade Arctic soil organic carbon (OC) and potentially release vast quantitates of CO2 and CH4. Previously, it has been shown that warming of Arctic soils leads to microbes respiring older carbon. To examine this process, we studied the microbial carbon usage and its relationship to the soil OC composition in active layer soils at five locations along a latitudinal transect on the North Slope of Alaska using the compound specific radiocarbon signatures of the viable microbial community using phospholipid fatty acids (PLFA). Additional geochemical parameters (C/N, 13C, 15N and 14C) of bulk soils were measured. Overall there was a greater change with depth than location. Organic rich surface soils are rich in vegetation and have high PLFA based cell densities, while deeper in the active layer geochemical parameters indicated soil OC was degraded and cell densities decreased. As expected, PLFA indicative of Fungi and Protozoa species dominated in surface soils, methyl-branched PLFAs, indicative of bacterial origin, increased in deeper in the active layer. A group of previously unreported PLFAs, believed to correlate to anaerobic microbes, increased at the transition between the surface and deep microbial communities. Cluster analysis based on individual PLFAs of samples confirmed compositional differences as a function of depth dominated with no site to site differences. Radiocarbon data of soil OC and PLFA show the preferential consumption of younger soil OC by microbes at all sites and older OC being eaten in deep soils. However, in deeper soil, where the C/N ratio suggests lower bioavailability, less soil OC was incorporated into the microbes as indicating by greater differences between bulk and PLFA radiocarbon ages.

[Species composition and diversity of soil mesofauna in the 'Holy Hills' fragmentary tropical rain forest of Xishuangbanna, China].

PubMed

Yang, X; Sha, L

2001-04-01

The species composition and diversity of soil mesofauna were examined in fragmented dry tropical seasonal rainforest of tow 'Holy Hills' of Dai nationality, compared with the continuous moist tropical seasonal rain forest of Nature Reserve in Xishuangbanna area. 5 sample quadrats were selected along the diagonal of 20 m x 20 m sampling plot, and the samples of litterfall and 0-3 cm soil were collected from each 50 cm x 10 cm sample quadrat. Animals in soil sample were collected by using dry-funnel(Tullgren's), were identified to their groups according to the order. The H' index, D.G index and the pattern of relative abundance of species were used to compare the diversity of soil mesofauna. The results showed that the disturbance of vegetation and soil resulted by tropical rainforest fragmentation was the major factor affecting the diversity of soil mesofauna. Because the fragmented forest was intruded by some pioneer tree species and the "dry and warm" effect operated, this forest had more litterfall on the floor and more humus in the soil than the continuous moist rain forest. The soil condition with more soil organic matter, total N and P, higher pH value and lower soil bulk density became more favorable to the soil mesofauna. Therefore, the species richness, abundance and diversity of soil mesofauna in fragmented forests were higher than those in continuous forest, but the similarity of species composition in fragmented forest to the continuous forest was minimal. Soil mesofauna diversity in fragmented forests did not change with decreasing fragmented area, indicating that there was no species-area effect operation in this forest. The pattern of relative abundance of species in these forest soils was logarithmic series distribution.

Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China

PubMed Central

Wang, Shaojun; Chen, Han Y. H.; Tan, Yan; Fan, Huan; Ruan, Honghua

2016-01-01

Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon’s and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability. PMID:26857390

Fertilizer regime impacts on abundance and diversity of soil fauna across a poplar plantation chronosequence in coastal Eastern China.

PubMed

Wang, Shaojun; Chen, Han Y H; Tan, Yan; Fan, Huan; Ruan, Honghua

2016-02-09

Soil fauna are critical for ecosystem function and sensitive to the changes of soil fertility. The effects of fertilization on soil fauna communities, however, remain poorly understood. We examined the effects of fertilization form and quantity on the abundance, diversity and composition of soil fauna across an age-sequence of poplar plantations (i.e., 4-, 9- and 20-yr-old) in the coastal region of eastern China. We found that the effects of fertilization on faunal abundance, diversity, and composition differed among stand ages. Organic fertilizers increased the total abundance of soil fauna, whereas low level inorganic fertilizers imparted increases only in the 4- and 9-yr-old stands. The number of faunal groups did not change with fertilization, but Shannon's and Margalef diversity indices increased under low level organic fertilization, and decreased under inorganic fertilization in the 9- and 20-yr-old stands. Community composition of soil fauna differed strongly with fertilization and stand age. The changes in soil fauna were strongly associated with the changes in microbial biomass carbon, dissolved organic carbon and nitrogen, and available phosphorus and potassium. Our findings suggest that the responses of soil fauna to fertilization may be mediated through the fertilization effects on soil nutrient availability.

[Effects of tree species transition on soil microbial community composition and functions in subtropical China].

PubMed

Ding, Guo Chang; Wang, Xiao Hua; Yang, Qi Fan; Lin, Qun Xing; Huang, Zhi Qun

2017-11-01

We employed a comparative study to examine the effects of tree species transition on soil microbial biomass, community composition and enzymes activities under Cunninghamia lanceolata (Lamb.) Hook, Eucalyptus grandis and a N-fixing species, Acacia melanoxylon in subtropical China. Results showed that the effect of tree species on soil microbial community and enzymes activities was significant only in the 0-10 cm soil layer. Reforestation with N-fixing species A. melanoxylon on the C. lanceolata harvest site significantly increased the total phospholipid fatty acid (PLFA), fungal PLFAs, Gram-positive bacterial PLFAs, Gram-negative bacterial PLFAs and actinomycetes biomasses in the 0-10 cm soil layer. The principal component analysis (PCA) showed that the soil microbial community composition in A. melanoxylon soil differed significantly from that in C. lanceolata and E. grandis soils. N-fixing species (A. melanoxylon) significantly enhanced the percent abundance of Gram-positive bacteria, Gram-negative bacteria and actinomycetes. Activities of cellobiohydrolase, N-acetyl-β-d-glucosaminidase and acid phosphatase were significantly higher under A. melanoxylon than under C. lanceolata and E. grandis plantations. Our results suggested that reforestation with N-fixing species, A. melanoxylon on C. lanceolata harvest site could increase soil microbial biomass, enzyme activities and soil organic matter content.

An evaluation of methods for identifying and interpreting buried soils in late Quaternary loess in Alaska: A section in Geologic studies in Alaska by the U.S. Geological Survey, 1998

USGS Publications Warehouse

Muhs, Daniel R.; Ager, Thomas A.; Been, Josh M.; Rosenbaum, Joseph G.; Reynolds, Richard J.

2000-01-01

The presence of buried soils in Alaskan loess is controversial, and therefore criteria for identifying buried soils in these deposits need to be evaluated. In this paper, morphologic and chemical criteria for identifying buried soils are evaluated by studying modern soils developed mostly in Holocene loess under tundra, boreal forest, and transitional coastal-boreal forest vegetation in different parts of Alaska. Data from modern Alaskan soils that developed under vegetation similar to that of the present indicate that soil morphology, organic-matter concentrations, and P concentrations can be useful diagnostic tools for identifying buried soils. Soil morphologic criteria, particularly horizon colors and horizon sequences, are essential for identifying buried soils, but some minimally developed soils may resemble organic-rich alluvial, colluvial, or lacustrine deposits. Organic matter and total P contents and distributions can aid in such studies because in well-drained soils these constituents show rapid declines with depth. However, neither of these techniques may work if the upper genetic horizons of buried soils are eroded.If buried soils are present in Alaskan loess, it would also be desirable to have techniques for determining the dominant vegetation under which the soils formed. Such techniques could then be used to reconstruct former vegetation types and paleoclimates in Alaska. A previous study suggested that tundra and boreal forest vegetation have distinctive carbon isotopic compositions, although both are dominated by C3 plants. If this is the case, then the carbon isotopic composition of organic matter in buried soils could be used to reconstruct former vegetation types. A larger suite of modern soils from Alaskan tundra and forest were analyzed to test this hypothesis. Results indicate that modern soil O horizons in these two biomes have the same range of δ13C values, and therefore carbon isotope compositions cannot be used to reconstruct former tundra or boreal forest.

Linking soil bacterial biodiversity and soil carbon stability.

PubMed

Mau, Rebecca L; Liu, Cindy M; Aziz, Maliha; Schwartz, Egbert; Dijkstra, Paul; Marks, Jane C; Price, Lance B; Keim, Paul; Hungate, Bruce A

2015-06-01

Native soil carbon (C) can be lost in response to fresh C inputs, a phenomenon observed for decades yet still not understood. Using dual-stable isotope probing, we show that changes in the diversity and composition of two functional bacterial groups occur with this 'priming' effect. A single-substrate pulse suppressed native soil C loss and reduced bacterial diversity, whereas repeated substrate pulses stimulated native soil C loss and increased diversity. Increased diversity after repeated C amendments contrasts with resource competition theory, and may be explained by increased predation as evidenced by a decrease in bacterial 16S rRNA gene copies. Our results suggest that biodiversity and composition of the soil microbial community change in concert with its functioning, with consequences for native soil C stability.

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

PubMed

Shang, Shuanghua; Yi, Yanli

2015-12-01

The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

Extracting Quantitative Data from Lunar Soil Spectra

NASA Technical Reports Server (NTRS)

Noble, S. K.; Pieters, C. M.; Hiroi, T.

2005-01-01

Using the modified Gaussian model (MGM) developed by Sunshine et al. [1] we compared the spectral properties of the Lunar Soil Characterization Consortium (LSCC) suite of lunar soils [2,3] with their petrologic and chemical compositions to obtain quantitative data. Our initial work on Apollo 17 soils [4] suggested that useful compositional data could be elicited from high quality soil spectra. We are now able to expand upon those results with the full suite of LSCC soils that allows us to explore a much wider range of compositions and maturity states. The model is shown to be sensitive to pyroxene abundance and can evaluate the relative portion of high-Ca and low-Ca pyroxenes in the soils. In addition, the dataset has provided unexpected insights into the nature and causes of absorption bands in lunar soils. For example, it was found that two distinct absorption bands are required in the 1.2 m region of the spectrum. Neither of these bands can be attributed to plagioclase or agglutinates, but both appear to be largely due to pyroxene.

Bacterial phylogeny structures soil resistomes across habitats

PubMed Central

Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

2014-01-01

Summary Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil1–3, including genes identical to those in human pathogens4. Despite the apparent overlap between soil and clinical resistomes4–6, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown3. General metagenome functions often correlate with the underlying structure of bacterial communities7–12. However, ARGs are hypothesized to be highly mobile4,5,13, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions13,14. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2895 ARGs we discovered were predominantly novel, and represent all major resistance mechanisms15. We demonstrate that distinct soil types harbor distinct resistomes, and that nitrogen fertilizer amendments strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements syntenic with ARGs were rare in soil compared to sequenced pathogens, suggesting that ARGs in the soil may not transfer between bacteria as readily as is observed in the clinic. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny13,14. PMID:24847883

Bacterial phylogeny structures soil resistomes across habitats

NASA Astrophysics Data System (ADS)

Forsberg, Kevin J.; Patel, Sanket; Gibson, Molly K.; Lauber, Christian L.; Knight, Rob; Fierer, Noah; Dantas, Gautam

2014-05-01

Ancient and diverse antibiotic resistance genes (ARGs) have previously been identified from soil, including genes identical to those in human pathogens. Despite the apparent overlap between soil and clinical resistomes, factors influencing ARG composition in soil and their movement between genomes and habitats remain largely unknown. General metagenome functions often correlate with the underlying structure of bacterial communities. However, ARGs are proposed to be highly mobile, prompting speculation that resistomes may not correlate with phylogenetic signatures or ecological divisions. To investigate these relationships, we performed functional metagenomic selections for resistance to 18 antibiotics from 18 agricultural and grassland soils. The 2,895 ARGs we discovered were mostly new, and represent all major resistance mechanisms. We demonstrate that distinct soil types harbour distinct resistomes, and that the addition of nitrogen fertilizer strongly influenced soil ARG content. Resistome composition also correlated with microbial phylogenetic and taxonomic structure, both across and within soil types. Consistent with this strong correlation, mobility elements (genes responsible for horizontal gene transfer between bacteria such as transposases and integrases) syntenic with ARGs were rare in soil by comparison with sequenced pathogens, suggesting that ARGs may not transfer between soil bacteria as readily as is observed between human pathogens. Together, our results indicate that bacterial community composition is the primary determinant of soil ARG content, challenging previous hypotheses that horizontal gene transfer effectively decouples resistomes from phylogeny.

Amplicon-Based Sequencing of Soil Fungi from Wood Preservative Test Sites

PubMed Central

Kirker, Grant T.; Bishell, Amy B.; Jusino, Michelle A.; Palmer, Jonathan M.; Hickey, William J.; Lindner, Daniel L.

2017-01-01

Soil samples were collected from field sites in two AWPA (American Wood Protection Association) wood decay hazard zones in North America. Two field plots at each site were exposed to differing preservative chemistries via in-ground installations of treated wood stakes for approximately 50 years. The purpose of this study is to characterize soil fungal species and to determine if long term exposure to various wood preservatives impacts soil fungal community composition. Soil fungal communities were compared using amplicon-based DNA sequencing of the internal transcribed spacer 1 (ITS1) region of the rDNA array. Data show that soil fungal community composition differs significantly between the two sites and that long-term exposure to different preservative chemistries is correlated with different species composition of soil fungi. However, chemical analyses using ICP-OES found levels of select residual preservative actives (copper, chromium and arsenic) to be similar to naturally occurring levels in unexposed areas. A list of indicator species was compiled for each treatment-site combination; functional guild analyses indicate that long-term exposure to wood preservatives may have both detrimental and stimulatory effects on soil fungal species composition. Fungi with demonstrated capacity to degrade industrial pollutants were found to be highly correlated with areas that experienced long-term exposure to preservative testing. PMID:29093702

Altered precipitation regime affects the function and composition of soil microbial communities on multiple time scales.

PubMed

Zeglin, L H; Bottomley, P J; Jumpponen, A; Rice, C W; Arango, M; Lindsley, A; McGowan, A; Mfombep, P; Myrold, D D

2013-10-01

Climate change models predict that future precipitation patterns will entail lower-frequency but larger rainfall events, increasing the duration of dry soil conditions. Resulting shifts in microbial C cycling activity could affect soil C storage. Further, microbial response to rainfall events may be constrained by the physiological or nutrient limitation stress of extended drought periods; thus seasonal or multiannual precipitation regimes may influence microbial activity following soil wet-up. We quantified rainfall-driven dynamics of microbial processes that affect soil C loss and retention, and microbial community composition, in soils from a long-term (14-year) field experiment contrasting "Ambient" and "Altered" (extended intervals between rainfalls) precipitation regimes. We collected soil before, the day following, and five days following 2.5-cm rainfall events during both moist and dry periods (June and September 2011; soil water potential = -0.01 and -0.83 MPa, respectively), and measured microbial respiration, microbial biomass, organic matter decomposition potential (extracellular enzyme activities), and microbial community composition (phospholipid fatty acids). The equivalent rainfall events caused equivalent microbial respiration responses in both treatments. In contrast, microbial biomass was higher and increased after rainfall in the Altered treatment soils only, thus microbial C use efficiency (CUE) was higher in Altered than Ambient treatments (0.70 +/- 0.03 > 0.46 +/- 0.10). CUE was also higher in dry (September) soils. C-acquiring enzyme activities (beta-glucosidase, cellobiohydrolase, and phenol oxidase) increased after rainfall in moist (June), but not dry (September) soils. Both microbial biomass C:N ratios and fungal:bacterial ratios were higher at lower soil water contents, suggesting a functional and/or population-level shift in the microbiota at low soil water contents, and microbial community composition also differed following wet-up and between seasons and treatments. Overall, microbial activity may directly (C respiration) and indirectly (enzyme potential) reduce soil organic matter pools less in drier soils, and soil C sequestration potential (CUE) may be higher in soils with a history of extended dry periods between rainfall events. The implications include that soil C loss may be reduced or compensated for via different mechanisms at varying time scales, and that microbial taxa with better stress tolerance or growth efficiency may be associated with these functional shifts.

Microbial community composition explains soil respiration responses to changing carbon inputs along an Andes-to-Amazon elevation gradient

PubMed Central

Whitaker, Jeanette; Ostle, Nicholas; Nottingham, Andrew T; Ccahuana, Adan; Salinas, Norma; Bardgett, Richard D; Meir, Patrick; McNamara, Niall P; Austin, Amy

2014-01-01

1. The Andes are predicted to warm by 3–5 °C this century with the potential to alter the processes regulating carbon (C) cycling in these tropical forest soils. This rapid warming is expected to stimulate soil microbial respiration and change plant species distributions, thereby affecting the quantity and quality of C inputs to the soil and influencing the quantity of soil-derived CO2 released to the atmosphere. 2. We studied tropical lowland, premontane and montane forest soils taken from along a 3200-m elevation gradient located in south-east Andean Peru. We determined how soil microbial communities and abiotic soil properties differed with elevation. We then examined how these differences in microbial composition and soil abiotic properties affected soil C-cycling processes, by amending soils with C substrates varying in complexity and measuring soil heterotrophic respiration (RH). 3. Our results show that there were consistent patterns of change in soil biotic and abiotic properties with elevation. Microbial biomass and the abundance of fungi relative to bacteria increased significantly with elevation, and these differences in microbial community composition were strongly correlated with greater soil C content and C:N (nitrogen) ratios. We also found that RH increased with added C substrate quality and quantity and was positively related to microbial biomass and fungal abundance. 4. Statistical modelling revealed that RH responses to changing C inputs were best predicted by soil pH and microbial community composition, with the abundance of fungi relative to bacteria, and abundance of gram-positive relative to gram-negative bacteria explaining much of the model variance. 5. Synthesis. Our results show that the relative abundance of microbial functional groups is an important determinant of RH responses to changing C inputs along an extensive tropical elevation gradient in Andean Peru. Although we do not make an experimental test of the effects of climate change on soil, these results challenge the assumption that different soil microbial communities will be ‘functionally equivalent’ as climate change progresses, and they emphasize the need for better ecological metrics of soil microbial communities to help predict C cycle responses to climate change in tropical biomes. PMID:25520527

Soil-plant-microbial relations in hydrothermally altered soils of Northern California

USDA-ARS?s Scientific Manuscript database

Soils developed on relict hydrothermally altered soils throughout the Western United States present unique opportunities to study the role of geology on above and belowground biotic activity and composition. Soil and vegetation samples were taken at three unaltered andesite and three hydrothermally ...

Land use influences arbuscular mycorrhizal fungal communities in the farming-pastoral ecotone of northern China.

PubMed

Xiang, Dan; Verbruggen, Erik; Hu, Yajun; Veresoglou, Stavros D; Rillig, Matthias C; Zhou, Wenping; Xu, Tianle; Li, Huan; Hao, Zhipeng; Chen, Yongliang; Chen, Baodong

2014-12-01

We performed a landscape-scale investigation to compare the arbuscular mycorrhizal fungal (AMF) communities between grasslands and farmlands in the farming-pastoral ecotone of northern China. AMF richness and community composition were examined with 454 pyrosequencing. Structural equation modelling (SEM) and multivariate analyses were applied to disentangle the direct and indirect effects (mediated by multiple environmental factors) of land use on AMF. Land use conversion from grassland to farmland significantly reduced AMF richness and extraradical hyphal length density, and these land use types also differed significantly in AMF community composition. SEM showed that the effects of land use on AMF richness and hyphal length density in soil were primarily mediated by available phosphorus and soil structural quality. Soil texture was the strongest predictor of AMF community composition. Soil carbon, nitrogen and soil pH were also significantly correlated with AMF community composition, indicating that these abiotic variables could be responsible for some of the community composition differences among sites. Our study shows that land use has a partly predictable effect on AMF communities across this ecologically relevant area of China, and indicates that high soil phosphorus concentrations and poor soil structure are particularly detrimental to AMF in this fragile ecosystem. © 2014 The Author. New Phytologist © 2014 New Phytologist Trust.

Nutrient addition dramatically accelerates microbial community succession.

PubMed

Knelman, Joseph E; Schmidt, Steven K; Lynch, Ryan C; Darcy, John L; Castle, Sarah C; Cleveland, Cory C; Nemergut, Diana R

2014-01-01

The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients--important drivers of plant succession--affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession.

Nutrient Addition Dramatically Accelerates Microbial Community Succession

PubMed Central

Knelman, Joseph E.; Schmidt, Steven K.; Lynch, Ryan C.; Darcy, John L.; Castle, Sarah C.; Cleveland, Cory C.; Nemergut, Diana R.

2014-01-01

The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients – important drivers of plant succession – affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession. PMID:25050551

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

NASA Astrophysics Data System (ADS)

Wang, Haitao; Marshall, Christopher W.; Cheng, Minying; Xu, Huijuan; Li, Hu; Yang, Xiaoru; Zheng, Tianling

2017-03-01

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Greenhouse gas emissions from a Cu-contaminated soil remediated by in situ stabilization and phytomanaged by a mixed stand of poplar, willows, and false indigo-bush.

PubMed

Šimek, M; Elhottová, D; Mench, M; Giagnoni, L; Nannipieri, P; Renella, G

2017-11-02

Phytomanagement of trace element-contaminated soils can reduce soil toxicity and restore soil ecological functions, including the soil gas exchange with the atmosphere. We studied the emission rate of the greenhouse gases (GHGs) CO 2 , CH 4 , and N 2 O; the potential CH 4 oxidation; denitrification enzyme activity (DEA), and glucose mineralization of a Cu-contaminated soil amended with dolomitic limestone and compost, alone or in combination, after a 2-year phytomanagement with a mixed stand of Populus nigra, Salix viminalis, S. caprea, and Amorpha fruticosa. Soil microbial biomass and microbial community composition after analysis of the phospholipid fatty acids (PLFA) profile were determined. Phytomanagement significantly reduced Cu availability and soil toxicity, increased soil microbial biomass and glucose mineralization capacity, changed the composition of soil microbial communities, and increased the CO 2 and N 2 O emission rates and DEA. Despite such increases, microbial communities were evolving toward less GHG emission per unit of microbial biomass than in untreated soils. Overall, the aided phytostabilization option would allow methanotrophic populations to establish in the remediated soils due to decreased soil toxicity and increased nutrient availability.

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

PubMed Central

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-01-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition. PMID:27256545

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition.

PubMed

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-03

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Differential effects of conifer and broadleaf litter inputs on soil organic carbon chemical composition through altered soil microbial community composition

NASA Astrophysics Data System (ADS)

Wang, Hui; Liu, Shi-Rong; Wang, Jing-Xin; Shi, Zuo-Min; Xu, Jia; Hong, Pi-Zheng; Ming, An-Gang; Yu, Hao-Long; Chen, Lin; Lu, Li-Hua; Cai, Dao-Xiong

2016-06-01

A strategic selection of tree species will shift the type and quality of litter input, and subsequently magnitude and composition of the soil organic carbon (SOC) through soil microbial community. We conducted a manipulative experiment in randomized block design with leaf litter inputs of four native subtropical tree species in a Pinus massoniana plantation in southern China and found that the chemical composition of SOC did not differ significantly among treatments until after 28 months of the experiment. Contrasting leaf litter inputs had significant impacts on the amounts of total microbial, Gram-positive bacterial, and actinomycic PLFAs, but not on the amounts of total bacterial, Gram-negative bacterial, and fungal PLFAs. There were significant differences in alkyl/O-alkyl C in soils among the leaf litter input treatments, but no apparent differences in the proportions of chemical compositions (alkyl, O-alkyl, aromatic, and carbonyl C) in SOC. Soil alkyl/O-alkyl C was significantly related to the amounts of total microbial, and Gram-positive bacterial PLFAs, but not to the chemical compositions of leaf litter. Our findings suggest that changes in forest leaf litter inputs could result in changes in chemical stability of SOC through the altered microbial community composition.

Transport mechanisms of soil-bound mercury in the erosion process during rainfall-runoff events.

PubMed

Zheng, Yi; Luo, Xiaolin; Zhang, Wei; Wu, Xin; Zhang, Juan; Han, Feng

2016-08-01

Soil contamination by mercury (Hg) is a global environmental issue. In watersheds with a significant soil Hg storage, soil erosion during rainfall-runoff events can result in nonpoint source (NPS) Hg pollution and therefore, can extend its environmental risk from soils to aquatic ecosystems. Nonetheless, transport mechanisms of soil-bound Hg in the erosion process have not been explored directly, and how different fractions of soil organic matter (SOM) impact transport is not fully understood. This study investigated transport mechanisms based on rainfall-runoff simulation experiments. The experiments simulated high-intensity and long-duration rainfall conditions, which can produce significant soil erosion and NPS pollution. The enrichment ratio (ER) of total mercury (THg) was the key variable in exploring the mechanisms. The main study findings include the following: First, the ER-sediment flux relationship for Hg depends on soil composition, and no uniform ER-sediment flux function exists for different soils. Second, depending on soil composition, significantly more Hg could be released from a less polluted soil in the early stage of large rainfall events. Third, the heavy fraction of SOM (i.e., the remnant organic matter coating on mineral particles) has a dominant influence on the enrichment behavior and transport mechanisms of Hg, while clay mineral content exhibits a significant, but indirect, influence. The study results imply that it is critical to quantify the SOM composition in addition to total organic carbon (TOC) for different soils in the watershed to adequately model the NPS pollution of Hg and spatially prioritize management actions in a heterogeneous watershed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of 10-Year Management Regimes on the Soil Seed Bank in Saline-Alkaline Grassland

PubMed Central

Ma, Hongyuan; Yang, Haoyu; Liang, Zhengwei; Ooi, Mark K. J.

2015-01-01

Background Management regimes for vegetation restoration of degraded grasslands can significantly affect the process of ecological succession. However, few studies have focused on variation in the soil seed bank during vegetation restoration under different management regimes, especially in saline-alkaline grassland habitats. Our aim was to provide insights into the ecological effects of grassland management regimes on soil seed bank composition and vegetation establishment in mown, fenced, transplanted and natural grassland sites, all dominated by the perennial rhizomatous grass Leymus chinensis. Methodology We studied species composition and diversity in both the soil seed bank and aboveground vegetation in differently managed grasslands in Northeast China. An NMDS (nonmetric multidimensional scaling) was used to evaluate the relationship between species composition, soil seed banks, aboveground vegetation and soil properties. Principal Findings Fenced and mown grassland sites had high density and species richness in both the soil seed bank and aboveground vegetation. The Transplanted treatment exhibited the highest vegetation growth and seed production of the target species L. chinensis. Seeds of L. chinensis in the soil occurred only in transplanted and natural grassland. Based on the NMDS analysis, the number of species in both the soil seed bank and aboveground vegetation were significantly related to soil Na+, Cl-, RSC (residual sodium carbonate), alkalinity, ESP (exchangeable sodium percentage) and AP (available phosphorus). Conclusions Soil seed bank composition and diversity in the saline-alkaline grassland were significantly affected by the management regimes implemented, and were also significantly related to the aboveground vegetation and several soil properties. Based on vegetative growth, reproductive output and maintenance of soil seed bank, the transplanting was identified as the most effective method for relatively rapid restoration of the target species L. chinensis. This approach could be beneficial for the restoration of dominant species in a wide range of degraded grassland ecosystems. PMID:25902145

Soil Microbe Active Community Composition and Capability of Responding to Litter Addition after 12 Years of No Inputs

PubMed Central

Brewer, Elizabeth; Yarwood, Rockie; Lajtha, Kate; Myrold, David

2013-01-01

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. PMID:23263952

Comparison of aboveground vegetation and soil seed bank composition at sites of different grazing intensity around a savanna-woodland watering point in West Africa.

PubMed

Sanou, Lassina; Zida, Didier; Savadogo, Patrice; Thiombiano, Adjima

2018-06-11

Grazing removes a plant's aboveground vegetative and reproductive tissues and can modify the soil seed bank, potentially impacting the restoration of preferred species. Knowledge about aboveground vegetation and species composition of soil seed bank and the processes that contribute to vegetation recovery on and surrounding watering points subjected to grazing is lacking. Successful restoration strategies hinge on addressing these knowledge gaps. We assessed the effects of livestock grazing on aboveground vegetation and soil seed bank characteristics along a river bank and surrounding areas subject to different grazing intensities and draw implications for restoration. Plots (50 × 50 m) were established along five transects representing differing levels of grazing intensity. Soil samples were taken from three layers within each plot to determine soil properties and species composition of soil seed bank using the seedling emergence method. Heavy grazing resulted in the disappearance of perennial grasses, a reduction in species diversity and a decrease in soil nutrients with increased soil depth. Overall, the similarity between the extant aboveground vegetation and flora within the soil seed bank was low. The soil seed bank was dominated by herbaceous species and two woody species, suggesting that many woody species are not accumulating in the soil. With increasing soil depth, the seed density and richness declined. Canonical correspondence analyses (CCAs) showed that emerged seedlings from the soil seed bank were significantly influenced by soil carbon, organic matter, total nitrogen, total potassium and soil cation exchange capacity. This finding suggests that current grazing practices have a negative impact on the vegetation surrounding watering points; hence there is a need for improved grazing management strategies and vegetation restoration in these areas. The soil seed bank alone cannot restore degraded river banks; active transfer of propagules from adjacent undisturbed forest areas is essential.

Unravelling Linkages between Plant Community Composition and the Pathogen-Suppressive Potential of Soils

PubMed Central

Latz, Ellen; Eisenhauer, Nico; Rall, Björn Christian; Scheu, Stefan; Jousset, Alexandre

2016-01-01

Plant diseases cause dramatic yield losses worldwide. Current disease control practices can be deleterious for the environment and human health, calling for alternative and sustainable management regimes. Soils harbour microorganisms that can efficiently suppress pathogens. Uncovering mediators driving their functioning in the field still remains challenging, but represents an essential step in order to develop strategies for increased soil health. We set up plant communities of varying richness to experimentally test the potential of soils differing in plant community history to suppress the pathogen Rhizoctonia solani. The results indicate that plant communities shape soil-disease suppression via changes in abiotic soil properties and the abundance of bacterial groups including species of the genera Actinomyces, Bacillus and Pseudomonas. Further, the results suggest that pairwise interactions between specific plant species strongly affect soil suppressiveness. Using structural equation modelling, we provide a pathway orientated framework showing how the complex interactions between plants, soil and microorganisms jointly shape soil suppressiveness. Our results stress the importance of plant community composition as a determinant of soil functioning, such as the disease suppressive potential of soils. PMID:27021053

Soil quality changes in response to their pollution by heavy metals, Georgia.

PubMed

Matchavariani, Lia; Kalandadze, Besik; Lagidze, Lamzira; Gokhelashvili, Nino; Sulkhanishvili, Nino; Paichadze, Nino; Dvalashvili, Giorgi

2015-01-01

The present study deals with the composition, migration and accumulation of heavy metals in irrigated soils, plants and partially natural waters; and also, establishing the possible sources of pollution and their impact on environmental situation. The content of toxic elements in the irrigated soils adjacent to ore mining and processing enterprise were studied. Content of toxic elements in the irrigated soils adjacent to ore mining, showed that more than half of territory was seriously polluted by copper and zinc. Some part of the area were considered catastrophically polluted. Expressed technogenesis taking place influenced irrigation. Heavy metals like copper, zinc and manganese negative by effected the properties of soil, thus composition and soil-forming processes taking place in the soil. It was especially well represented in the deterioration of hydro-physical potential of the soil. Irrigation of agricultural land plots by water, polluted with heavy metals changed the pH. Balanced correlation among solid, liquid and gas phases was disrupted. In highly polluted soil, the cementing processes took place that sharply increased the bulk density of the soil, deteriorated the porosity of soil and reduced water permeability critically.

Effect of reclamation of abandoned salinized farmland on soil bacterial communities in arid northwest China.

PubMed

Cheng, Zhibo; Chen, Yun; Zhang, Fenghua

2018-07-15

Understanding the impact of reclamation of abandoned salinized farmland on soil bacterial community is of great importance for maintaining soil health and sustainability in arid regions. In this study, we used field sampling and 454 pyrosequencing methods to investigate the effects of 5-year reclamation treatments on soil properties, bacterial community composition and diversity. The four reclamation treatments are: abandoned salinized farmland (CK), cropland (CL), grassland (GL) and woodland (WL). We have found soil properties are significantly altered by abandoned salinized farmland reclamation. In particular, the lowest soil pH and electrical conductivity (EC) values are observed in CL (P<0.05). The dominant phyla are Firmicutes, Proteobacteria, Chloroflexi, Actinobacteria and Acidobacteria in all treatments. At the genus levels, the relative abundance of Bacillus, Lactococcus, Streptococcus and Enterococcus in CK, GL and WL is significantly higher than in CL. Bacterial diversity indices (i.e. ACE, Chao and Shannon) dramatically increase after the reclamation, with the highest in CL. Similar patterns of bacterial communities have been observed in CK, GL and WL soils, but significantly different from CL. Regression analyses indicate that the relative abundance of these phyla are significantly correlated with soil Fe, pH and EC. Results from non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) indicate that soil Fe content, EC and pH are the most important factors in shaping soil bacterial communities. Overall, results indicate that abandoned salinized farmland reclaimed for CL significantly decrease soil pH and EC, and increase soil bacterial community diversity. Soil Fe concentration, EC and pH are the dominant environmental factors affecting soil bacterial community composition. The important role of Fe concentration in shaping bacterial community composition is a new discovery among the similar studies. Copyright © 2018. Published by Elsevier B.V.

Microbial and geochemical assessment of bauxitic un-mined and post-mined chronosequence soils from Mocho Mountains, Jamaica.

PubMed

Lewis, Dawn E; Chauhan, Ashvini; White, John R; Overholt, Will; Green, Stefan J; Jasrotia, Puja; Wafula, Denis; Jagoe, Charles

2012-10-01

Microorganisms are very sensitive to environmental change and can be used to gauge anthropogenic impacts and even predict restoration success of degraded environments. Here, we report assessment of bauxite mining activities on soil biogeochemistry and microbial community structure using un-mined and three post-mined sites in Jamaica. The post-mined soils represent a chronosequence, undergoing restoration since 1987, 1997, and 2007. Soils were collected during dry and wet seasons and analyzed for pH, organic matter (OM), total carbon (TC), nitrogen (TN), and phosphorus. The microbial community structure was assessed through quantitative PCR and massively parallel bacterial ribosomal RNA (rRNA) gene sequencing. Edaphic factors and microbial community composition were analyzed using multivariate statistical approaches and revealed a significant, negative impact of mining on soil that persisted even after greater than 20 years of restoration. Seasonal fluctuations contributed to variation in measured soil properties and community composition, but they were minor in comparison to long-term effects of mining. In both seasons, post-mined soils were higher in pH but OM, TC, and TN decreased. Bacterial rRNA gene analyses demonstrated a general decrease in diversity in post-mined soils and up to a 3-log decrease in rRNA gene abundance. Community composition analyses demonstrated that bacteria from the Proteobacteria (α, β, γ, δ), Acidobacteria, and Firmicutes were abundant in all soils. The abundance of Firmicutes was elevated in newer post-mined soils relative to the un-mined soil, and this contrasted a decrease, relative to un-mined soils, in proteobacterial and acidobacterial rRNA gene abundances. Our study indicates long-lasting impacts of mining activities to soil biogeochemical and microbial properties with impending loss in soil productivity.

Differential Response of Acidobacteria Subgroups to Forest-to-Pasture Conversion and Their Biogeographic Patterns in the Western Brazilian Amazon

PubMed Central

Navarrete, Acacio A.; Venturini, Andressa M.; Meyer, Kyle M.; Klein, Ann M.; Tiedje, James M.; Bohannan, Brendan J. M.; Nüsslein, Klaus; Tsai, Siu M.; Rodrigues, Jorge L. M.

2015-01-01

Members of the phylum Acidobacteria are among the most abundant soil bacteria on Earth, but little is known about their response to environmental changes. We asked how the relative abundance and biogeographic patterning of this phylum and its subgroups responded to forest-to-pasture conversion in soils of the western Brazilian Amazon. Pyrosequencing of 16S rRNA genes was employed to assess the abundance and composition of the Acidobacteria community across 54 soil samples taken using a spatially nested sampling scheme at the landscape level. Numerically, Acidobacteria represented 20% of the total bacterial community in forest soils and 11% in pasture soils. Overall, 15 different Acidobacteria subgroups of the current 26 subgroups were detected, with Acidobacteria subgroups 1, 3, 5, and 6 accounting together for 87% of the total Acidobacteria community in forest soils and 75% in pasture soils. Concomitant with changes in soil chemistry after forest-to-pasture conversion—particularly an increase in properties linked to soil acidity and nutrient availability—we observed an increase in the relative abundances of Acidobacteria subgroups 4, 10, 17, and 18, and a decrease in the relative abundances of other Acidobacteria subgroups in pasture relative to forest soils. The composition of the total Acidobacteria community as well as the most abundant Acidobacteria subgroups (1, 3, 5, and 6) was significantly more similar in composition across space in pasture soils than in forest soils. These results suggest that preponderant responses of Acidobacteria subgroups, especially subgroups 1, 3, 4, 5, and 6, to forest-to-pasture conversion effects in soils could be used to define management-indicators of agricultural practices in the Amazon Basin. These acidobacterial responses are at least in part through alterations on acidity- and nutrient-related properties of the Amazon soils. PMID:26733981

Soil pH is a Key Determinant of Soil Fungal Community Composition in the Ny-Ålesund Region, Svalbard (High Arctic)

PubMed Central

Zhang, Tao; Wang, Neng-Fei; Liu, Hong-Yu; Zhang, Yu-Qin; Yu, Li-Yan

2016-01-01

This study assessed the fungal community composition and its relationships with properties of surface soils in the Ny-Ålesund Region (Svalbard, High Arctic). A total of thirteen soil samples were collected and soil fungal community was analyzed by 454 pyrosequencing with fungi-specific primers targeting the rDNA internal transcribed spacer (ITS) region. The following eight soil properties were analyzed: pH, organic carbon (C), organic nitrogen (N), ammonium nitrogen (NH4+-N), silicate silicon (SiO42--Si), nitrite nitrogen (NO2--N), phosphate phosphorus (PO43--P), and nitrate nitrogen (NO3--N). A total of 57,952 reads belonging to 541 operational taxonomic units (OTUs) were found. of these OTUs, 343 belonged to Ascomycota, 100 to Basidiomycota, 31 to Chytridiomycota, 22 to Glomeromycota, 11 to Zygomycota, 10 to Rozellomycota, whereas 24 belonged to unknown fungi. The dominant orders were Helotiales, Verrucariales, Agaricales, Lecanorales, Chaetothyriales, Lecideales, and Capnodiales. The common genera (>eight soil samples) were Tetracladium, Mortierella, Fusarium, Cortinarius, and Atla. Distance-based redundancy analysis (db-rda) and analysis of similarities (ANOSIM) revealed that soil pH (p = 0.001) was the most significant factor in determining the soil fungal community composition. Members of Verrucariales were found to predominate in soils of pH 8–9, whereas Sordariales predominated in soils of pH 7–8 and Coniochaetales predominated in soils of pH 6–7. The results suggest the presence and distribution of diverse soil fungal communities in the High Arctic, which can provide reliable data for studying the ecological responses of soil fungal communities to climate changes in the Arctic. PMID:26955371

Genesis of peat-bog soils in the northern taiga spruce forests of the Kola Peninsula

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nikonov, V.V.

1981-01-01

The characteristics of soil formation processes in the Peat-Bog soils of waterlogged spruce phytocenoses on the Kola Peninsula are investigated. It is found that the ash composition of the peat layer is determined primarily by the composition of the buried plant residues. The effect of the chemical composition of water feeding the peat bogs is determined. (Refs. 7).

Microbial Community Composition Affects Soil Fungistasis†

PubMed Central

de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J. A.; Kowalchuk, George A.; van Veen, Johannes A.

2003-01-01

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis. PMID:12571002

Bacteria as Emerging Indicators of Soil Condition

PubMed Central

Hermans, Syrie M.; Buckley, Hannah L.; Case, Bradley S.; Curran-Cournane, Fiona; Taylor, Matthew

2016-01-01

ABSTRACT Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. IMPORTANCE The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future. PMID:27793827

The effect of soil biodiversity on soil quality after agricultural reclamation at the eastern coast of China

NASA Astrophysics Data System (ADS)

Wang, Xiaohan; Yang, Jianghua; Pu, Lijie; Chen, Xinjian

2017-04-01

Large area of tidal flats in Chinese coast has been reclaimed to support agriculture and urban development because of rapid population and economic growth. Knowledge of soil development mechanisms is essential for efficient management of land resources in coastal zone. So far, most studies have focused on consequences of soil physico-chemical properties on soil quality evolution after tideland reclamation for cultivation; yet a large part of soil bioprocess drives many soil processes. The effect of organism composition on the performance of soil development remains unclear. The purpose of our work was to reveal the organism composition change and its influence on soil quality impotent. In this study, we choose seven reclamation districts along a chronosequence in eastern coast of China, which were respectively reclaimed in 1956, 1971, 1980, 1997, 2009, 2013 and unenclosed tidal flat. The latest districts reclaimed in 2013 were left to succession fallow which were covered with halophytic vegetation and the rest districts were agriculturally managed. Soil samples at 0-20 cm were collected in each district. Soil physical, chemical and biological properties and wheat yields were measured. The result showed after the transformation from tidal flat to cropland, longer tillage time (>5 year) lead to higher soil clay and silt, SOC contents and lower bulk density, while soil clay and C contents declined within the first 5 years after reclamation. Agricultural reclamation significantly improved SOC contents of 0-20 cm depth form 0.11±0.05% to 0.77±0.10%. It needs about 35 years to achieve stable yield level after reclamation. Meanwhile, the soil community composition changed strongly over time. More significant relationships were found among soil physicochemical properties and bacteria community. And the variation trend of soil community richness (chao1) is similar to soil C contents, dropped at first 5 years and then significantly increased. Our results indicate that the soil biodiversity growth promotes the soil quality recovery after crop cultivation. Both the soil physical environment and fertility were improved.

Bacteria as Emerging Indicators of Soil Condition.

PubMed

Hermans, Syrie M; Buckley, Hannah L; Case, Bradley S; Curran-Cournane, Fiona; Taylor, Matthew; Lear, Gavin

2017-01-01

Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of Pirellulaceae and soil pH, members of Gaiellaceae and carbon-to-nitrogen ratios, members of Bradyrhizobium and the levels of Olsen P (a measure of plant available phosphorus), and members of Chitinophagaceae and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition. The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future. Copyright © 2016 American Society for Microbiology.

Soil biogeochemistry properties vary between two boreal forest ecosystems in Quebec: significant differences in soil carbon, available nutrients and iron and aluminium crystallinity

NASA Astrophysics Data System (ADS)

Bastianelli, Carole; Ali, Adam A.; Beguin, Julien; Bergeron, Yves; Grondin, Pierre; Hély, Christelle; Paré, David

2017-04-01

At the northernmost extent of the managed forest in Quebec, the boreal forest is currently undergoing an ecological transition from closed-canopy black spruce-moss forests towards open-canopy lichen woodlands, which spread southward. Our study aim was to determine whether this shift could impact soil properties on top of its repercussions on forest productivity or carbon storage. We studied the soil biogeochemical composition of three pedological layers in moss forests (MF) and lichen woodlands (LW) north of the Manicouagan crater in Quebec. The humus layer (FH horizons) was significantly thicker and held more carbon, nitrogen and exchangeable Ca and Mg in MF plots than in LW plots. When considering mineral horizons, we found that the deep C horizon had a very close composition in both ecosystem plots, suggesting that the parent material was of similar geochemical nature. This was expected as all selected sites developed from glacial deposit. Multivariate analysis of surficial mineral B horizon showed however that LW B horizon displayed higher concentrations of Al and Fe oxides than MF B horizon, particularly for inorganic amorphous forms. Conversely, main exchangeable base cations (Ca, Mg) were higher in B horizon of MF than that of LW. Ecosystem types explained much of the variations in the B horizon geochemical composition. We thus suggest that the differences observed in the geochemical composition of the B horizon have a biological origin rather than a mineralogical origin. We also showed that total net stocks of carbon stored in MF soils were three times higher than in LW soils (FH + B horizons, roots apart). Altogether, we suggest that variations in soil properties between MF and LW are linked to a cascade of events involving the impacts of natural disturbances such as wildfires on forest regeneration that determines the of vegetation structure (stand density) and composition (ground cover type) and their subsequent consequences on soil environmental parameters (moisture, radiation rate, redox conditions, etc.). Our data underline significant differences in soil biogeochemistry under different forest ecosystems and reveal the importance of interactions in the soil-vegetation-climate system for the determination of soil composition.

Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce

PubMed Central

Nacke, Heiko; Goldmann, Kezia; Schöning, Ingo; Pfeiffer, Birgit; Kaiser, Kristin; Castillo-Villamizar, Genis A.; Schrumpf, Marion; Buscot, François; Daniel, Rolf; Wubet, Tesfaye

2016-01-01

The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species (Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0–10, 10–20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0–10 vs. 10–20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees. PMID:28066384

Fine Spatial Scale Variation of Soil Microbial Communities under European Beech and Norway Spruce.

PubMed

Nacke, Heiko; Goldmann, Kezia; Schöning, Ingo; Pfeiffer, Birgit; Kaiser, Kristin; Castillo-Villamizar, Genis A; Schrumpf, Marion; Buscot, François; Daniel, Rolf; Wubet, Tesfaye

2016-01-01

The complex interactions between trees and soil microbes in forests as well as their inherent seasonal and spatial variations are poorly understood. In this study, we analyzed the effects of major European tree species ( Fagus sylvatica L. and Picea abies (L.) Karst) on soil bacterial and fungal communities. Mineral soil samples were collected from different depths (0-10, 10-20 cm) and at different horizontal distances from beech or spruce trunks (0.5, 1.5, 2.5, 3.5 m) in early summer and autumn. We assessed the composition of soil bacterial and fungal communities based on 16S rRNA gene and ITS DNA sequences. Community composition of bacteria and fungi was most strongly affected by soil pH and tree species. Different ectomycorrhizal fungi (e.g., Tylospora ) known to establish mutualistic associations with plant roots showed a tree species preference. Moreover, bacterial and fungal community composition showed spatial and seasonal shifts in soil surrounding beech and spruce. The relative abundance of saprotrophic fungi was higher at a depth of 0-10 vs. 10-20 cm depth. This was presumably a result of changes in nutrient availability, as litter input and organic carbon content decreased with soil depth. Overall bacterial community composition showed strong variations under spruce with increasing distance from the tree trunks, which might be attributed in part to higher fine root biomass near spruce trunks. Furthermore, overall bacterial community composition was strongly affected by season under deciduous trees.

The influence of litter composition across the litter–soil interface on mass loss, nitrogen dynamics and the decomposer community

EPA Science Inventory

Many studies have investigated the influence of plant litter species composition on decomposition, but results have been context-dependent. Litter and soil are considered to constitute a decomposition continuum, but whether litter and soil ecosystems respond to litter identity an...

Seasonal switchgrass ecotype contributions to soil organic carbon, deep soil microbial community composition and rhizodeposit uptake during an extreme drought

USDA-ARS?s Scientific Manuscript database

The importance of rhizodeposit C and associated microbial communities in deep soil C stabilization is relatively unknown. Phenotypic variability in plant root biomass could impact C cycling through belowground plant allocation, rooting architecture, and microbial community abundance and composition...

[Thermodynamic forecasting of reagents composition for soils decontamination].

PubMed

Nikolaev, V P; Nikolaevskiĭ, V B; Chirkina, I V; Shcheglov, M Iu

2009-01-01

Based on thermodynamic studies, the authors conducted laboratory experiments on searching optimal composition of leaching reagents solution for soils decontamination, when contaminated with Cs-137, of activity coefficient for caesium sulfate microquantities in macrocomponents solutions. The method could be used for modelling the radionuclides phase equillibrium and relocations in soils.

Effects of soil water repellency on microbial community structure and functions in Mediterranean pine forests

NASA Astrophysics Data System (ADS)

Lozano, Elena; Grayston, Sue J.; Mataix-Solera, Jorge; Arcenegui, Victoria; Jimenez-Pinilla, Patricia; Mataix-Beneyto, Jorge

2015-04-01

Soil water repellency (SWR) is a property commonly observed in forest areas showing wettable and water repellent patches with high spatial variability. SWR can greatly influence the hydrology and the ecology of forest soils. The capacity of soil microorganisms to degrade different organic compounds depends upon species composition, so this may affect changes in SWR on the microsite scale (such as the presence of soil water repellent patches; Mülleret al., 2010). In the Mediterranean forest context, SWR has been found to be related to microbial community composition. The accumulation of different hydrophobic compounds might be causing the shifts in microbial community structure (Lozano et al., 2014). In this study we investigated the effects of SWR persistence on soil microbial community structure and enzyme activity under Pinus halepensis forest in three different sites: Petrer, Gorga and Jávea (Alicante, E Spain). Soil samples were classified into three different water repellency classes (wettable, slight or strongly water repellent samples) depending on the SWR persistence. The soil microbial community was determined through phospholipid fatty acids (PLFAs). Enzyme activities chosen for this study were cellulase, β-glucosidase and N-acetyl-β-glucosaminide (NAG). The relationships between microbiological community structure and some soil properties such as pH, Glomalin Related Soil Protein, soil organic matter content and soil respiration were also studied. Redundancy analyses and decomposition of the variances were performed to clarify how microbial community composition and enzyme activities are affected by SWR and soil properties. The effect of SWR on microbial community composition differed between locations. This effect was clearer in the Petrer site. Enzyme activity varied considerably depending on SWR persistence. The highest activities were found in slightly SWR samples and the lowest mostly in the strongly water repellent ones. These preliminary results suggest a possible influence of SWR on microbial structure and its activity in soils. References: Lozano, E., García-Orenes, F., Bárcenas-Moreno, G., Jiménez-Pinilla, P., Mataix-Solera, J., Arcenegui, V., Morugán-Coronado, A., Mataix-Beneyto, J., 2014. Relationships between soil water repellency and microbial community composition under different plant species in a Mediterranean semiarid forest. J. Hydrol. Hydromech., 62, 101-107 Müller, K., Deurer, M., Newton, P.C.D., 2010. Is there a link between elevated atmospheric carbon dioxide concentration, soil water repellency and soil carbon mineralization? Agric. Ecosyst. Environ., 139, 98-109. Acknowledgements: to the "Ministerio de Economía and Competitividad" of Spanish Government for finance the POSTFIRE project (CGL2013- 47862-C2-1-R), Generalitat Valenciana for PhD grant, and Spanish Soil Science Society and FUEGORED for their support.

An integrated view of the chemistry and mineralogy of martian soils

USGS Publications Warehouse

Yen, A. S.; Gellert, Ralf; Schroder, C.; Morris, R.V.; Bell, J.F.; Knudson, A.T.; Clark, B. C.; Ming, D. W.; Crisp, J.A.; Arvidson, R. E.; Blaney, D.; Brückner, J.; Christensen, P.R.; DesMarais, D.J.; De Souza, P.A.; Economou, T.E.; Ghosh, A.; Hahn, B.C.; Herkenhoff, K. E.; Haskin, L.A.; Hurowitz, J.A.; Joliff, B.L.; Johnson, J. R.; Klingelhofer, G.; Madsen, M.B.; McLennan, S.M.; McSween, H.Y.; Richter, L.; Rieder, R.; Rodionov, D.; Soderblom, L.; Squyres, S. W.; Tosca, N.J.; Wang, A.; Wyatt, M.; Zipfel, J.

2005-01-01

The mineralogical and elemental compositions of the martian soil are indicators of chemical and physical weathering processes. Using data from the Mars Exploration Rovers, we show that bright dust deposits on opposite sides of the planet are part of a global unit and not dominated by the composition of local rocks. Dark soil deposits at both sites have similar basaltic mineralogies, and could reflect either a global component or the general similarity in the compositions of the rocks from which they were derived. Increased levels of bromine are consistent with mobilization of soluble salts by thin films of liquid water, but the presence of olivine in analysed soil samples indicates that the extent of aqueous alteration of soils has been limited. Nickel abundances are enhanced at the immediate surface and indicate that the upper few millimetres of soil could contain up to one per cent meteoritic material.

Soil spectral characterization

NASA Technical Reports Server (NTRS)

Stoner, E. R.; Baumgardner, M. F.

1981-01-01

The spectral characterization of soils is discussed with particular reference to the bidirectional reflectance factor as a quantitative measure of soil spectral properties, the role of soil color, soil parameters affecting soil reflectance, and field characteristics of soil reflectance. Comparisons between laboratory-measured soil spectra and Landsat MSS data have shown good agreement, especially in discriminating relative drainage conditions and organic matter levels in unvegetated soils. The capacity to measure both visible and infrared soil reflectance provides information on other soil characteristics and makes it possible to predict soil response to different management conditions. Field and laboratory soil spectral characterization helps define the extent to which intrinsic spectral information is available from soils as a consequence of their composition and field characteristics.

STABLE CARBON ISOTOPE RATIO AND COMPOSITION OF MICROBIAL FATTY ACIDS IN TROPICAL SOILS

EPA Science Inventory

The soil microbial community plays a critical part in tropical ecosystem functioning through its role in the soil organic matter (SOM) cycle. This study evaluates the relative effects of soil type and land use on: (1) soil microbial community structure and (2) the contribution o...

Influence of site and soil properties on the DRIFT spectra of northern cold-region soils

USDA-ARS?s Scientific Manuscript database

We investigated the influence of site characteristics and soil properties on the chemical composition of organic matter in soils collected from a latitudinal transect across Alaska through analysis of diffuse reflectance infrared Fourier transform mid infrared (MidIR) spectra of bulk soils. The stud...

[Effect of Long-Term Fertilization on Organic Nitrogen Functional Groups in Black Soil as Revealed by Synchrotron-Based X-Ray Absorption Near-Edge Structure Spectroscopy].

PubMed

Li, Hui; Gao, Qiang; Wang, Shuai; Zhu, Ping; Zhang, Jin-jing; Zhao, Yi-dong

2015-07-01

Nitrogen (N) is a common limiting nutrient in crop production. The N content of soil has been used as an important soil fertility index. Organic N is the major form of N in soil. In most agricultural surface soils, more than 90% of total N occurs in organic forms. Therefore, understanding the compositional characteristics of soil organic N functional groups can provide the scientific basis for formulating the reasonable farmland management strategies. Synchrotron radiation soft X-ray absorption near-edge structure (N K-edge XANES) spectroscopy is the most powerful tool to characterize in situ organic N functional groups compositions in soil. However, to our most knowledge, no studies have been conducted to examine the organic N functional groups compositions of soil using N K-edge XANES spectroscopy under long-term fertilization practices. Based on a long-term field experiment (started in 1990) in a black soil (Gongzhuling, Northeast China), we investigated the differences in organic N functional groups compositions in bulk soil and clay-size soil fraction among fertilization patterns using synchrotron-based N K- edge XANES spectroscopy. Composite soil samples (0-20 cm) were collected in 2008. The present study included six treatments: farmland fallow (FALL), no-fertilization control (CK), chemical nitrogen, phosphorus, and potassium fertilization (NPK), NPK in combination with organic manure (NPKM), 1.5 times of NPKM (1.5 NPKM), and NPK in combination with maize straw (NPKS). The results showed that N K-edge XANES spectra of all the treatments under study exhibited characteristic absorption peaks in the ranges of 401.2-401.6 and 402.7-403.1 eV, which were assigned as amides/amine-N and pyrrole-N, respectively. These characteristic absorption peaks were more obvious in clay-size soil fraction than in bulk soil. The results obtained from the semi-quantitative analysis of N K-edge XANES spectra indicated that the relative proportion of amides/amine-N was the highest in both bulk soil and clay-size soil fraction, and it was the most major forms in soil organic nitrogen functional groups. Compared with the FALL treatment, the relative proportion of amide/amine-N was lower whereas that of Pyrrole-N was higher in the CK treatment. In the treatments with combined chemical fertilizers and organic manure, the relative proportion of amide/amine-N decreased with increasing application rates of organic manure, while that of Pyrrole-N had an opposite trend. In bulk soil, the relative proportion of amide/amine-N was the highest for the NPKS treatment than for the other treatments. On the other hand, the relative proportion of nitrile/aromatic-N was the highest for the Fallow treatment than for the other treatments in clay-size soil fraction. It is feasible to use N K-edge XANES spectroscopy for characterizing in situ the changes of organic N functional groups in soil under different fertilization practices.

Chemical composition of rocks and soils at Taurus-Littrow

NASA Technical Reports Server (NTRS)

Rose, H. J., Jr.; Cuttitta, F.; Berman, S.; Brown, F. W.; Carron, M. K.; Christian, R. P.; Dwornik, E. J.; Greenland, L. P.

1974-01-01

Seventeen soils and seven rock samples were analyzed for major elements, minor elements, and trace elements. Unlike the soils at previous Apollo sites, which showed little difference in composition at each collection area, the soils at Taurus-Littrow vary widely. Three soil types are evident, representative of (1) the light mantle at the South Massif, (2) the dark mantle in the valley, and (3) the surface material at the North Massif. The dark-mantle soils are chemically similar to those at Tranquillitatis. Basalt samples from the dark mantle are chemically similar although they range from fine to coarse grained. It is suggested that they originated from the same source but crystallized at varying depths from the surface.

Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

NASA Astrophysics Data System (ADS)

Wang, Qiufeng; Tian, Jing; Yu, Guirui

2014-05-01

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils

PubMed Central

Koyama, Akihiro; Wallenstein, Matthew D.; Simpson, Rodney T.; Moore, John C.

2014-01-01

The pool of soil organic carbon (SOC) in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity. We investigated how nutrients limit bacterial and fungal biomass and community composition in organic and mineral soils within moist acidic tussock tundra ecosystems. We sampled two experimental arrays of moist acidic tussock tundra that included fertilized and non-fertilized control plots. One array included plots that had been fertilized annually since 1989 and the other since 2006. Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site. The relative abundance of copiotrophic α-Proteobacteria and β-Proteobacteria was higher in fertilized than control soils, and oligotrophic Acidobacteria were less abundant in fertilized than control soils at the 1989 site. Fungal community composition was less sensitive to increased nutrient availability, and fungal responses to fertilization were not consistent between soil horizons and sites. We detected two ectomycorrhizal genera, Russula and Cortinarius spp., associated with shrubs. Their relative abundance was not affected by fertilization despite increased dominance of their host plants in the fertilized plots. Our results indicate that fertilization, which has been commonly used to simulate warming in Arctic tundra, has limited applicability for investigating fungal dynamics under warming. PMID:25324836

Soil networks become more connected and take up more carbon as nature restoration progresses.

PubMed

Morriën, Elly; Hannula, S Emilia; Snoek, L Basten; Helmsing, Nico R; Zweers, Hans; de Hollander, Mattias; Soto, Raquel Luján; Bouffaud, Marie-Lara; Buée, Marc; Dimmers, Wim; Duyts, Henk; Geisen, Stefan; Girlanda, Mariangela; Griffiths, Rob I; Jørgensen, Helene-Bracht; Jensen, John; Plassart, Pierre; Redecker, Dirk; Schmelz, Rűdiger M; Schmidt, Olaf; Thomson, Bruce C; Tisserant, Emilie; Uroz, Stephane; Winding, Anne; Bailey, Mark J; Bonkowski, Michael; Faber, Jack H; Martin, Francis; Lemanceau, Philippe; de Boer, Wietse; van Veen, Johannes A; van der Putten, Wim H

2017-02-08

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.

Impact of temperature on the biological properties of soil

NASA Astrophysics Data System (ADS)

Borowik, Agata; Wyszkowska, Jadwiga

2016-01-01

The aim of the study was to determine the response of soil microorganisms and enzymes to the temperature of soil. The effect of the temperatures: 5, 10, 15, 20, and 25°C on the biological properties of soil was investigated under laboratory conditions. The study was performed using four different soils differing in their granulometric composition. It was found that 15°C was the optimal temperature for the development of microorganisms in soil. Typically, in the soil, the highest activity of dehydrogenases was observed at 10-15°C, catalase and acid phosphatase - at 15°C, alkaline phosphatase at 20°C, urease and β-glucosidase at 25°C. The highest colony development index for heterotrophic bacteria was recorded in soils incubated at 25°C, while for actinomycetes and fungi at 15°C. The incubation temperature of soil only slightly changed the ecophysiological variety of the investigated groups of microorganisms. Therefore, the observed climate changes might have a limited impact on the soil microbiological activity, because of the high ability of microorganisms to adopt. The response of soil microorganisms and enzymes was more dependent on the soil granulometric composition, organic carbon, and total nitrogen than on its temperature.

Altered soil microbial community at elevated CO2 leads to loss of soil carbon

PubMed Central

Carney, Karen M.; Hungate, Bruce A.; Drake, Bert G.; Megonigal, J. Patrick

2007-01-01

Increased carbon storage in ecosystems due to elevated CO2 may help stabilize atmospheric CO2 concentrations and slow global warming. Many field studies have found that elevated CO2 leads to higher carbon assimilation by plants, and others suggest that this can lead to higher carbon storage in soils, the largest and most stable terrestrial carbon pool. Here we show that 6 years of experimental CO2 doubling reduced soil carbon in a scrub-oak ecosystem despite higher plant growth, offsetting ≈52% of the additional carbon that had accumulated at elevated CO2 in aboveground and coarse root biomass. The decline in soil carbon was driven by changes in soil microbial composition and activity. Soils exposed to elevated CO2 had higher relative abundances of fungi and higher activities of a soil carbon-degrading enzyme, which led to more rapid rates of soil organic matter degradation than soils exposed to ambient CO2. The isotopic composition of microbial fatty acids confirmed that elevated CO2 increased microbial utilization of soil organic matter. These results show how elevated CO2, by altering soil microbial communities, can cause a potential carbon sink to become a carbon source. PMID:17360374

Stabilization of polar soils organic matter: insights from 13-C NMR and ESR spectroscopy

NASA Astrophysics Data System (ADS)

Abakumov, Evgeny

2017-04-01

Polar soils play a key role in the global carbon balance, as they contain maximum stocks of soil organic matter (SOM) within the whole pedosphere. Low temperature and severe conditions provides the accumulation of large amounts of organic matter in permafrost soils over thousands of years. The quality and composition of organic matter of polar soils is underestimated. In order to better understand the implication of permafrost SOM to greenhouse gas emissions, an accurate knowledge of its spatial distribution, both in terms of quantity and quality (i.e. biodegradability, chemical composition and humification degree) is needed. The chemical composition of SOM determines its decomposability and, therefore, it determines the rate at which carbon may be transferred from soils to the atmosphere under warming conditions. Biodegradability of SOM has been related to humification degree, as more advanced stages in the humification process imply a depletion of the labile molecules, as well as an increase in the bulk aromaticity, which provides a higher stability of the SOM. Soils from Antarctic and different sectors of Arctic biome were investigated by 13-C NMR and electron spin resonance spectroscopy. It was shown, that the characteristic feature of polar soils humic acids is the dominance of aliphatic compounds on the aromatic one. This is related to the humification precursors component composition, namely to dominance of the remnants of lower plants, especially in Antarctic and low period of biological activity, which regulates the humification rate. Humic acids of Antarctic and various Arctic soils show the portion of aromatic components not more than 30 %. ESR spectroscopy shown that the concentration of free radicals is proportional to the humic acids stabilization degree. Less humified organic materials show the highest portion of free radical content, while the most developed soils and buried organic layers show decreased contents of free radicals. The database on soil organic matter composition of polar soil should be created with aim to evaluate current state of the humosphere and to provide the prognostic scenarios of possible mineralisation of humus.

Sediment composition for the assessment of water erosion and nonpoint source pollution in natural and fire-affected landscapes.

PubMed

Carkovic, Athena B; Pastén, Pablo A; Bonilla, Carlos A

2015-04-15

Water erosion is a leading cause of soil degradation and a major nonpoint source pollution problem. Many efforts have been undertaken to estimate the amount and size distribution of the sediment leaving the field. Multi-size class water erosion models subdivide eroded soil into different sizes and estimate the aggregate's composition based on empirical equations derived from agricultural soils. The objective of this study was to evaluate these equations on soil samples collected from natural landscapes (uncultivated) and fire-affected soils. Chemical, physical, and soil fractions and aggregate composition analyses were performed on samples collected in the Chilean Patagonia and later compared with the equations' estimates. The results showed that the empirical equations were not suitable for predicting the sediment fractions. Fine particles, including primary clay, primary silt, and small aggregates (<53 μm) were over-estimated, and large aggregates (>53 μm) and primary sand were under-estimated. The uncultivated and fire-affected soils showed a reduced fraction of fine particles in the sediment, as clay and silt were mostly in the form of large aggregates. Thus, a new set of equations was developed for these soils, where small aggregates were defined as particles with sizes between 53 μm and 250 μm and large aggregates as particles>250 μm. With r(2) values between 0.47 and 0.98, the new equations provided better estimates for primary sand and large aggregates. The aggregate's composition was also well predicted, especially the silt and clay fractions in the large aggregates from uncultivated soils (r(2)=0.63 and 0.83, respectively) and the fractions of silt in the small aggregates (r(2)=0.84) and clay in the large aggregates (r(2)=0.78) from fire-affected soils. Overall, these new equations proved to be better predictors for the sediment and aggregate's composition in uncultivated and fire-affected soils, and they reduce the error when estimating soil loss in natural landscapes. Copyright © 2015 Elsevier B.V. All rights reserved.

Impact of tree cutting on water-soluble organic compounds in podzolic soils of the European North-East

NASA Astrophysics Data System (ADS)

Lapteva, Elena; Bondarenko, Natalia; Shamrikova, Elena; Kubik, Olesya; Punegov, Vasili

2016-04-01

Water-soluble organic compounds (WOCs) and their single components, i.e. low-molecular organic acids, alcohols, and carbohydrates, attain a great deal of attention among soil scientists. WOCs are an important component of soil organic matter (SOM) and form as a results of different biological and chemical processes in soils. These processes are mainly responsible for formation and development of soils in aboveground ecosystems. The purpose of the work was identifying qualitative and quantitative composition of low-molecular organic substances which form in podzolic loamy soils against natural reforestation after spruce forest cutting. The studies were conducted on the territory of the European North-East of Russia, in the middle taiga subzone (Komi Republic, Ust-Kulom region). The study materials were soil of undisturbed bilberry spruce forest (Sample Plot 1 (SP1)) and soils of different-aged tree stands where cutting activities took place in winter 2001/2002 (SP2) and 1969/1970 (SP3). Description of soils and vegetation cover on the plots is given in [1]. Low-molecular organic compounds in soil water extracts were identified by the method of gas chromatography mass-spectrometry [2, 3]. Finally, reforestationafterspruceforestcutting was found to be accompanied by different changes in soil chemical composition. In contrast with soils under undisturbed spruce forest, organic soil horizons under different-aged cuts decreased in organic carbon reserves and production of low-molecular organic compounds, changed in soil acidity. Within the soil series of SP1→SP2→SP3, the highest content of WOCs was identified for undisturbed spruce forest (738 mg kg-1 soil). In soils of coniferous-deciduous forests on SP1 and SP3, WOC content was 294 and 441 mg kg-1 soil, correspondingly. Soils at cuts decreased in concentration of any water-soluble low-molecular SOM components as low-molecular acids, alcohols, and carbohydrates. Structure of low-molecular WOCs in the study podzolic soils was dominated by carbohydrates with ratio from 49% (SP1) to 63-66% (SP2, SP3) of total content of all identified compounds. The increase in relative content in carbohydrates observed for soils under cuts was possibly affected by vegetation cover change after clear-cutting and presence of birch and aspen leaves in plant waste composition (due to tree species change). At SP2 and SP3 cuts, content of alcohols and low-molecular carboxylic acids fell by almost twice as compared with SP1. Tree cuts changed not only in total content of water-soluble compounds but also in ratio of individual low-molecular compounds in water extracts composition. Totally, we identified 26 various compounds, including 12 low-molecular organic (carboxylic) acids, 10 carbohydrates, and 4 alcohols. Composition of carboxylic acids was dominated by aliphatic substituted acids (mainly 2-oxyacetic acid, 2-oxypropane, and 2,3-dioxypropane acids). Total number of aliphatic substituted acids, as well as aliphatic non-substituted and aromatic carboxylic acids, decreased in soils under cuts at initial reforestation stages (SP2). Content of all mentioned acids gradually rose with time (SP3). Soils under cut forests were observed for a decrease of erythrite ratio in composition of water-soluble alcohols (from 52 to 40% of total alcohols) and an increase of glycerin ratio (from 46 to 72%). 10 of identified mono- and disaccharides were dominated by mannose, galactopyranose, and D-ribose. Disturbed soils were identified for increased ratio of galactopyranose and D-ribose and for by almost twice as decreased ratio of mannose. References 1. Dymov, A. A. Changes in the organic matter of taiga soils during the natural reaforestation after cutting in the middle taigaof the Komi Republic / A. A. Dymov, E. Yu. Milanovskii // Eurasian Soil Science, 2013. Vol. 46. № 12. P. 1164-1171. 2. Shamrikova E.V., Punegov V.V., Gruzdev I.V., Vanchikova E.V., Vetoshkina A.A. Individual organic compounds in water extracts from podzolic soils of the Komi Republic // Eurasian Soil Science, 2012. T. 45. № 10. C. 939-946. 3. Shamrikova E.V., Gruzdev I.V., Punegov V.V., Khabibullina F.M., Kubik O.S. Water-soluble low-molecular-weight organic acids in automorphic loamy soils of the tundra and taiga zones // Eurasian Soil Science, 2013. T. 46.№ 6. C. 654-659.

The effect of Bahiagrass roots on soil erosion resistance of Aquults in subtropical China

NASA Astrophysics Data System (ADS)

Ye, Chao; Guo, Zhonglu; Li, Zhaoxia; Cai, Chongfa

2017-05-01

Herbaceous species, especially their roots, are believed to have an important role in enhancing soil strength and protecting soil against erosion. This study evaluated the effects of root distribution characteristics on soil shear resistance and soil detachment rates, correlations among root mechanical properties, root chemical composition and root parameters, and whether the Wu-Waldron model can accurately estimate soil reinforcement by roots. Bahiagrass (Paspalum notatum) was planted in planter boxes by overlapping four rectangle frames (0.4 × 0.1 × 0.1 m). A series of laboratory tests of direct shear strength and soil detachment were conducted on two soils that were derived from granite and shale with different soil depths and sowing densities. The results indicated that soil aggregate stability was positively correlated with root characteristics. Over 70% of the total measured root parameters were distributed in the upper 20 cm of the soil, and they decreased with increasing soil depth and decreasing sowing density. The tensile properties (root tensile strength and root tensile force) were significantly correlated with root diameter. The contents of root main chemical compositions were significantly correlated with root diameter while hemicellulose showed no obvious trend with root diameter (P = 0.12). Root tensile strength and root tensile force were also significantly correlated with the contents of these four compositions, except hemicellulose. The relative soil detachment demonstrated a significant negative correlation with root parameters with sowing densities from 5 to 30 g m- 2, and it remained at a relatively low value when the sowing density was > 20 g m- 2. The soil detachment rate, erodibility factor and critical flow shear stress were well correlated with the root area ratio, sowing density, and soil depth. The Wu-Waldron model was found to be inappropriate for these soils, as it overestimated additional soil shear strength due to roots by 152-366% in the upper 20 cm, and 11-48% in deeper soil layers. This study demonstrated that the root area ratio was a more suitable root characteristic parameter that contributes to soil reinforcement.

Provenance and geochemical behavior of fluorine in the soils of an endemic fluorosis belt, central Iran

NASA Astrophysics Data System (ADS)

Dehbandi, Reza; Moore, Farid; Keshavarzi, Behnam

2017-05-01

The concentration of fluorine, major, trace and rare earth elements (REEs) were used to estimate the probable sources and provenance of fluorine in the soils of an endemic fluorosis belt in central Iran. Total fluorine (TF) in soils varied from 146 to 406 mg/kg with a mean of 277.5 mg/kg. Calculated enrichment factor (EF) and single factor pollution index (SFPI) revealed that the majority of soil samples were moderately contaminated by fluorine. The very strong positive correlation of TF with weathering indices and soil's fine sized fractions indicated that chemical weathering and alteration of parent rocks/soils are the main controlling factors of fluorine behavior in soils. Fluorine affinity to immobile transition trace elements and REEs suggested the role of heavy minerals as the potential F host phases. Modal mineralogy along with SEM-EDX analysis indicated that apatite, fluorapophyllite, epidote, biotite, muscovite and chlorite, as well as, clay minerals are the main F-bearing minerals in the studied soils. Discriminant, bivariate and ternary diagrams of elemental compositions displayed similar geochemical signature of soils to intermediate-acidic rocks and local shales. Based on the weathering indices, soils were immature and showed a non-steady state weathering trend from upper continental crust (UCC), acidic and intermediate igneous source rocks towards shale composition possibly due to mixing of moderately weathered and un-weathered sources of different primary compositions.

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

PubMed Central

Lupatini, Manoeli; Korthals, Gerard W.; de Hollander, Mattias; Janssens, Thierry K. S.; Kuramae, Eiko E.

2017-01-01

Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms. PMID:28101080

Characterization of PCC Cement by Addition of Napa Soil from Subdistrict Sarilamak 50 Kota District as Alternative Additional Material for Semen Padang

NASA Astrophysics Data System (ADS)

Mawardi, M.; Deyundha, D.; Zainul, R.; Zalmi P, R.

2018-04-01

The study has been conducted to determine characteristics of the portland composite cement by the addition of napa soil from Sarilamak subdistrict, 50 Kota District as an alternative additional material at PT. Semen Padang. Napa soil is a natural material highly containing silica and alumina minerals so that it can be one of material in producing cement. This study aims to determine the effect of napa soil on the quality of portland composite cement. Napa soil used in the variation compositions 0%, 4%, 8%, 12% and 16%, for control of cement used 8 % of pozzolan and 0 % of napa soil. Determination of cement quality by testing cement characteristics include blaine test, sieving, lost of ignition or LOI, insoluble residue, normal consistency, setting time and compressive strength. Cement was characterized using XRF. Fineness of cement decreases with the addition of napa soil. Lost of Ignition of cement decreased, while the insoluble residue increased with the addition of napa soil. Normal consistency of cement increasing, so does initial setting time and final setting time of cement. While the resultant compressive strength decreases with the addition of napa soil on 28 days, 342, 325, 307, 306, and 300 kg / cm2.

Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region.

PubMed

Wu, Wencheng; Dong, Changxun; Wu, Jiahui; Liu, Xiaowen; Wu, Yingxin; Chen, Xianbin; Yu, Shixiao

2017-12-01

Soil microbes play vital roles in ecosystem functions, and soil microbial communities may be strongly structured by land use patterns associated with electronic waste (e-waste) recycling activities, which can increase the heavy metal concentration in soils. In this study, a suite of soils from five land use types (paddy field, vegetable field, dry field, forest field, and e-waste recycling site) were collected in Longtang Town, Guangdong Province, South China. Soil physicochemical properties and heavy metal concentrations were measured, and the indigenous microbial assemblages were profiled using 16S rRNA high-throughput sequencing and clone library analyses. The results showed that mercury concentration was positively correlated with both Faith's PD and Chao1 estimates, suggesting that the soil microbial alpha diversity was predominantly regulated by mercury. In addition, redundancy analysis indicated that available phosphorus, soil moisture, and mercury were the three major drivers affecting the microbial assemblages. Overall, the microbial composition was determined primarily by land use patterns, and this study provides a novel insight on the composition and diversity of microbial communities in soils associated with e-waste recycling activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities.

PubMed

Liu, Jun; He, Xiao-Xin; Lin, Xue-Rui; Chen, Wen-Ce; Zhou, Qi-Xing; Shu, Wen-Sheng; Huang, Li-Nan

2015-06-02

The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate.

PubMed

Yan, Lijuan; Sinkko, Hanna; Penttinen, Petri; Lindström, Kristina

2016-01-15

The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial community responses to 17 years of altered precipitation are seasonally dependent and coupled to co-varying effects of water content on vegetation and soil C

USGS Publications Warehouse

Sorensen, Patrick O.; Germino, Matthew J.; Feris, Kevin P.

2013-01-01

Precipitation amount and seasonal timing determine the duration and distribution of water available for plant and microbial activity in the cold desert sagebrush steppe. In this study, we sought to determine if a sustained shift in the amount and timing of precipitation would affect soil microbial diversity, community composition, and soil carbon (C) storage. Field plots were irrigated (+200 mm) during the dormant or growing-season for 17 years. Microbial community responses were assessed over the course of a year at two depths (15–20 cm, 95–100 cm) by terminal restriction fragment length polymorphism (T-RFLP), along with co-occurring changes in plant cover and edaphic properties. Bacterial richness, Shannon Weaver diversity, and composition in shallow soils (15–20 cm) as well as evenness in deep soils (95–100 cm) differed across irrigation treatments during July. Irrigation timing affected fungal community diversity and community composition during the dormant season and most strongly in deep soils (95–100 cm). Dormant-season irrigation increased the ratio of shrubs to forbs and reduced soil C in shallow soils by 16% relative to ambient conditions. It is unclear whether or not soil C will continue to decline with continued treatment application or if microbial adaptation could mitigate sustained soil C losses. Future changes in precipitation timing will affect soil microbes in a seasonally dependent manner and be coupled to co-varying effects of water content on vegetation and soil C.

Soil-foraging animals alter the composition and co-occurrence of microbial communities in a desert shrubland

PubMed Central

Eldridge, David J; Woodhouse, Jason N; Curlevski, Nathalie J A; Hayward, Matthew; Brown, Mark V; Neilan, Brett A

2015-01-01

Animals that modify their physical environment by foraging in the soil can have dramatic effects on ecosystem functions and processes. We compared bacterial and fungal communities in the foraging pits created by bilbies and burrowing bettongs with undisturbed surface soils dominated by biocrusts. Bacterial communities were characterized by Actinobacteria and Alphaproteobacteria, and fungal communities by Lecanoromycetes and Archaeosporomycetes. The composition of bacterial or fungal communities was not observed to vary between loamy or sandy soils. There were no differences in richness of either bacterial or fungal operational taxonomic units (OTUs) in the soil of young or old foraging pits, or undisturbed soils. Although the bacterial assemblage did not vary among the three microsites, the composition of fungi in undisturbed soils was significantly different from that in old or young foraging pits. Network analysis indicated that a greater number of correlations between bacterial OTUs occurred in undisturbed soils and old pits, whereas a greater number of correlations between fungal OTUs occurred in undisturbed soils. Our study suggests that digging by soil-disturbing animals is likely to create successional shifts in soil microbial and fungal communities, leading to functional shifts associated with the decomposition of organic matter and the fixation of nitrogen. Given the primacy of organic matter decomposition in arid and semi-arid environments, the loss of native soil-foraging animals is likely to impair the ability of these systems to maintain key ecosystem processes such as the mineralization of nitrogen and the breakdown of organic matter, and to recover from disturbance. PMID:25932616

Experimental protocol for manipulating plant-induced soil heterogeneity.

PubMed

Brandt, Angela J; del Pino, Gaston A; Burns, Jean H

2014-03-13

Coexistence theory has often treated environmental heterogeneity as being independent of the community composition; however biotic feedbacks such as plant-soil feedbacks (PSF) have large effects on plant performance, and create environmental heterogeneity that depends on the community composition. Understanding the importance of PSF for plant community assembly necessitates understanding of the role of heterogeneity in PSF, in addition to mean PSF effects. Here, we describe a protocol for manipulating plant-induced soil heterogeneity. Two example experiments are presented: (1) a field experiment with a 6-patch grid of soils to measure plant population responses and (2) a greenhouse experiment with 2-patch soils to measure individual plant responses. Soils can be collected from the zone of root influence (soils from the rhizosphere and directly adjacent to the rhizosphere) of plants in the field from conspecific and heterospecific plant species. Replicate collections are used to avoid pseudoreplicating soil samples. These soils are then placed into separate patches for heterogeneous treatments or mixed for a homogenized treatment. Care should be taken to ensure that heterogeneous and homogenized treatments experience the same degree of soil disturbance. Plants can then be placed in these soil treatments to determine the effect of plant-induced soil heterogeneity on plant performance. We demonstrate that plant-induced heterogeneity results in different outcomes than predicted by traditional coexistence models, perhaps because of the dynamic nature of these feedbacks. Theory that incorporates environmental heterogeneity influenced by the assembling community and additional empirical work is needed to determine when heterogeneity intrinsic to the assembling community will result in different assembly outcomes compared with heterogeneity extrinsic to the community composition.

Effects of atmospheric deposition nitrogen flux and its composition on soil solution chemistry from a red soil farmland, southeast China.

PubMed

Cui, Jian; Zhou, Jing; Peng, Ying; Chan, Andrew; Mao, Jingdong

2015-12-01

A detailed study on the solution chemistry of red soil in South China is presented. Data are collected from two simulated column-leaching experiments with an improved setup to evaluate the effects of atmospheric N deposition (ADN) composition and ADN flux on agricultural soil acidification using a (15)N tracer technique and an in situ soil solution sampler. The results show that solution pH values decline regardless of the increase of the NH4(+)/NO3(-) ratio in the ADN composition or ADN flux, while exchangeable Al(3+), Ca(2+), Mg(2+), and K(+) concentrations increase at different soil depths (20, 40, and 60 cm). Compared with the control, ADN (60 kg per ha per year N, NH4(+)/NO3(-) ratio of 2 : 1) decreases solution pH values, increases solution concentrations of NO3(-)-N, Al(3+), Ca(2+) and Mg(2+) at the middle and lower soil depths, and promotes their removal. NH4(+)-N was not detected in red soil solutions of all the three soil layers, which might be attributed to effects of nitrification, absorption and fixation in farmland red soil. Some of the NO3(-)-N concentrations at 40-60 cm soil depth exceed the safe drinking level of 10 mg L(-1), especially when the ADN flux is beyond 60 kg ha(-1) N. These features are critical for understanding the ADN agro-ecological effects, and for future assessment of ecological critical loads of ADN in red soil farmlands.

Biodegradation of poly(hydroxy butanoic acid) copolymer mulch films in soil

NASA Astrophysics Data System (ADS)

Kukade, Pranav

Agricultural mulch films that are used to cover soil of crop rows contribute to earlier maturation of crops and higher yield. Incineration and landfill disposals are the most common means of disposal of the incumbent polyethylene (PE) mulch films; however, these are not environment friendly options. Biodegradable mulch films that can be rototilled into the soil after crop harvest are a promising alternative to offset problems such as landfill disposal, film retrieval and disposal costs. In this study, an in-house laboratory scale test method was developed in which the rate of disintegration, as a result of biodegradation of films based on polyhydroxybutanoic acid (PHB) copolymers was investigated in a soil environment using the residual weight loss method. The influence of soil composition, moisture levels in the soil, and industry-standard anti-microbial additive in the film composition on the rate of disintegration of PHB copolymer films was investigated. The soil composition has significant effect on the disintegration kinetics of PHB copolymer films, since the increasing compost levels in the soil lowered the rate of disintegration of the film. Also, with the increase in moisture level up to a threshold limit, the microbial activity and, hence, the rate of disintegration increased. Lastly, the developed lab-scale test protocol was found to be sensitive to even small concentrations of industry-standard antimicrobial additive in the film composition.

Soil Bacterial Community Response to Differences in Agricultural Management along with Seasonal Changes in a Mediterranean Region

PubMed Central

Bevivino, Annamaria; Paganin, Patrizia; Bacci, Giovanni; Florio, Alessandro; Pellicer, Maite Sampedro; Papaleo, Maria Cristiana; Mengoni, Alessio; Ledda, Luigi; Fani, Renato; Benedetti, Anna; Dalmastri, Claudia

2014-01-01

Land-use change is considered likely to be one of main drivers of biodiversity changes in grassland ecosystems. To gain insight into the impact of land use on the underlying soil bacterial communities, we aimed at determining the effects of agricultural management, along with seasonal variations, on soil bacterial community in a Mediterranean ecosystem where different land-use and plant cover types led to the creation of a soil and vegetation gradient. A set of soils subjected to different anthropogenic impact in a typical Mediterranean landscape, dominated by Quercus suber L., was examined in spring and autumn: a natural cork-oak forest, a pasture, a managed meadow, and two vineyards (ploughed and grass covered). Land uses affected the chemical and structural composition of the most stabilised fractions of soil organic matter and reduced soil C stocks and labile organic matter at both sampling season. A significant effect of land uses on bacterial community structure as well as an interaction effect between land uses and season was revealed by the EP index. Cluster analysis of culture-dependent DGGE patterns showed a different seasonal distribution of soil bacterial populations with subgroups associated to different land uses, in agreement with culture-independent T-RFLP results. Soils subjected to low human inputs (cork-oak forest and pasture) showed a more stable bacterial community than those with high human input (vineyards and managed meadow). Phylogenetic analysis revealed the predominance of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes phyla with differences in class composition across the site, suggesting that the microbial composition changes in response to land uses. Taken altogether, our data suggest that soil bacterial communities were seasonally distinct and exhibited compositional shifts that tracked with changes in land use and soil management. These findings may contribute to future searches for bacterial bio-indicators of soil health and sustainable productivity. PMID:25144665

Influence of soil solution cation composition on boron adsorption by soils

USDA-ARS?s Scientific Manuscript database

Boron (B) adsorption on five arid-zone soil samples from California was investigated as a function of solution pH (4-10) and cation composition (Na, Ca, or Mg). Boron adsorption increased with increasing solution pH, reached an adsorption maximum near pH 9, and decreased with further increases with...

Effects of waste water irrigation on soil properties and soil fauna of spinach fields in a West African urban vegetable production system.

PubMed

Stenchly, Kathrin; Dao, Juliane; Lompo, Désiré Jean-Pascal; Buerkert, Andreas

2017-03-01

The usage of inadequately processed industrial waste water (WW) can lead to strong soil alkalinity and soil salinization of agricultural fields with negative consequences on soil properties and biota. Gypsum as a soil amendment to saline-sodic soils is widely used in agricultural fields to improve their soil physical, chemical and hence biological properties. This study aimed at analysing the effects of intensive WW irrigation on the structure and composition of soil-dwelling arthropods on spinach fields (Spinacia oleracea L.) in a West African urban vegetable production system. We used gypsum as a soil amendment with the potential to alleviate soil chemical stress resulting in a potentially positive impact on soil arthropods. A total of 32 plots were established that showed a gradient in soil pH ranging from slight to strong soil alkalinity and that were irrigated with WW (n = 12) or clean water (CW; n = 20), including eight plots into which gypsum was incorporated. Our study revealed a high tolerance of soil-dwelling arthropods for alkaline soils, but spinach fields with increased soil electrical conductivity (EC) showed a reduced abundance of Hymenoptera, Diptera and Auchenorrhyncha. Arthropod abundance was positively related to a dense spinach cover that in turn was not affected by WW irrigation or soil properties. Gypsum application reduced soil pH but increased soil EC. WW irrigation and related soil pH affected arthropod composition in the investigated spinach fields which may lead to negative effects on agronomical important arthropod groups such as pollinators and predators. Copyright © 2017 Elsevier Ltd. All rights reserved.

Land-use history has a stronger impact on soil microbial community composition than aboveground vegetation and soil properties

USDA-ARS?s Scientific Manuscript database

The response of soil microbial communities following soil disturbances is poorly understood. The development of soil microbial communities in two restoration gradients was studied to investigate the impact of land-management regime at the W. K. Kellogg Biological Station, Michigan. The first restora...

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by vineyard management

USDA-ARS?s Scientific Manuscript database

Here, we demonstrate how vineyard management practices influence shifts in soil resources, which in turn affects shifts in soil-borne bacterial communities. The objective is to determine the hierarchical effects of management practices, soil attributes and location factors on the structure of soil-b...

Cover cropping frequency is the main driver of soil microbial changes during six years of organic vegetable production

USDA-ARS?s Scientific Manuscript database

Soil microbes play a key role in soil health, and understanding the functional role of this living component of soil organic matter is critical to developing sustainable systems in major vegetable production regions like Salinas, California. Soil microbial community size and composition was evaluat...

Digging a Little Deeper: Microbial Communities, Molecular Composition and Soil Organic Matter Turnover along Tropical Forest Soil Depth Profiles

NASA Astrophysics Data System (ADS)

Pett-Ridge, J.; McFarlane, K. J.; Heckman, K. A.; Reed, S.; Green, E. A.; Nico, P. S.; Tfaily, M. M.; Wood, T. E.; Plante, A. F.

2016-12-01

Tropical forest soils store more carbon (C) than any other terrestrial ecosystem and exchange vast amounts of CO2, water, and energy with the atmosphere. Much of this C is leached and stored in deep soil layers where we know little about its fate or the microbial communities that drive deep soil biogeochemistry. Organic matter (OM) in tropical soils appears to be associated with mineral particles, suggesting deep soils may provide greater C stabilization. However, few studies have evaluated sub-surface soils in tropical ecosystems, including estimates of the turnover times of deep soil C, the sensitivity of this C to global environmental change, and the microorganisms involved. We quantified bulk C pools, microbial communities, molecular composition of soil organic matter, and soil radiocarbon turnover times from surface soils to 1.5m depths in multiple soil pits across the Luquillo Experimental Forest, Puerto Rico. Soil C, nitrogen, and root and microbial biomass all declined exponentially with depth; total C concentrations dropped from 5.5% at the surface to <0.5% at 140cm depth. High-throughput sequencing highlighted distinct microbial communities in surface soils (Acidobacteria and Proteobacteria) versus those below the active rooting zone (Verrucomicrobia and Thaumarchaea). High resolution mass spectrometry (FTICR-MS) analyses suggest a shift in the composition of OM with depth (especially in the water soluble fraction), an increase in oxidation, and decreasing H/C with depth (indicating higher aromaticity). Additionally, surface samples were rich in lignin-like compounds of plant origin that were absent with depth. Soil OM 14C and mean turnover times were variable across replicate horizons, ranging from 3-1500 years at the surface, to 5000-40,000 years at depth. In comparison to temperate deciduous forests, these 14C values reflect far older soil C. Particulate organic matter (free light fraction), with a relatively modern 14C was found in low but measureable concentration in even the deepest soil horizons. Our results indicate these tropical subsoils contain small but metabolically active microbial communities that are highly OM limited and may persist via degradation of recent inputs.

Microbial and physical properties as indicators of sandy soil quality under cropland and grassland

NASA Astrophysics Data System (ADS)

Frac, Magdalena; Lipiec, Jerzy; Usowicz, Boguslaw; Oszust, Karolina; Brzezinska, Malgorzata

2017-04-01

Land use is one of the key factor driving changes in soil properties influencing on soil health and quality. Microbial diversity and physical properties are sensitive indicators for assessing soil health and quality. The alterations of microbial diversity and physical properties following land use changes have not been sufficiently elucidated, especially for sandy soils. We investigated microbial diversity indicators including fungal communities composition and physical properties of sandy acid soil under cropland and more than 20-yr-old grassland (after cropland) in Trzebieszów, Podlasie Region, Poland (N 51° 59' 24", E 22° 33' 37"). The study included four depths within 0-60 cm. Microbial genetic diversity was assessed by terminal restriction fragment length polymorphism (t-RFLP) analysis, fungal community composition was evaluated by next generation sequencing (NGS) analysis and functional diversity was determined by Biolog EcoPlate method. Overall microbial activity was assessed by soil enzymes (dehydrogenases, β-glucosidase) and respiration test. At the same places soil texture, organic carbon content, pH, bulk density, water holding capacity were determined. Our results showed that grassland soil was characterized by higher activity of soil enzymes than cropland. The average well color development of soil microorganisms, the microbial functional diversity and the number of carbon source utilization were significantly affected by land use type and were differentiated among soil depths. In grassland compared to cropland soil a significant increase of carboxylic acids and decrease of amino acids utilization was observed. The quantitative and qualitative differences were found in community of ammonia oxidizing archaea in cropland and grassland soil. The results of fungal community composition help to explain the soil health of grassland and cropland based on the appearance of phytopathogenic and antagonistic fungi. In general bulk density and field water capacity were greater and saturated hydraulic conductivity was lower under grassland than cropland soil. The study was funded by HORIZON 2020, European Commission, Programme: H2020-SFS-4-2014: Soil quality and function, project No. 635750, Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience (iSQAPER, 2015-2020).

Estimation of the efficiency of hydrocarbon mineralization in soil by measuring CO2-emission and variations in the isotope composition of carbon dioxide

NASA Astrophysics Data System (ADS)

Dubrovskaya, Ekaterina; Turkovskaya, Olga

2010-05-01

Estimation of the efficiency of hydrocarbon mineralization in soil by measuring CO2-emission and variations in the isotope composition of carbon dioxide E. Dubrovskaya1, O. Turkovskaya1, A. Tiunov2, N. Pozdnyakova1, A. Muratova1 1 - Institute of Biochemistry and Physiology of Plants and Microorganisms, RAS, Saratov, 2 - A.N. Severtsov Institute of Ecology and Evolution, RAS, Moscow, Russian Federation Hydrocarbon mineralization in soil undergoing phytoremediation was investigated in a laboratory experiment by estimating the variation in the 13С/12С ratio in the respired СО2. Hexadecane (HD) was used as a model hydrocarbon pollutant. The polluted soil was planted with winter rye (Secale cereale) inoculated with Azospirillum brasilense strain SR80, which combines the abilities to promote plant growth and to degrade oil hydrocarbon. Each vegetated treatment was accompanied with a corresponding nonvegetated one, and uncontaminated treatments were used as controls. Emission of carbon dioxide, its isotopic composition, and the residual concentration of HD in the soil were examined after two and four weeks. At the beginning of the experiment, the CO2-emission level was higher in the uncontaminated than in the contaminated soil. After two weeks, the quantity of emitted carbon dioxide decreased by about three times and did not change significantly in all uncontaminated treatments. The presence of HD in the soil initially increased CO2 emission, but later the respiration was reduced. During the first two weeks, nonvegetated soil had the highest CO2-emission level. Subsequently, the maximum increase in respiration was recorded in the vegetated contaminated treatments. The isotope composition of plant material determines the isotope composition of soil. The soil used in our experiment had an isotopic signature typical of soils formed by C3 plants (δ13C,-22.4‰). Generally, there was no significant fractionation of the carbon isotopes of the substrates metabolized by the soil microbiota. The plants and microorganisms used had the isotopic signatures similar to that of the soil, whereas the δ13C of HD was -47.9‰. The HD mineralization level was assessed by determining the difference between the isotopic compositions of soil CO2 immediately after pollution and during remediation. In the unvegetated soil, about 13% of initially added HD was mineralized, the phytoremediation increased the total decomposition of the contaminant to 19%, and an additional plant inoculation with strain SR80 raised it to 33%. The GC analysis of soil demonstrated that contaminant loss in the plant treatments and in the inoculated plant treatment was 71 and 72%, respectively, whereas in the nonvegetated treatments, it was 64 and 66%, respectively. Thus, the elimination of the contaminant resulted from its total mineralization (CO2 emission) and partial chemical transformation.

Geochemical variability of natural soils and reclaimed minespoil soils in the San Juan Basin, New Mexico

USGS Publications Warehouse

Gough, L.P.; Severson, R.C.

1981-01-01

An inventory of total-and extractable-element concentrations in soils was made for three areas of the San Juan Basin in New Mexico: (1) the broad area likely to be affected by energy-related development. (2) an area of soils considered to have potential for use as topsoil in mined-land reclamation. and (3) an area of the San Juan coal mine that has been regraded. topsoiled, and revegetated. Maps made of concentrations of 16 elements in area 1 soils show no gradational pattern across the region. Further. these maps do not correspond to those showing geology or soil types. Sodic or saline problems, and a possible but unproven deficiency of zinc available to plants. may make some of the soils in this area undesirable for use as topsoil in mined-land reclamation. Taxonomic great groups of soil in this area cannot be distinguished because each great group tends to have a large within-group variability if compared to the between-group variability. In area 2 the major soils sampled were of the Sheppard. Shiprock. and Doak association. These soils are quite uniform in chemical composition and are not greatly saline or sodic. As in area 1 soils. zinc deficiency may cause a problem in revegetating most of these soils. It is difficult to distinguish soil taxonomic families by using their respective chemical compositions. because of small between-family variability. Topsoil from a reclaimed area of the San Juan mine (area 3) most closely resembles the chemical composition of natural C horizons of soil from area 1. Spoil material that has not been topsoiled is likely to cause sodic-and saline-related problems in revegetation and may cause boron toxicity in plants. Topsoiling has apparently ameliorated these potential problems for plant growth on mine spoil. Total and extractable concentrations for elements and other parameters for each area of the San Juan Basin provide background information for the evaluation of the chemical quality of soils in each area.

Impact of Land Use Management and Soil Properties on Denitrifier Communities of Namibian Savannas.

PubMed

Braker, Gesche; Matthies, Diethart; Hannig, Michael; Brandt, Franziska Barbara; Brenzinger, Kristof; Gröngröft, Alexander

2015-11-01

We studied potential denitrification activity and the underlying denitrifier communities in soils from a semiarid savanna ecosystem of the Kavango region in NE Namibia to help in predicting future changes in N(2)O emissions due to continuing changes of land use in this region. Soil type and land use (pristine, fallow, and cultivated soils) influenced physicochemical characteristics of the soils that are relevant to denitrification activity and N(2)O fluxes from soils and affected potential denitrification activity. Potential denitrification activity was assessed by using the denitrifier enzyme activity (DEA) assay as a proxy for denitrification activity in the soil. Soil type and land use influenced C and N contents of the soils. Pristine soils that had never been cultivated had a particularly high C content. Cultivation reduced soil C content and the abundance of denitrifiers and changed the composition of the denitrifier communities. DEA was strongly and positively correlated with soil C content and was higher in pristine than in fallow or recently cultivated soils. Soil type and the composition of both the nirK- and nirS-type denitrifier communities also influenced DEA. In contrast, other soil characteristics like N content, C:N ratio, and pH did not predict DEA. These findings suggest that due to greater availability of soil organic matter, and hence a more effective N cycling, the natural semiarid grasslands emit more N(2)O than managed lands in Namibia.

Bacterial community structure and soil properties of a subarctic tundra soil in Council, Alaska.

PubMed

Kim, Hye Min; Jung, Ji Young; Yergeau, Etienne; Hwang, Chung Yeon; Hinzman, Larry; Nam, Sungjin; Hong, Soon Gyu; Kim, Ok-Sun; Chun, Jongsik; Lee, Yoo Kyung

2014-08-01

The subarctic region is highly responsive and vulnerable to climate change. Understanding the structure of subarctic soil microbial communities is essential for predicting the response of the subarctic soil environment to climate change. To determine the composition of the bacterial community and its relationship with soil properties, we investigated the bacterial community structure and properties of surface soil from the moist acidic tussock tundra in Council, Alaska. We collected 70 soil samples with 25-m intervals between sampling points from 0-10 cm to 10-20 cm depths. The bacterial community was analyzed by pyrosequencing of 16S rRNA genes, and the following soil properties were analyzed: soil moisture content (MC), pH, total carbon (TC), total nitrogen (TN), and inorganic nitrogen (NH4+ and NO3-). The community compositions of the two different depths showed that Alphaproteobacteria decreased with soil depth. Among the soil properties measured, soil pH was the most significant factor correlating with bacterial community in both upper and lower-layer soils. Bacterial community similarity based on jackknifed unweighted unifrac distance showed greater similarity across horizontal layers than through the vertical depth. This study showed that soil depth and pH were the most important soil properties determining bacterial community structure of the subarctic tundra soil in Council, Alaska. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of the Federation of European Microbiological Societies.

Natural attenuation is enhanced in previously contaminated and coniferous forest soils.

PubMed

Kauppi, Sari; Romantschuk, Martin; Strömmer, Rauni; Sinkkonen, Aki

2012-01-01

Prevalence of organic pollutants or their natural analogs in soil is often assumed to lead to adaptation in the bacterial community, which results in enhanced bioremediation if the soil is later contaminated. In this study, the effects of soil type and contamination history on diesel oil degradation and bacterial adaptation were studied. Mesocosms of mineral and organic forest soil (humus) were artificially treated with diesel oil, and oil hydrocarbon concentrations (GC-FID), bacterial community composition (denaturing gradient gel electrophoresis, DGGE), and oil hydrocarbon degraders (DGGE + sequencing of 16S rRNA genes) were monitored for 20 weeks at 16°C. Degradation was advanced in previously contaminated soils as compared with pristine soils and in coniferous organic forest soil as compared with mineral soil. Contamination affected bacterial community composition especially in the pristine mineral soil, where diesel addition increased the number of strong bands in the DGGE gel. Sequencing of cloned 16S rRNA gene fragments and DGGE bands showed that potential oil-degrading bacteria were found in mineral and organic soils and in both pristine and previously contaminated mesocosms. Fast oil degradation was not associated with the presence of any particular bacterial strain in soil. We demonstrate at the mesocosm scale that previously contaminated and coniferous organic soils are superior environments for fast oil degradation as compared with pristine and mineral soil environments. These results may be utilized in preventing soil pollution and planning soil remediation.

[Impact of land-use type changes on soil nitrification and ammonia-oxidizing bacterial community composition].

PubMed

Yang, Li-Lin; Mao, Ren-Zhao; Liu, Jun-Jie; Liu, Xiao-Jing

2011-11-01

A comparative study was conducted to determine nitrification potentials and ammonia-oxidizing bacterial (AOB) community composition in 0-20 cm soil depth in adjacent native forest,natural grassland, and cropland soils on the Tibetan Plateau, by incubation experiment and by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA, respectively. Cropland has the highest nitrification potential and nitrate concentration among the three land-use types (LUT), approximately 9 folds and more than 11 folds than that of the forests and grasslands, respectively. NO3(-) -N accounted for 70%-90% of inorganic N in cropland soil, while NH4(+) -N was the main form of inorganic N in forest and grassland soils. Nitrification potentials and nitrate concentrations showed no significant difference between native forest and grassland soils. The native forest showed the lowest nitrification potentials and the lowest AOB diversity and community composition among the three LUT. Conversions from natural grasslands to croplands remarkably decreased the AOB diversity and composition, but croplands remain high similarity in AOB community composition compared with grasslands. The minimal and the lowest diversity of AOB in native forests directly resulted to the lowest nitrification potentials compared to natural grasslands and croplands. From the fact of the highest nitrification potentials and nitrate concentrations in croplands indicated that there were the most substantial AOB with higher activity and priority. The results provide evidence that changes of land-use type can affect both soil nitrogen internal cycling process, the diversity, community and activity of AOB, which further affect soil environment quality and the long-term sustainability of ecosystems.

Soil bacterial diversity in degraded and restored lands of Northeast Brazil.

PubMed

Araújo, Ademir Sérgio Ferreira; Borges, Clovis Daniel; Tsai, Siu Mui; Cesarz, Simone; Eisenhauer, Nico

2014-11-01

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.

Effects of short- and long-term disturbance resulting from military maneuvers on vegetation and soils in a mixed prairie area

USGS Publications Warehouse

Leis, S.A.; Engle, David M.; Leslie, David M.; Fehmi, J.S.

2005-01-01

Loss of grassland species resulting from activities such as off-road vehicle use increases the need for models that predict effects of anthropogenic disturbance. The relationship of disturbance by military training to plant species richness and composition on two soils (Foard and Lawton) in a mixed prairie area was investigated. Track cover (cover of vehicle disturbance to the soil) and soil organic carbon were selected as measures of short- and long-term disturbance, respectively. Soil and vegetation data, collected in 1-m 2 quadrats, were analyzed at three spatial scales (60, 10, and 1 m2). Plant species richness peaked at intermediate levels of soil organic carbon at the 10-m2 and 1-m2 spatial scales on both the Lawton and Foard soils, and at intermediate levels of track cover at all three spatial scales on the Foard soil. Species composition differed across the disturbance gradient on the Foard soil but not on the Lawton soil. Disturbance increased total plant species richness on the Foard soil. The authors conclude that disturbance up to intermediate levels can be used to maintain biodiversity by enriching the plant species pool. ?? 2005 Springer Science+Business Media, Inc.

Review of progress in soil inorganic carbon research

NASA Astrophysics Data System (ADS)

Bai, S. G.; Jiao, Y.; Yang, W. Z.; Gu, P.; Yang, J.; Liu, L. J.

2017-12-01

Soil inorganic carbon is one of the main carbon banks in the near-surface environment, and is the main form of soil carbon library in arid and semi-arid regions, which plays an important role in the global carbon cycle. This paper mainly focuses on the inorganic dynamic process of soil inorganic carbon in soil environment in arid and semi-arid regions, and summarized the composition and source of soil inorganic carbon, influence factors and soil carbon sequestration.

Durability of Starch Based Biodegradable Plastics Reinforced with Manila Hemp Fibers.

PubMed

Ochi, Shinji

2011-02-25

The biodegradability of Manila hemp fiber reinforced biodegradable plastics was studied for 240 days in a natural soil and 30 days in a compost soil. After biodegradability tests, weights were measured and both tensile strength tests and microscopic observation were performed to evaluate the biodegradation behavior of the composites. The results indicate that the tensile strength of the composites displays a sharp decrease for up to five days, followed by a gradual decrease. The weight loss and the reduction in tensile strength of biodegradable composite materials in the compost soil are both significantly greater than those buried in natural soil. The biodegradability of these composites is enhanced along the lower portion because this area is more easily attacked by microorganisms.

Durability of Starch Based Biodegradable Plastics Reinforced with Manila Hemp Fibers

PubMed Central

Ochi, Shinji

2011-01-01

The biodegradability of Manila hemp fiber reinforced biodegradable plastics was studied for 240 days in a natural soil and 30 days in a compost soil. After biodegradability tests, weights were measured and both tensile strength tests and microscopic observation were performed to evaluate the biodegradation behavior of the composites. The results indicate that the tensile strength of the composites displays a sharp decrease for up to five days, followed by a gradual decrease. The weight loss and the reduction in tensile strength of biodegradable composite materials in the compost soil are both significantly greater than those buried in natural soil. The biodegradability of these composites is enhanced along the lower portion because this area is more easily attacked by microorganisms. PMID:28880000

Membrane-Soil Composite Layers in the Design, Construction, and Performance of an Expedient Bridge and Approach.

DTIC Science & Technology

1982-09-01

Engineering News-Record 1977). The concept is that of a composite soil-membrane system with tensile and flexural strengths greater than soil alone can...uniformity 2 Mean diameter 0.5 mm Sandbags 31. Sandbags used in this project were 14 x 26 in. in size and were made of jute or kenaf burlap...support 4. Converted airfield index penetrometer readings for the upper 6 in. of foundation soil indicated similar relative strengths at the base of

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest.

PubMed

Schilling, Erik M; Waring, Bonnie G; Schilling, Jonathan S; Powers, Jennifer S

2016-09-01

We investigated how forest composition, litter quality, and rainfall interact to affect leaf litter decomposition across three successional tropical dry forests in Costa Rica. We monitored litter stocks and bulk litter turnover in 18 plots that exhibit substantial variation in soil characteristics, tree community structure, fungal communities (including forests dominated by ecto- or arbuscular mycorrhizal host trees), and forest age. Simultaneously, we decomposed three standard litter substrates over a 6-month period spanning an unusually intense drought. Decay rates of standard substrates depended on the interaction between litter identity and forest type. Decomposition rates were correlated with tree and soil fungal community composition as well as soil fertility, but these relationships differed among litter types. In low fertility soils dominated by ectomycorrhizal oak trees, bulk litter turnover rates were low, regardless of soil moisture. By contrast, in higher fertility soils that supported mostly arbuscular mycorrhizal trees, bulk litter decay rates were strongly dependent on seasonal water availability. Both measures of decomposition increased with forest age, as did the frequency of termite-mediated wood decay. Taken together, our results demonstrate that soils and forest age exert strong control over decomposition dynamics in these tropical dry forests, either directly through effects on microclimate and nutrients, or indirectly by affecting tree and microbial community composition and traits, such as litter quality.

Ca, Sr and Ba stable isotopes reveal the fate of soil nutrients along a tropical climosequence

USGS Publications Warehouse

Bullen, Thomas D.; Chadwick, Oliver A.

2016-01-01

Nutrient biolifting is an important pedogenic process in which plant roots obtain inorganic nutrients such as phosphorus (P) and calcium (Ca) from minerals at depth and concentrate those nutrients at the surface. Here we use soil chemistry and stable isotopes of the alkaline earth elements Ca, strontium (Sr) and barium (Ba) to test the hypothesis that biolifting of P has been an important pedogenic process across a soil climosequence developed on volcanic deposits at Kohala Mountain, Hawaii. The geochemical linkage between these elements is revealed as generally positive site-specific relationships in soil mass gains and losses, particularly for P, Ba and Ca, using the ratio of immobile elements titanium and niobium (Ti/Nb) to link individual soil samples to a restricted compositional range of the chemically and isotopically diverse volcanic parent materials. At sites where P is enriched in surface soils relative to abundances in deeper soils, the isotope compositions of exchangeable Ca, Sr and Ba in the shallowest soil horizons (< 10 cm depth) are lighter than those of the volcanic parent materials and trend toward those of plants growing on fresh volcanic deposits. In contrast the isotope composition of exchangeable Ba in deeper soil horizons (> 10 cm depth) at those sites is consistently heavier than the volcanic parent materials. The isotope compositions of exchangeable Ca and Sr trend toward heavier compositions with depth more gradually, reflecting increasing leakiness from these soils in the order Ba < Sr < Ca and downward transfer of light biocycled Ca and Sr to deeper exchange sites. Given the long-term stability of ecosystem properties at the sites where P is enriched in surface soils, a simple box model demonstrates that persistence of isotopically light exchangeable Ca, Sr and Ba in the shallowest soil horizons requires that the uptake flux to plants from those near-surface layers is less than the recycling flux returned to the surface as litterfall. This observation implicates an uptake flux from an additional source which we attribute to biolifting. We view the heavy exchangeable Ba relative to soil parent values in deeper soils at sites where P is enriched in surface soils, and indeed at all but the wettest site across the climosequence, to represent the complement of an isotopically light Ba fraction removed from these soils by plant roots consistent with the biolifting hypothesis. We further suggest that decreasing heaviness of depth-integrated exchangeable Ba in deeper soils with increasing median annual precipitation across the climosequence reflects greater reliance on shallow nutrient sources as site water balance increases. While the Ca, Sr and Ba isotopes considered together were useful in confirming an important role for nutrient biolifting across the climosequence, the Ba isotopes provided the most robust tracer of biolifting and have the greatest potential to find application as an isotopic proxy for P dynamics in soils.

Modeling as a tool for management of saline soils and irrigation waters

USDA-ARS?s Scientific Manuscript database

Optimal management of saline soils and irrigation waters requires consideration of many interrelated factors including, climate, water applications and timing, water flow, plant water uptake, soil chemical reactions, plant response to salinity and solution composition, soil hydraulic properties and ...

Nutrient properties of five West Virginia forest soils

Treesearch

L. R. Auchmoody

1972-01-01

Nutrient levels in five well-drained forest soils of the northern mountain section of West Virginia were generally associated with the type of parent rocks from which the soils had formed. But in some instances, different rock types yielded soils of similar nutrient composition. Soils formed from limestone and calcareous shale were usually higher in fertility than...

Influence of site and soil properties on the DRIFT spectra of northern cold-region soils [Influence of site and soil properties on the mid-infrared spectra of northern cold-region soils

DOE PAGES

Matamala, Roser; Calderon, Francisco J.; Jastrow, Julie D.; ...

2017-06-05

Here, we investigated the influence of site characteristics and soil properties on the chemical composition of organic matter in soils collected from a latitudinal transect across Alaska through analysis of diffuse reflectance Fourier transform mid infrared (MidIR) spectra of bulk soils. The study included 119 soil samples collected from 28 sites including tundra, boreal forest, and grassland ecosystems. Organic, mineral, and cryoturbated soil horizons, both seasonally and perennially frozen, from a variety of depths and edaphic conditions were examined. The amount and chemical composition of organic matter as well as site and soil properties exerted a strong influence on themore » MidIR spectra. The spectra were highly sensitive to the extent of organic matter decomposition, enabling the ordination of Oi, Oe and Oa organic horizons. Differences in absorbance intensity for several spectral bands indicated that Oi horizons contained greater abundance of relatively fresh residues, phenolic-OH compounds, aliphatic compounds (waxes, lipids and fats), and carbohydrates. In contrast, Oa horizons had a greater presence of amide groups (possibly from microbial residues), aromatics, C=C bonds, carboxylates and carboxylic acids. Another significant factor differentiating these horizons was the incorporation of clays and silicates into the decomposing organic matter of Oa horizons. Calculated height peak ratios showed a clear trend to greater decomposition among Oi, Oe and Oa. The MidIR spectra were related to many site/soil attributes including land cover type, parent material, and associated factors, such as permafrost presence/absence, soil drainage, horizon depth, bulk density, cation exchange capacity, and pH. Single MidIR spectral bands were identified that might be used in future studies to quickly estimate the organic and inorganic carbon, total nitrogen, and carbon:nitrogen ratios of soils from northern latitudes. Lastly, our results demonstrate that the information contained in MidIR spectra of bulk soil integrates the quantity and chemical composition of soil organic matter with soil forming factors and highlights the potential for using this information to assess the degradation state of organic matter stored in northern cold-region soils.« less

Compositon of sediments transported by the wind at different heights

NASA Astrophysics Data System (ADS)

Iturri, Antonela; Funk, Roger; Leue, Martin; Sommer, Michael; Buschiazzo, Daniel

2017-04-01

Wind erosion (WE) is one of the most important degradation process of soils in arid- and semiarid environments in the world, affecting soil properties and adjacent ecosystems, including human health. Estimations about the amount of eroded soil are available in Argentina and in the world, but the quality of the eroded sediments, particularly the sorting effects in agricultural soils, has been scarcely studied. The trend of the different mineral and organic soil compounds, which enrich in different size classes, can define height distribution profiles. Therefore, the uppermost 2.5 cm of four agricultural loess soils that differ in granulometric composition were used for WE simulations in a wind tunnel. Particles with a diameter smaller than 10 µm (PM10) were collected with a laboratory dust generator. The bulk soil and all the sediment samples were characterized by the granulometric composition, the soil organic carbon (SOC) content and the mineral and organic functional groups. Despite different texture, the soils were subjected to similar sorting processes in height, but differed depending on their granulometry. There was a separation between coarser and finer soil particles in coarser textured soils, while finer textured soils were more homogeneous in all heights. This correlated with the preferential transport of Si-O from quartz and C-H, C=O and C-C from soil organic matter (SOM), which were transported in larger and/or denser particles at lower heights. O-H from clay minerals and C-O-C and C-O from polysaccharides, carbohydrates and derivatives from SOM were transported in higher heights. Despite similar SOC content in the bulk soils, both the amount and composition in the PM10 fractions was different. The SOC transported at higher heights was mostly composed of polysaccharides, carbohydrates and derivatives associated with clay minerals. The SOC in PM10 fractions of coarser-textured soils was dominated by labile C-H groups. According to the determined height distribution profiles, it can be deduced that WE may affect both soil quality and the soil C balance due to the sorting effects during transport.

Influence of site and soil properties on the DRIFT spectra of northern cold-region soils [Influence of site and soil properties on the mid-infrared spectra of northern cold-region soils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matamala, Roser; Calderon, Francisco J.; Jastrow, Julie D.

Here, we investigated the influence of site characteristics and soil properties on the chemical composition of organic matter in soils collected from a latitudinal transect across Alaska through analysis of diffuse reflectance Fourier transform mid infrared (MidIR) spectra of bulk soils. The study included 119 soil samples collected from 28 sites including tundra, boreal forest, and grassland ecosystems. Organic, mineral, and cryoturbated soil horizons, both seasonally and perennially frozen, from a variety of depths and edaphic conditions were examined. The amount and chemical composition of organic matter as well as site and soil properties exerted a strong influence on themore » MidIR spectra. The spectra were highly sensitive to the extent of organic matter decomposition, enabling the ordination of Oi, Oe and Oa organic horizons. Differences in absorbance intensity for several spectral bands indicated that Oi horizons contained greater abundance of relatively fresh residues, phenolic-OH compounds, aliphatic compounds (waxes, lipids and fats), and carbohydrates. In contrast, Oa horizons had a greater presence of amide groups (possibly from microbial residues), aromatics, C=C bonds, carboxylates and carboxylic acids. Another significant factor differentiating these horizons was the incorporation of clays and silicates into the decomposing organic matter of Oa horizons. Calculated height peak ratios showed a clear trend to greater decomposition among Oi, Oe and Oa. The MidIR spectra were related to many site/soil attributes including land cover type, parent material, and associated factors, such as permafrost presence/absence, soil drainage, horizon depth, bulk density, cation exchange capacity, and pH. Single MidIR spectral bands were identified that might be used in future studies to quickly estimate the organic and inorganic carbon, total nitrogen, and carbon:nitrogen ratios of soils from northern latitudes. Lastly, our results demonstrate that the information contained in MidIR spectra of bulk soil integrates the quantity and chemical composition of soil organic matter with soil forming factors and highlights the potential for using this information to assess the degradation state of organic matter stored in northern cold-region soils.« less

Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

Treesearch

Mitchell A. Pavao-Zuckerman; David C. Coleman

2007-01-01

We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR FIELD COLLECTION OF YARD COMPOSITE SOIL SAMPLES (UA-F-5.1)

EPA Science Inventory

The purpose of this SOP is to establish a uniform procedure for the collection of yard composite soil samples in the field. This procedure was followed to ensure consistent and reliable collection of outdoor soil samples during the Arizona NHEXAS project and the "Border" study. ...

Eukaryal composition and diversity in anaerobic soils influenced by the novel chiral insecticide Paichongding.

PubMed

Zhu, Xiaolin; Zhou, Shaomin; Guo, Jing; Zhao, Xiyue; Yang, Guanghua; Cai, Zhiqiang

2018-04-18

Paichongding (IPP) is a neonicotinoid chiral insecticide with independent intellectual property in China. IPP application can increase crop yield, and also lead to insecticide residue and pollution in soils, which will affect microbial population and community composition in soils. In this study, four different types of soils were employed to inquire into the impact of IPP on eukaryal community and species-group through pyrosequencing of 18S rRNA gene amplicons. Fungal population differed in different soils at different days after IPP treatment (DAT). Eukaryal community species in CK (control check) groups were more rich than that with Paichongding sprayed at 5 DAT, while eukaryal species in CK soils at 60 DAT was relatively slight. Shannon's H' analysis indicated fungal species in CK soils were also higher at 5 DAT and relative lower at 60 DAT, except in soil C. There are also differences in the phyla and genus levels of the eukaryotic communities in the soil. After IPP application, the relative abundance of Nectriaceae increased 3-4 times in soil C. In soil F, Phaeosphaeriaceae increased to 57.3% at 5 DAT. The genus of Guehomyces, Aspergillus and Alternaria increased from 3.1 to 9.7, 1.1 to 4.6, 1.5 to 6.7% in soil H, respectively.

Effect of long-term industrial waste effluent pollution on soil enzyme activities and bacterial community composition.

PubMed

Subrahmanyam, Gangavarapu; Shen, Ju-Pei; Liu, Yu-Rong; Archana, Gattupalli; Zhang, Li-Mei

2016-02-01

Although numerous studies have addressed the influence of exogenous pollutants on microorganisms, the effect of long-term industrial waste effluent (IWE) pollution on the activity and diversity of soil bacteria was still unclear. Three soil samples characterized as uncontaminated (R1), moderately contaminated (R2), and highly contaminated (R3) receiving mixed organic and heavy metal pollutants for more than 20 years through IWE were collected along the Mahi River basin, Gujarat, western India. Basal soil respiration and in situ enzyme activities indicated an apparent deleterious effect of IWE on microbial activity and soil function. Community composition profiling of soil bacteria using 16S rRNA gene amplification and denaturing gradient gel electrophoresis (DGGE) method indicated an apparent bacterial community shift in the IWE-affected soils. Cloning and sequencing of DGGE bands revealed that the dominated bacterial phyla in polluted soil were affiliated with Firmicutes, Acidobacteria, and Actinobacteria, indicating that these bacterial phyla may have a high tolerance to pollutants. We suggested that specific bacterial phyla along with soil enzyme activities could be used as relevant biological indicators for long-term pollution assessment on soil quality. Graphical Abstract Bacterial community profiling and soil enzyme activities in long-term industrial waste effluent polluted soils.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil

PubMed Central

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009–2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0–20 cm, 20–40 cm, and 40–60 cm), e.g., the relative abundance of bio-control bacteria (Xanthomonadales, Lysobacter, Pseudomonas, and Bacillus), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria, and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter, and Ohtaekwangia. These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity. PMID:27965631

Soil pollution by petroleum products, III. Kerosene stability in soil columns as affected by volatilization

NASA Astrophysics Data System (ADS)

Galin, Ts.; Gerstl, Z.; Yaron, B.

1990-05-01

The stability of kerosene in soils as affected by volatization was determined in a laboratory column experiment by following the losses in the total concentration and the change in composition of the residuals in a dune sand, a loamy sand, and a silty loam soil during a 50-day period. Seven major compounds ranging between C 9 and C 15 were selected from a large variety of hydrocarbons forming kerosene and their presence in the remaining petroleum product was determined. The change in composition of kerosene during the experimental period was determined by gas chromatography and related to the seven major compounds selected. The experimental conditions — air-dairy soil and no subsequent addition of water—excluded both biodegradative and leaching. losses. The losses of kerosene in air-dried soil columns during the 50-day experimental period and the changes in the composition of the remaining residues due to volatilization are reported. The volatilization of all the components determined was greater from the dune sand and loamy sand soils than from the silty loam soil. It was assumed that the reason for this behavior was that the dune sand and the loamy sand soils contain a greater proportion of large pores (>4.5 μm) than the silty loam soil, even though the total porosity of the loamy sand and the silty loam is similar. In all the soils in the experiment, the components with a high carbon number formed the main fraction of the kerosene residues after 50 days of incubation.

Long-Term Application of Bioorganic Fertilizers Improved Soil Biochemical Properties and Microbial Communities of an Apple Orchard Soil.

PubMed

Wang, Lei; Yang, Fang; E, Yaoyao; Yuan, Jun; Raza, Waseem; Huang, Qiwei; Shen, Qirong

2016-01-01

Soil biochemical properties and microbial communities are usually considered as important indicators of soil health because of their association with plant nutrition. In this study, we investigated the impact of long-term application of bioorganic fertilizer (BOF) on soil biochemical properties and microbial communities in the apple orchard soil of the Loess Plateau. The experiment included three treatments: (1) control without fertilization (CK); (2) chemical fertilizer application (CF); and (3) bioorganic fertilizer application (BOF). The high throughput sequencing was used to examine the bacterial and fungal communities in apple orchard soil. The results showed that the BOF treatment significantly increased the apple yield during the experimental time (2009-2015). The application of BOF significantly increased the activities of catalase and invertase compared to those in CK and CF treatments. The high throughput sequencing data showed that the application of BOF changed the microbial community composition of all soil depths considered (0-20 cm, 20-40 cm, and 40-60 cm), e.g., the relative abundance of bio-control bacteria ( Xanthomonadales, Lysobacter, Pseudomonas , and Bacillus ), Proteobacteria, Bacteroidetes, Ohtaekwangia, Ilyonectria , and Lecanicillium was increased while that of Acidobacteria, Chloroflexi, Gp4, Gp6 and Sphaerobacter was decreased. The increase in apple yield after the application of BOF might be due to increase in organic matter, total nitrogen and catalase and invertase activities of soil and change in the bacterial community composition by enriching Bacillus, Pseudomonas, Lysobacter , and Ohtaekwangia . These results further enhance the understanding on how BOFs alter soil microbial community composition to stimulate soil productivity.

Variation of Soil Bacterial Communities in a Chronosequence of Rubber Tree (Hevea brasiliensis) Plantations

PubMed Central

Zhou, Yu-Jie; Li, Jian-Hua; Ross Friedman, Cynthia; Wang, Hua-Feng

2017-01-01

Regarding rubber tree plantations, researchers lack a basic understanding of soil microbial communities; specifically, little is known about whether or not soil microbial variation is correlated with succession in these plantations. In this paper, we used high-throughput sequencing of the 16S rRNA gene to investigate the diversity and composition of the soil bacterial communities in a chronosequence of rubber tree plantations that were 5, 10, 13, 18, 25, and 30 years old. We determined that: (1) Soil bacterial diversity and composition show changes over the succession stages of rubber tree plantations. The diversity of soil bacteria were highest in 10, 13, and 18 year-old rubber tree plantations, followed by 30 year-old rubber tree plantations, whereas 5 and 25 year-old rubber tree plantations had the lowest values for diversity. A total of 438,870 16S rDNA sequences were detected in 18 soil samples from six rubber tree plantations, found in 28 phyla, 66 classes, 139 orders, 245 families, 355 genera, and 645 species, with 1.01% sequences from unclassified bacteria. The dominant phyla were Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria, and Verrucomicrobia (relative abundance large than 3%). There were differences in soil bacterial communities among different succession stages of rubber tree plantation. (2) Soil bacteria diversity and composition in the different stages was closely related to pH, vegetation, soil nutrient, and altitude, of which pH, and vegetation were the main drivers. PMID:28611794

Organic Amendments to Avocado Crops Induce Suppressiveness and Influence the Composition and Activity of Soil Microbial Communities

PubMed Central

Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B.; Gaju, Nuria; Cazorla, Francisco M.

2015-01-01

One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. PMID:25769825

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter.

PubMed

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; Koechli, Chantal; Campbell, Ashley; Buckley, Daniel H; Lehmann, Johannes

2016-12-01

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.

Soil factors involved in the diversity and structure of soil bacterial communities in commercial organic olive orchards in Southern Spain.

PubMed

Landa, B B; Montes-Borrego, M; Aranda, S; Soriano, M A; Gómez, J A; Navas-Cortés, J A

2014-04-01

Nowadays, there is a tendency in olive production systems to reduce tillage or keep a vegetative cover to reduce soil erosion and degradation. However, there is scarce information on the effects of different soil management systems (SMS) in soil bacterial community composition of olive groves. In this study, we have evaluated the effects of soil type and different SMS implemented to control weeds in the structure and diversity of bacterial communities of 58 soils in the two geographic areas that best represent the organic olive production systems in Spain. Bacterial community composition assessed by frequency and intensity of occurrence of terminal restriction profiles (TRFs) derived from terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified 16S ribosomal deoxyribonucleic acid were strongly correlated with soil type/field site (Eutric/Calcaric) that differed mainly in soil particle size distribution and soil pH, followed by a strong effect of SMS, in that order. Canonical discriminant (CD) analysis of TRFs properly classified all of the olive orchard soils as belonging to their respective soil type or SMS. Furthermore, only a small set of TRFs were enough to clearly and significantly differentiate soil samples according to soil type or SMS. Those specific TRFs could be used as bioindicators to assess the effect of changes in SMS aimed to enhance soil quality in olive production systems. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Molecular composition of soil organic matter with land-use change along a bi-continental mean annual temperature gradient.

PubMed

Pisani, Oliva; Haddix, Michelle L; Conant, Richard T; Paul, Eldor A; Simpson, Myrna J

2016-12-15

Soil organic matter (SOM) is critical for maintaining soil fertility and long-term agricultural sustainability. The molecular composition of SOM is likely altered due to global climate and land-use change; but rarely are these two aspects studied in tandem. Here we used molecular-level techniques to examine SOM composition along a bi-continental (from North to South America) mean annual temperature (MAT) gradient from seven native grassland/forest and cultivated/pasture sites. Biomarker methods included solvent extraction, base hydrolysis and cupric (II) oxide oxidation for the analysis of free lipids of plant and microbial origin, ester-bound lipids from cutin and suberin, and lignin-derived phenols, respectively. Solid-state 13 C nuclear magnetic resonance (NMR) was used to examine the overall composition of SOM. Soil cultivation was found to increase the amount of microbial-derived compounds at warmer temperatures (up to 17% increase). The cultivated soils were characterized by much lower contributions of plant-derived SOM components compared to the native soils (up to 64% lower at the coldest site). In addition, cultivation caused an increase in lignin and cutin degradation (up to 68 and 15% increase, respectively), and an increase in the amount of suberin-derived inputs (up to 54% increase). Clear differences in the molecular composition of SOM due to soil cultivation were observed in soils of varying mineral composition and were attributed to disturbance, different vegetation inputs, soil aggregate destruction and MAT. A high organic allophanic tropical soil was characterized by its protection of carbohydrates and nitrogen-containing compounds. The conversion of native to cultivated land shows significant shifts in the degradation stage of SOM. In particular, cutin-derived compounds which are believed to be part of the stable SOM pool may undergo enhanced degradation with long-term cultivation and disruption of soil aggregates. On a per year basis, the total amount of cutin decreased only at the two forest sites that were converted to pasture, likely due to cutin degradation or to changes in vegetation and litter quality associated with land-use change. Overall, our study highlights that the implementation of different agricultural management practices enhances the degradation of recalcitrant SOM compounds that may become a source of atmospheric CO 2 with increasing land-use and climate change. Copyright © 2016 Elsevier B.V. All rights reserved.

Interactive effects between plant functional types and soil factors on tundra species diversity and community composition.

PubMed

Iturrate-Garcia, Maitane; O'Brien, Michael J; Khitun, Olga; Abiven, Samuel; Niklaus, Pascal A; Schaepman-Strub, Gabriela

2016-11-01

Plant communities are coupled with abiotic factors, as species diversity and community composition both respond to and influence climate and soil characteristics. Interactions between vegetation and abiotic factors depend on plant functional types (PFT) as different growth forms will have differential responses to and effects on site characteristics. However, despite the importance of different PFT for community assembly and ecosystem functioning, research has mainly focused on vascular plants. Here, we established a set of observational plots in two contrasting habitats in northeastern Siberia in order to assess the relationship between species diversity and community composition with soil variables, as well as the relationship between vegetation cover and species diversity for two PFT (nonvascular and vascular). We found that nonvascular species diversity decreased with soil acidity and moisture and, to a lesser extent, with soil temperature and active layer thickness. In contrast, no such correlation was found for vascular species diversity. Differences in community composition were found mainly along soil acidity and moisture gradients. However, the proportion of variation in composition explained by the measured soil variables was much lower for nonvascular than for vascular species when considering the PFT separately. We also found different relationships between vegetation cover and species diversity according the PFT and habitat. In support of niche differentiation theory, species diversity and community composition were related to edaphic factors. The distinct relationships found for nonvascular and vascular species suggest the importance of considering multiple PFT when assessing species diversity and composition and their interaction with edaphic factors. Synthesis : Identifying vegetation responses to edaphic factors is a first step toward a better understanding of vegetation-soil feedbacks under climate change. Our results suggest that incorporating differential responses of PFT is important for predicting vegetation shifts, primary productivity, and in turn, ecosystem functioning in a changing climate.

The effects of grassland degradation on plant diversity, primary productivity, and soil fertility in the alpine region of Asia's headwaters.

PubMed

Wang, Xuexia; Dong, Shikui; Yang, Bing; Li, Yuanyuan; Su, Xukun

2014-10-01

A 3-year survey was conducted to explore the relationships among plant composition, productivity, and soil fertility characterizing four different degradation stages of an alpine meadow in the source region of the Yangtze and Yellow Rivers, China. Results showed that plant species diversity, productivity, and soil fertility of the top 30-cm soil layer significantly declined with degradation stages of alpine meadow over the study period. The productivity of forbs significantly increased with degradation stages, and the soil potassium stock was not affected by grassland degradation. The vegetation composition gradually shifted from perennial graminoids (grasses and sedges) to annual forbs along the degradation gradient. The abrupt change of response in plant diversity, plant productivity, and soil nutrients was demonstrated after heavy grassland degradation. Moreover, degradation can indicate plant species diversity and productivity through changing soil fertility. However, the clear relationships are difficult to establish. In conclusion, degradation influenced ecosystem function and services, such as plant species diversity, productivity, and soil carbon and nitrogen stocks. Additionally, both plant species diversity and soil nutrients were important predictors in different degradation stages of alpine meadows. To this end, heavy degradation grade was shown to cause shift of plant community in alpine meadow, which provided an important basis for sustaining ecosystem function, manipulating the vegetation composition of the area and restoring the degraded alpine grassland.

Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri.

PubMed

Stein, Ricardo J; Höreth, Stephan; de Melo, J Romário F; Syllwasschy, Lara; Lee, Gwonjin; Garbin, Mário L; Clemens, Stephan; Krämer, Ute

2017-02-01

Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Evaluating the Effects of Metals on Microorganisms in Flooded Paddy Soils Using the SEM/AVS-Based Approach and Measurements of Exchangeable Metal Concentrations.

PubMed

Kunito, Takashi; Toya, Hitomi; Sumi, Hirotaka; Ishikawa, Yuichi; Toda, Hideshige; Nagaoka, Kazunari; Saeki, Kazutoshi; Aikawa, Yoshio; Matsumoto, Satoshi

2017-04-01

We examined possible adverse effects of heavy metals on microbial activity, biomass, and community composition using the simultaneously extracted metals (SEM)/acid-volatile sulfide (AVS)-based approach and measurements of exchangeable metal concentrations in three paddy soils (wastewater-contaminated soil, mine-contaminated soil, and noncontaminated soil) incubated for 60 days under flooded conditions. Incubation under flooding increased pH and decreased Eh in all samples. AVS increased when Eh decreased to approximately -200 mV for the mine-contaminated and noncontaminated soils, while the wastewater-contaminated soil originally had a high concentration of AVS despite its air-dried condition. Addition of rice straw or alkaline material containing calcium carbonate and gypsum increased AVS levels under flooded conditions. We observed no apparent relationship between soil enzyme activity (β-D-glucosidase and acid phosphatase) and concentrations of SEM, [∑SEM - AVS], and exchangeable metals. Bacterial and fungal community composition, assessed using polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) analysis targeting rRNA genes, was largely influenced by site of collection and incubation time, but metal contamination did not influence community composition. We observed significant negative correlations between biomass C and [∑SEM - AVS] and between biomass C and ∑SEM, suggesting that [∑SEM - AVS] and ∑SEM might reflect the bioavailability of organic matter to microorganisms in these soils.

Suitability of the microbial community composition and function in a semiarid mine soil for assessing phytomanagement practices based on mycorrhizal inoculation and amendment addition.

PubMed

Kohler, J; Caravaca, F; Azcón, R; Díaz, G; Roldán, A

2016-03-15

The recovery of species composition and functions of soil microbial community of degraded lands is crucial in order to guarantee the long-term self-sustainability of the ecosystems. A field experiment was carried out to test the influence of combining fermented sugar beet residue (SBR) addition and inoculation with the arbuscular mycorrhizal (AM) fungus Funneliformis mosseae on the plant growth parameters and microbial community composition and function in the rhizosphere of two autochthonous plant species (Dorycnium pentaphyllum L. and Asteriscus maritimus L.) growing in a semiarid soil contaminated by heavy metals. We analysed the phospholipid fatty acids (PLFAs), neutral lipids fatty acids (NLFAs) and enzyme activities to study the soil microbial community composition and function, respectively. The combined treatment was not effective for increasing plant growth. The SBR promoted the growth of both plant species, whilst the AM fungus was effective only for D. pentaphyllum. The effect of the treatments on plant growth was linked to shifts in the rhizosphere microbial community composition and function. The highest increase in dehydrogenase and β-glucosidase activities was recorded in SBR-amended soil. The SBR increased the abundance of marker PLFAs for saprophytic fungi, Gram+ and Gram- bacteria and actinobacteria, whereas the AM fungus enhanced the abundance of AM fungi-related NLFA and marker PLFAs for Gram- bacteria. Measurement of the soil microbial community composition and function was useful to assess the success of phytomanagement technologies in a semiarid, contaminated soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Agricultural legacies in forest environments: tree communities, soil properties, and light availability.

PubMed

Flinn, Kathryn M; Marks, P L

2007-03-01

Temperate deciduous forests across much of Europe and eastern North America reflect legacies of past land use, particularly in the diversity and composition of plant communities. Intense disturbances, such as clearing forests for agriculture, may cause persistent environmental changes that continue to shape vegetation patterns as landscapes recover. We assessed the long-term consequences of agriculture for environmental conditions in central New York forests, including tree community structure and composition, soil physical and chemical properties, and light availability. To isolate the effects of agriculture, we compared 20 adjacent pairs of forests that were never cleared for agriculture (primary forests) and forests that established 85-100 years ago on plowed fields (secondary forests). Tree communities in primary and secondary forests had similar stem density, though secondary forests had 14% greater basal area. Species composition differed dramatically between the two forest types, with primary forests dominated by Acer saccharum and Fagus grandifolia and secondary forests by Acer rubrum and Pinus strobus. Primary and secondary forests showed no consistent differences in soil physical properties or in the principal gradient of soil fertility associated with soil pH. Within stands, however, soil water content and pH were more variable in primary forests. Secondary forest soils had 15% less organic matter, 16% less total carbon, and 29% less extractable phosphorus in the top 10 cm than adjacent primary stands, though the ranges of the forest types mostly overlapped. Understory light availability in primary and secondary forests was similar. These results suggest that, within 100 years, post-agricultural stands have recovered conditions comparable to less disturbed forests in many attributes, including tree size and number, soil physical properties, soil chemical properties associated with pH, and understory light availability. The principal legacies of agriculture that remain in these forests are the reduced levels of soil organic matter, carbon, and phosphorus; the spatial homogenization of soil properties; and the altered species composition of the vegetation.

Multi-factorial drivers of ammonia oxidizer communities: evidence from a national soil survey.

PubMed

Yao, Huaiying; Campbell, Colin D; Chapman, Stephen J; Freitag, Thomas E; Nicol, Graeme W; Singh, Brajesh K

2013-09-01

The factors driving the abundance and community composition of soil microbial communities provide fundamental knowledge on the maintenance of biodiversity and the ecosystem services they underpin. Several studies have suggested that microbial communities are spatially organized, including functional groups and much of the observed variation is explained by geographical location or soil pH. Soil ammonia-oxidizing archaea (AOA) and bacteria (AOB) are excellent models for such study due to their functional, agronomic and environmental importance and their relative ease of characterization. To identify the dominant drivers of different ammonia oxidizers, we used samples (n = 713) from the National Soil Inventory of Scotland (NSIS). Our results indicate that 40-45% of the variance in community compositions can be explained by 71 environmental variables. Soil pH and substrate, which have been regarded as the two main drivers, only explained 13-16% of the total variance. We provide strong evidence of multi-factorial drivers (land use, soil type, climate and N deposition) of ammonia-oxidizing communities, all of which play a significant role in the creation of specific niches that are occupied by unique phylotypes. For example, one AOA phylotype was strongly linked to woodland/semi-natural grassland, rainfall and N deposition. Some soil typologies, namely regosols, have a novel AOA community composition indicating typology as one of the factors which defines this ecological niche. AOA abundance was high and strongly linked the rate of potential nitrification in the highly acidic soils supporting the argument that AOA are main ammonia oxidizers in acidic soils. However, for AOB, soil pH and substrate (ammonia) were the main drivers for abundance and community composition. These results highlight the importance of multiple drivers of microbial niche formation and their impact on microbial biogeography that have significant consequences for ecosystem functioning. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Fire Frequency and Vegetation Composition Influence Soil Nitrogen Cycling and Base Cations in an Oak Savanna Ecosystem

NASA Astrophysics Data System (ADS)

McLauchlan, K. K.; Nelson, D. M.; Perakis, S.; Marcotte, A. L.

2017-12-01

Fire frequency is crucial for maintaining savannas in the transition between forests and grasslands. In general, increasing fire frequency has two effects: it increases herbaceous plant cover more than woody plant cover, and it lowers soil organic matter stocks. These effects have been demonstrated at a long-term prescribed fire experiment in an oak savanna ecosystem at Cedar Creek Ecosystem Science Reserve, Minnesota, U.S.A. The fire experiment began in 1964 and oak savannas are burned at various frequencies ranging from every year to not at all. This has led to changes in vegetation ranging from almost 100% grassland to 100% oak forest. Additionally, nitrogen stocks almost doubled in the sites that were not burned, as it accumulated in the trees, leaf litter, and soil. We addressed additional soil changes taking place at this experiment by asking the question: How have fire and oak-grass balance affected soil nutrients, specifically nitrogen and base cations? Surface soils were collected from 12 plots on the oak savanna burn experiment. Soils were collected in increments to 100 cm depth, from under grass-dominated vegetation and from under tree-dominated vegetation. We non-destructively estimated soil base cations by measuring elemental concentrations of dried soil subsamples with a handheld x-ray fluorescence analyzer. We also measured carbon and nitrogen concentrations and isotopic composition of the soil samples. Soils in plots with high fire frequency had higher concentrations of calcium than soils in unburned plots (low fire frequency). Similar trends were seen for soil potassium, magnesium, and phosphorus concentrations. In contrast, soils in plots with high fire frequency had dramatically lowered nitrogen cycling rates and stocks across the oak savanna. The contrast between the responses of different nutrients to changing fire frequency has important implications for the consequences of fire and tree-grass composition on nutrient cycling dynamics.

Effects of simulated acid rain on soil fauna community composition and their ecological niches.

PubMed

Wei, Hui; Liu, Wen; Zhang, Jiaen; Qin, Zhong

2017-01-01

Acid rain is one of the severest environmental issues globally. Relative to other global changes (e.g., warming, elevated atmospheric [CO 2 ], and nitrogen deposition), however, acid rain has received less attention than its due. Soil fauna play important roles in multiple ecological processes, but how soil fauna community responds to acid rain remains less studied. This microcosm experiment was conducted using latosol with simulated acid rain (SAR) manipulations to observe potential changes in soil fauna community under acid rain stress. Four pH levels, i.e., pH 2.5, 3.5, 4.5, and 5.5, and a neutral control of pH 7.0 were set according to the current pH condition and acidification trend of precipitation in southern China. As expected, we observed that the SAR treatments induced changes in soil fauna community composition and their ecological niches in the tested soil; the treatment effects tended to increase as acidity increased. This could be attributable to the environmental stresses (such as acidity, porosity and oxygen supply) induced by the SAR treatments. In addition to direct acidity effect, we propose that potential changes in permeability and movability of water and oxygen in soils induced by acid rain could also give rise to the observed shifts in soil fauna community composition. These are most likely indirect pathways of acid rain to affect belowground community. Moreover, we found that nematodes, the dominating soil fauna group in this study, moved downwards to mitigate the stress of acid rain. This is probably detrimental to soil fauna in the long term, due to the relatively severer soil conditions in the deep than surface soil layer. Our results suggest that acid rain could change soil fauna community and the vertical distribution of soil fauna groups, consequently changing the underground ecosystem functions such as organic matter decomposition and greenhouse gas emissions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Sorption of atrazine and ametryn by carbonatic and non-carbonatic soils of varied origin.

PubMed

Kasozi, G N; Nkedi-Kizza, P; Li, Y; Zimmerman, A R

2012-10-01

Sorption of two s-triazines, atrazine and ametryn, by carbonatic soils, Histosols, Spodosols and Oxisols was examined. Linear isotherms were observed and sorption coefficients (K(d)) of both compounds were significantly lower (α = 0.05) onto carbonatic soils compared to non-carbonatic soils. Furthermore, among carbonatic soil types, the marl-carbonatic soils had the lowest sorption affinities. K(d) and organic carbon content were highly correlated, suggesting predominant influence of organic carbon in the sorption of the s-triazine, except in Oxisols and Spodosols where variations suggest other factors. Upon removal of organic matter (OM) using sodium hypochlorite and hydrogen peroxide, the K(d) values were reduced by ~90%, indicating minimal contribution of mineral surfaces. Thus OM compositional differences likely explain the large variation in s-triazine sorption within and between soil orders. This study highlights the need to consider OM composition in addition to quantity when determining pesticide applications rates, particularly for carbonatic soils. Copyright © 2012 Elsevier Ltd. All rights reserved.

Root uptake of 137Cs by natural and semi-natural grasses as a function of texture and moisture of soils.

PubMed

Grytsyuk, N; Arapis, G; Davydchuk, V

2006-01-01

This work studies the dependence of 137Cs root uptake on the structure of landscape, especially on texture and moisture of soils, under natural conditions, on abandoned radiopolluted lands in Northern Ukraine. Researches were carried out on a wide range of landscape conditions, at various levels of 137Cs contamination (from 20 up to 5000 kBqm(-2)), with different types of soils (approx. 20 soil varieties), which differ in texture, granulometric composition, degrees of gleyization and water regime, and anthropogenic transformation. The results showed that transfer factor (TF) values of 137Cs differ 50 times for the natural grassy coenoses and 8 times for the semi-natural ones. The lowest 137Cs TF values were measured in the herbages of dry meadows at automorphous loamy soils, while the highest were observed in wetland meadows at organic soils. Finally, the correlation between 137Cs TF values and granulometric composition of soil was determined for both automorphic and hydromorphic mineral soils.

Retrieval of Compositional End-Members From Mars Exploration Rover Opportunity Observations in a Soil-Filled Fracture in Marathon Valley, Endeavour Crater Rim

NASA Astrophysics Data System (ADS)

Stein, N. T.; Arvidson, R. E.; O'Sullivan, J. A.; Catalano, J. G.; Guinness, E. A.; Politte, D. V.; Gellert, R.; VanBommel, S. J.

2018-01-01

The Opportunity rover investigated a gentle swale on the rim of Endeavour crater called Marathon Valley where a series of bright planar outcrops are cut into polygons by fractures. A wheel scuff performed on one of the soil-filled fracture zones revealed the presence of three end-members identified on the basis of Pancam multispectral imaging observations covering 0.4 to 1 μm: red and dark pebbles, and a bright soil clod. Multiple overlapping Alpha Particle X-ray Spectrometer (APXS) measurements were collected on three targets within the scuff zone. The field of view of each APXS measurement contained various proportions of the Pancam-based end-members. Application of a log maximum likelihood method for retrieving the composition of the end-members using the 10 APXS measurements shows that the dark pebble end-member is compositionally similar to average Mars soil, with slightly elevated S and Fe. In contrast, the red pebble end-member exhibits enrichments in Al and Si and is depleted in Fe and Mg relative to average Mars soil. The soil clod end-member is enriched in Mg, S, and Ni. Thermodynamic modeling of the soil clod end-member composition indicates a dominance of sulfate minerals. We hypothesize that acidic fluids in fractures leached and oxidized the basaltic host rock, forming the red pebbles, and then evaporated to leave behind sulfate-cemented soil.

Elemental composition study of heavy metal (Ni, Cu, Zn) in riverbank soil by electrokinetic-assisted phytoremediation using XRF and SEM/EDX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jamari, Suhailly; Embong, Zaidi; Bakar, Ismail

Electrokinetic (EK)-assisted phytoremediation is one of the methods that have a big potential in enhancing the ability of plant uptake in soils remediation process. This research was conducted to investigate the difference in elemental composition concentration of riverbank soil and the change of pH between pre- and post-phytoremediation under the following condition: 1) control or as-receive sample; 2) Dieffenbachia spp plant with EK system (a pair of EK electrodes connected to a direct current (DC) power supply). After the electrodes were connected to a magnitude of 6V/cm{sup −1} electric field for 4 hours/day, the soil and plant samples were analyzedmore » using and X-ray Fluorescence Spectrometer (XRF) and Scanning Electron Microscope / Energy Dispersive X-ray Spectroscopy (SEM/EDX). The SEM/EDX analysis showed that concentration of elemental composition (Ni, Cu and Zn) in post-phytoremediation plant powder samples had increase while elemental concentrations in the post-phytoremediation soil samples were decreased. XRF analysis presented a variation in soil elemental composition concentration from anode to cathode where the concentration near anode region increased while decreased near the cathode region. A significant changes in soil pH were obtained where the soil pH increase in cathode region while decrease in anode region. The results reveal that the assistance of EK in phytoremediation process has increase the efficiency of plant uptake.« less

Soil disturbance effects on the composition of seed-dispersing ants in roadside environments.

PubMed

Palfi, Zsofia; Spooner, Peter G; Robinson, Wayne

2017-02-01

Myrmecochory (the dispersal of seeds by ants) is a significant ecological process in sclerophyll woodlands, but habitat disturbance is known to alter the extent and success of this mutualism. We investigated the influence of soil disturbance on the composition of the seed-dispersing ant community. Surveys were conducted in roadside verges where soils are regularly disturbed by road maintenance activities. Using a 'cafeteria' bait station approach, we selected 24 roads of different widths to investigate ant composition and abundance in relation to soil disturbance. We found ant species richness was greater in non-disturbed than disturbed zones, where road verge width significantly influenced results. The composition and abundance of individual seed-dispersing ant species varied between disturbed and non-disturbed zones. Rhytidoponera metallica were more abundant in non-disturbed sites, whereas Melophorus bruneus and Monomorium rothseini were more frequently recorded in disturbed areas. Commonly found Iridomyrmex purpureus was significantly more abundant in disturbed zones in narrow roadsides and vice versa in wide roadsides, and strongly influenced total community composition. Variation in the abundance of commonly recorded Iridomyrmex and Monomorium genera were related more to site conditions (roadside width and habitat) than soil disturbance. The rich composition of seed dispersing ants in roadside environments, and the effects of soil disturbances on these ant communities that we describe, provide a key insight to important seed dispersal vectors occurring in fragmented rural landscapes.

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

PubMed

Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

Regional-scale drivers of forest structure and function in northwestern Amazonia.

PubMed

Higgins, Mark A; Asner, Gregory P; Anderson, Christopher B; Martin, Roberta E; Knapp, David E; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest.

Soil warming alters microbial substrate use in alpine soils.

PubMed

Streit, Kathrin; Hagedorn, Frank; Hiltbrunner, David; Portmann, Magdalena; Saurer, Matthias; Buchmann, Nina; Wild, Birgit; Richter, Andreas; Wipf, Sonja; Siegwolf, Rolf T W

2014-04-01

Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C-rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007-2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO2 enrichment experiment using depleted (13)CO2 (δ(13)C = -30‰, 2001-2009). We traced this depleted (13)C label in phospholipid fatty acids (PLFA) of the organic layer (0-5 cm soil depth) and in C mineralized from root-free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 ('old'), from 2001 to 2009 ('new') or in 2010 ('recent'). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root-free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem. © 2013 John Wiley & Sons Ltd.

Biogeochemical drivers of microbial community convergence across actively retreating glaciers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castle, Sarah C.; Nemergut, Diana R.; Grandy, A. Stuart

The ecological processes that influence biogeographical patterns of microorganisms are actively debated. To investigate how such patterns emerge during ecosystem succession, we examined the biogeochemical drivers of bacterial community assembly in soils over two environmentally distinct, recently deglaciated chronosequences separated by a distance of more than 1,300 kilometers. Our results show that despite different geographic, climatic, and soil chemical and physical characteristics at the two sites, soil bacterial community structure and decomposer function converged during plant succession. In a comparative analysis, we found that microbial communities in early succession soils were compositionally distinct from a group of diverse, mature forestmore » soils, but that the differences between successional soils and mature soils decreased from early to late stages of succession. Differences in bacterial community composition across glacial sites were largely explained by pH. However, successional patterns and community convergence across sites were more consistently related to soil organic carbon and organic matter chemistry, which appeared to be tightly coupled with bacterial community structure across both young and mature soils.« less

A Critical Examination of Relative Concentrations of Volume-correlated and Surface-correlated Submicron Globules of Pure Fe-0 in Lunar Soils

NASA Technical Reports Server (NTRS)

Basu, A.; McKay, D. S.; Wentworth, S. J.

2003-01-01

Impacts on lunar soils produce melt and vapor in an approximate proportion of 7:1. The melt scavenges soil grains of diverse size, quenches and forms agglutinates, thereby converting surface correlated components of soil grains as volume correlated components; simultaneously, parts of the vapor may condense or escape. Cumulative small impacts increase the maturity of the soils, increase the abundance of agglutinates, and increase the concentration of vapor condensated material. Since the discovery of vapor deposited crystalline Fe-0 in vugs of regolith breccias and the theoretical anticipation of amorphous vapor deposits of diverse composition coating lunar soils grains, empirical evidence is gathering in support of such deposits, now commonly called vapor deposited patina (VDP). In addition, submicron globules of Fe-0 are seen to be ubiquitous in VDP. The amorphous VDP lowers the albedo of lunar soils, affects magnetic properties of soils, changes the slopes of uv-vis-ir reflectance spectra, and potentially also alters the gamma and x-ray spectra of lunar soils, compromising compositional inferences from remote sensing.

Climate change and physical disturbance manipulations result in distinct biological soil crust communities.

PubMed

Steven, Blaire; Kuske, Cheryl R; Gallegos-Graves, La Verne; Reed, Sasha C; Belnap, Jayne

2015-11-01

Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Climate change and physical disturbance manipulations result in distinct biological soil crust communities

USGS Publications Warehouse

Steven, Blaire; Kuske, Cheryl R.; Gallegos-Graves, La Verne; Reed, Sasha C.; Belnap, Jayne

2015-01-01

Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remain poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2 °C soil warming, altered summer precipitation (wetting), and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional change. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities and the community functional profile can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.

APXS-derived chemistry of the Bagnold dune sands: Comparisons with Gale Crater soils and the global Martian average

NASA Astrophysics Data System (ADS)

O'Connell-Cooper, C. D.; Spray, J. G.; Thompson, L. M.; Gellert, R.; Berger, J. A.; Boyd, N. I.; Desouza, E. D.; Perrett, G. M.; Schmidt, M.; VanBommel, S. J.

2017-12-01

We present Alpha-Particle X-ray Spectrometer (APXS) data for the active Bagnold dune field within the Gale impact crater (Mars Science Laboratory (MSL) mission). We derive an APXS-based average basaltic soil (ABS) composition for Mars based on past and recent data from the MSL and Mars Exploration Rover (MER) missions. This represents an update to the Taylor and McLennan (2009) average Martian soil and facilitates comparison across Martian data sets. The active Bagnold dune field is compositionally distinct from the ABS, with elevated Mg, Ni, and Fe, suggesting mafic mineral enrichment and uniformly low levels of S, Cl, and Zn, indicating only a minimal dust component. A relationship between decreasing grain size and increasing felsic content is revealed. The Bagnold sands possess the lowest S/Cl of all Martian unconsolidated materials. Gale soils exhibit relatively uniform major element compositions, similar to Meridiani Planum and Gusev Crater basaltic soils (MER missions). However, they show minor enrichments in K, Cr, Mn, and Fe, which may signify a local contribution. The lithified eolian Stimson Formation within the Gale impact crater is compositionally similar to the ABS and Bagnold sands, which provide a modern analogue for these ancient eolian deposits. Compilation of APXS-derived soil data reveals a generally homogenous global composition for Martian soils but one that can be locally modified due to past or extant geologic processes that are limited in both space and time.

How soil organic matter composition controls hexachlorobenzene-soil-interactions: adsorption isotherms and quantum chemical modeling.

PubMed

Ahmed, Ashour A; Kühn, Oliver; Aziz, Saadullah G; Hilal, Rifaat H; Leinweber, Peter

2014-04-01

Hazardous persistent organic pollutants (POPs) interact in soil with the soil organic matter (SOM) but this interaction is insufficiently understood at the molecular level. We investigated the adsorption of hexachlorobenzene (HCB) on soil samples with systematically modified SOM. These samples included the original soil, the soil modified by adding a hot water extract (HWE) fraction (soil+3 HWE and soil+6 HWE), and the pyrolyzed soil. The SOM contents increased in the order pyrolyzed soil

Comment on 'Shang S. 2012. Calculating actual crop evapotranspiration under soil water stress conditions with appropriate numerical methods and time step. Hydrological Processes 26: 3338-3343. DOI: 10.1002/hyp.8405'

NASA Technical Reports Server (NTRS)

Yatheendradas, Soni; Narapusetty, Balachandrudu; Peters-Lidard, Christa; Funk, Christopher; Verdin, James

2014-01-01

A previous study analyzed errors in the numerical calculation of actual crop evapotranspiration (ET(sub a)) under soil water stress. Assuming no irrigation or precipitation, it constructed equations for ET(sub a) over limited soil-water ranges in a root zone drying out due to evapotranspiration. It then used a single crop-soil composite to provide recommendations about the appropriate usage of numerical methods under different values of the time step and the maximum crop evapotranspiration (ET(sub c)). This comment reformulates those ET(sub a) equations for applicability over the full range of soil water values, revealing a dependence of the relative error in numerical ET(sub a) on the initial soil water that was not seen in the previous study. It is shown that the recommendations based on a single crop-soil composite can be invalid for other crop-soil composites. Finally, a consideration of the numerical error in the time-cumulative value of ET(sub a) is discussed besides the existing consideration of that error over individual time steps as done in the previous study. This cumulative ET(sub a) is more relevant to the final crop yield.

Soil aggregate stratification of nematodes and ammonia oxidizers affects nitrification in an acid soil.

PubMed

Jiang, Yuji; Jin, Chen; Sun, Bo

2014-10-01

Nitrification plays a central role in global nitrogen cycle, which is affected by interaction between soil microfauna and microorganisms. The impact of synchronized changes in nematodes and ammonia oxidizers within aggregate fractions on nitrification was investigated in an acid soil under 10-year manure application. Nematodes, ammonia oxidizers and potential nitrification activity (PNA) were examined in three soil aggregate fractions under four fertilization regimes. Pyrosequencing data revealed that the dominant bacterial amoA operational taxonomic units (OTUs) were related to Nitrosospira species, while archaeal OTUs were affiliated with Nitrososphaera and Nitrosotalea species. PNA was more strongly correlated with ammonia-oxidizing bacteria (AOB) abundance than ammonia-oxidizing archaea (AOA) abundance, although AOA were dominant in the acid soil. Plant parasites had a negative effect on AOB abundance; however, bacterivores stimulated AOB abundance and contributed more to PNA than plant parasites. Aggregate fractions exerted significant impacts on AOA abundance and AOB community composition. Total carbon content strongly affected the abundance and composition of AOA community, while soil pH primarily affected that of AOB community. Soil variables explained 62.7% and 58.1% variations, and nematode variables explained 11.7% and 19.5% variations in the AOA and AOB community composition respectively. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Out of sight - Profiling soil characteristics, nutrients and microbial communities affected by organic amendments down to one meter in a long-term maize cultivation experiment

NASA Astrophysics Data System (ADS)

Lehtinen, Taru; Mikkonen, Anu; Zavattaro, Laura; Grignani, Carlo; Baumgarten, Andreas; Spiegel, Heide

2016-04-01

Soil characteristics, nutrients and microbial activity in the deeper soil layers are topics not of-ten covered in agricultural studies since the main interest lies within the most active topsoils and deep soils are more time-consuming to sample. Studies have shown that deep soil does matter, although biogeochemical cycles are not fully understood yet. The main aim of this study is to investigate the soil organic matter dynamics, nutrients and microbial community composition in the first meter of the soil profiles in the long-term maize cropping system ex-periment Tetto Frati, in the vicinity of the Po River in Northern Italy. The trial site lies on a deep, calcareous, free-draining soil with a loamy texture. The following treatments have been applied since 1992: 1) maize for silage with 250 kg mineral N ha-1 (crop residue removal, CRR), 2) maize for grain with 250 kg mineral N ha-1 (crop residue incorporation, CRI), 3) maize for silage with 250 kg bovine slurry N ha-1 (SLU), 4) maize for silage with 250 kg farm yard manure N ha-1 (FYM). Soil characteristics (pH, carbonate content, soil organic carbon (SOC), aggregate stability (WSA)), and nutrients (total nitrogen (Nt), CAL-extractable phos-phorous (P) and potassium (K), potential N mineralisation) were investigated. Bacteri-al community composition was investigated with Ion PGM high-throughput sequencing at the depth of 8000 sequences per sample. Soil pH was moderately alkaline in all soil samples, in-creasing with increasing soil depth, as the carbonate content increased. SOC was significantly higher in the treatments with organic amendments (CRI, SLU and FYM) compared to CRR in 0-25 cm (11.1, 11.6, 14.7 vs. 9.8 g kg-1, respectively), but not in the deeper soil. At 50-75 cm soil depth FYM treatment revealed higher WSA compared to CRR, as well as higher CAL-extractable K (25 and 15 mg kg-1, respectively) and potential N mineralisation (11.30 and 8.78 mg N kg-1 7d-1, respectively). At 75-100 cm soil depth, SLU and FYM had the highest poten-tial N mineralisation. Microbial biomass and bacterial diversity decreased downwards the soil profile. Incorporation of crop residues alone showed no positive impacts on either biomass or diversity, whereas fertilization by FYM instead of mineral fertilizer did. Microbial community composition showed depth-related shifts: Proteobacteria and Actinobacteria dominated the upper layer, whereas Gemmatimonadetes showed the highest relative abundance in the mid-layers and Chloroflexi deeper in the soil profile. The main factor determining soil bacterial community composition in the entire dataset was not the treatments but the layers. Interesting-ly, the surface layers that we expected to be most impacted by the treatments were much more similar to each other, regardless of treatment or block, than samples from the deeper layers were to each other. This means that agricultural practices strongly influence the soil bacterial composition and reduce its wide natural heterogeneity. This calls for continuous efforts to study the deeper soil layers in the numerous long-term field experiments, where mostly the topsoils are currently studied in detail.

Effects of application of corn straw on soil microbial community structure during the maize growing season.

PubMed

Lu, Ping; Lin, Yin-Hua; Yang, Zhong-Qi; Xu, Yan-Peng; Tan, Fei; Jia, Xu-Dong; Wang, Miao; Xu, De-Rong; Wang, Xi-Zhuo

2015-01-01

This study investigated the influence of corn straw application on soil microbial communities and the relationship between such communities and soil properties in black soil. The crop used in this study was maize (Zea mays L.). The five treatments consisted of applying a gradient (50, 100, 150, and 200%) of shattered corn straw residue to the soil. Soil samples were taken from May through September during the 2012 maize growing season. The microbial community structure was determined using phospholipid fatty acid (PLFA) analysis. Our results revealed that the application of corn straw influenced the soil properties and increased the soil organic carbon and total nitrogen. Applying corn straw to fields also influenced the variation in soil microbial biomass and community composition, which is consistent with the variations found in soil total nitrogen (TN) and soil respiration (SR). However, the soil carbon-to-nitrogen ratio had no effect on soil microbial communities. The abundance of PLFAs, TN, and SR was higher in C1.5 than those in other treatments, suggesting that the soil properties and soil microbial community composition were affected positively by the application of corn straw to black soil. A Principal Component Analysis indicated that soil microbial communities were different in the straw decomposition processes. Moreover, the soil microbial communities from C1.5 were significantly different from those of CK (p < 0.05). We also found a high ratio of fungal-to-bacterial PLFAs in black soil and significant variations in the ratio of monounsaturated-to-branched fatty acids with different straw treatments that correlated with SR (p < 0.05). These results indicated that the application of corn straw positively influences soil properties and soil microbial communities and that these properties affect these communities. The individual PLFA signatures were sensitive indicators that reflected the changes in the soil environment condition. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The secret life of microbes: soil bacteria and fungi undaunted by the harvesting of fire-killed trees

Treesearch

Paul Meznarich; Jane Smith; Tara Jennings

2013-01-01

Soil health is fundamental to ecosystem health. Disturbances such as fire and timber harvesting can affect the abundance, activity, and composition of soil microbial communities and thus affect soil productivity. In response to forest managers, scientists with the Pacific Northwest Research Station compared health and productivity indicators between soils disturbed by...

Method comparison for forest soil carbon and nitrogen estimates in the Delaware River basin

Treesearch

B. Xu; Yude Pan; A.H. Johnson; A.F. Plante

2016-01-01

The accuracy of forest soil C and N estimates is hampered by forest soils that are rocky, inaccessible, and spatially heterogeneous. A composite coring technique is the standard method used in Forest Inventory and Analysis, but its accuracy has been questioned. Quantitative soil pits provide direct measurement of rock content and soil mass from a larger, more...

Similarities in chemical composition of soil organic matter across a millennia-old paddy soil chronosequence as revealed by advanced solid-state NMR spectroscopy

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) accumulation in paddy soils has aroused considerable attention due to its vital significance in global food, energy, climate, and environmental issues. Considerable progress has been made toward the understanding of changes in the quantity of SOM in paddy soils over a mille...

Influence of soil thickness on stand characteristics in a Sierra Nevada mixed-conifer forest

Treesearch

Marc D. Meyer; Malcolm P. North; Andrew N. Gray; Harold S. J. Zald

2007-01-01

Soil thickness can be an important factor influencing vegetation, yet few spatially explicit studies have examined soil horizon thickness and vegetation composition in summer drought forests. We compared seismic and soil penetration measurements of combined A + C and Cr horizon thickness, soil moisture and temperature, and stand variables in a contiguous 4-ha mixed-...

Distribution of tetraether lipids in agricultural soils - differentiation between paddy and upland management

NASA Astrophysics Data System (ADS)

Mueller-Niggemann, C.; Utami, S. R.; Marxen, A.; Mangelsdorf, K.; Bauersachs, T.; Schwark, L.

2015-10-01

Insufficient knowledge of the composition and variation of isoprenoid and branched glycerol dialkyl glycerol tetraethers (GDGTs) in agricultural soils exists, despite of the potential effect of different management types (e.g. soil/water and redox conditions, cultivated plants) on GDGT distribution. Here, we determined the influence of different soil management types on the GDGT composition in paddy (flooded) and adjacent upland (non-flooded) soils, and if available also forest, bushland and marsh soils. To compare the local effects on GDGT distribution patterns, we collected comparable soil samples in various locations from tropical (Indonesia, Vietnam and Philippines) and subtropical (China and Italy) sites. We found that differences in the distribution of isoprenoid GDGTs (iGDGTs) as well as of branched GDGTs (brGDGTs) are predominantly controlled by management type and only secondarily by climatic exposition. In general upland soil had higher crenarchaeol contents than paddy soil, which on the contrary was more enriched in GDGT-0. The GDGT-0 / crenarchaeol ratio was 3-27 times higher in paddy soil and indicates the enhanced presence of methanogenic archaea, which were additionally linked to the number of rice cultivation cycles per year (higher number of cycles was coupled with an increase in the ratio). The TEX86 values were 1.3 times higher in upland, bushland and forest soils than in paddy soils. In all soils brGDGT predominated over iGDGTs, with the relative abundance of brGDGTs increasing from subtropical to tropical soils. Higher BIT values in paddy soils compared to upland soils together with higher BIT values in soil from subtropical climates indicate effects on the amounts of brGDGT through differences in management as well as climatic zones. In acidic soil CBT values correlated well with soil pH. In neutral to alkaline soils, however, no apparent correlation but an offset between paddy and upland managed soils was detected, which may suggest that soil moisture may exert an additional control on the CBT in these soils. Lower MBT' values and calculated temperatures (TMC) in paddy soils compared to upland soils may indicate a management (e.g. enhanced soil moisture through flooding practises) induced effect on mean annual soil temperature (MST).

Geochemical characterization of elements in Vitis vinifera cv. Negroamaro grape berries grown under different soil managements.

PubMed

Pepi, Salvatore; Coletta, Antonio; Crupi, Pasquale; Leis, Marilena; Russo, Sabrina; Sansone, Luigi; Tassinari, Renzo; Chicca, Milvia; Vaccaro, Carmela

2016-04-01

The present geochemical study concerns the impact of viticultural practices in the chemical composition of the grape cultivar "Negroamaro" in Apulia, a southern Italian region renowned for its quality wine. Three types of soil management (SM), two cover cropping with different mixtures, and a soil tillage were considered. For each SM, the vines were irrigated according to two irrigation levels. Chemical composition of soil and of berries of Vitis vinifera cultivar "Negroamaro" were analyzed by X-ray fluorescence, inductively coupled plasma-mass spectrometry and multivariate statistics (linear discrimination analysis). In detail, we investigated major and trace elements behavior in the soil according to irrigation levels, the related index of bioaccumulation (BA) and the relationship between trace element concentration and soil management in "Negroamaro" grapes. The results indicate that soil management affects the mobility of major and trace elements. A specific assimilation of these elements in grapes from vines grown under different soil management was confirmed by BA. Multivariate statistics allowed to associate the vines to the type of soil management. This geochemical characterization of elements could be useful to develop fingerprints of vines of the cultivar "Negroamaro" according to soil management and geographical origin.

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent

PubMed Central

Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

2016-01-01

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se. PMID:26172210

Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

PubMed

Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

2016-02-01

Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

On quantifying active soil carbon using mid-infrared spectroscopy

EPA Science Inventory

Soil organic matter (SOM) is derived from plant or animal residues deposited to soil and is in various stages of decomposition and mineralization. Total SOM is a common measure of soil quality, although due to its heterogeneous composition SOM can vary dramatically in terms of i...

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR FIELD COLLECTION OF YARD COMPOSITE SOIL SAMPLES (UA-F-5.1)

EPA Science Inventory

The purpose of this SOP is to establish a uniform procedure for the collection of yard composite soil samples in the field. This procedure was followed to ensure consistent and reliable collection of outdoor soil samples during the Arizona NHEXAS project and the Border study. Ke...

Composition of soil seed banks in southern California coastal sage scrub and adjacent exotic grassland

Treesearch

Robert D. Cox; Edith B. Allen

2008-01-01

Soil seed banks are important to many plant communities and are recognized as an important component of management plans. Understanding seed bank composition and density is especially important when communities have been invaded by exotic species and must be managed to promote desirable species. We examined germinable soil seed banks in southern California coastal sage...

Soil bacterial community responses to revegetation of moving sand dune in semi-arid grassland.

PubMed

Cao, Chengyou; Zhang, Ying; Cui, Zhenbo; Feng, Shuwei; Wang, Tingting; Ren, Qing

2017-08-01

Grasslands in semi-arid Northern China are widely desertified, thus inducing the formation of a large area of moving sand lands. Revegetation of the sandy land is commonly adopted to restore degraded grasslands. The structure of the soil microbial community might dramatically change during degradation and recovery because microorganisms are one of the major drivers of ecological process through their interactions with plants and soil. Assuming that soil properties are the key determinants of the structure of soil bacterial community within the same soil type, whether the vegetation type causes the significant difference in the structure of soil bacterial community during revegetation and restoration of the degraded grasslands remains poorly understood. Our study aimed to (1) investigate the response of soil bacterial communities to the changes during vegetation degradation and recovery and (2) evaluate whether the soil bacterial communities under plantations return to their native state. We detected the shifts in diversities and compositions of the soil bacterial communities and the relative abundance of dominant bacterial taxa by using the high-throughput Illumina MiSeq sequencing technique in an area covered by 32-year-old Caragana microphylla, Artemisia halodendron, Hedysarum fruticosum, Pinus sylvestris var. mongolica, Populus simonii, and Salix gordejevii sand-fixing plantations and in the native community (NC) dominated by elm, and moving sandy dune (MS). We found that the obtained operational taxonomic units by 16S rRNA gene sequencing and diversity index in MS were all significantly lower than those in NC, and the number and composition of dominant genera were significantly different between NC and MS. Interestingly, the compositions of bacterial communities and the dominant genera in different sand-fixation plantations (C. microphylla, A. halodendron, H. fruticosum, P. sylvestris var. mongolica, P. simonii, and S. gordejevii) were all similar to those of the native soil of NC, suggesting that the plantation type and soil properties exhibit a minimal effect on the compositions of soil microbial communities within a continuous landscape. These results revealed that the structure of the soil bacterial community of degraded sandy grassland (even degenerated into a mobile sand dunes) in semi-arid region can be reversibly restored by planting indigenous shrub or semi-shrub plantation on human time scales.

Fate of organic carbon from different waste materials in cropland soils

NASA Astrophysics Data System (ADS)

Paetsch, Lydia; Mueller, Carsten; Rumpel, Cornelia; Houot, Sabine; Kögel-Knabner, Ingrid

2015-04-01

Organic amendments are widely used to enhance the fertility of cropland soils. However, there is only scarce knowledge about the long term impact of added organic matter (OM) on the soil organic carbon (SOC) pool. Therefore, we analyzed a long-term field experiment in Feucherolles (France), which regularly received three different composts (home sorted bio-waste mixed with green waste (BIO), municipal solid waste (MSW) and a mixture of green waste and sewage sludge (GWS) and cattle manure since 1998. With these organic materials approximately 4 Mg total OC were added to the soil in two year intervals. The experiment was fully randomized with 4 replicates for each amendment. In September 2013 we took samples from the surface soil (0-5 cm of Ap horizon) of all 4 treatments and the unamended control. To study the chemical alteration and the fate of the added OC into different soil compartments, we fractionated the soils by physical means using a combined density and particle size protocol. Carbon and N content were determined in bulk soils, amendments as well as in size fractions (fPOM, oPOM <20µm and oPOM >20µm, sand, silt and a combined fine silt-clay fraction). Chemical composition was determined by solid-state 13C CPMAS NMR spectroscopy. We found significant higher C contents for the oPOM small and sand fraction of BIO treated soil and for the clay fraction of GWS treated soils (p<0.05). Nitrogen contents were significantly higher for BIO treated soils in bulk soil, fPOM, oPOM small and for GWS treated soils in bulk soil, fPOM and oPOM. The NMR measurements revealed that only the chemical composition of the fPOM differed according to the treatment; towards the more altered fractions as the oPOM small, the compositional differences leveled out and became almost homogeneous. Furthermore, the NMR measurements indicate a similar OC composition within the independent field replicates regarding the different amendments and fractions. As previously shown, N was found to be concentrated in the clay fractions, but interestingly we were able to show this also for the oPOM small. Proteins and peptides, as indicated by the broad resonance between 30 and 55 ppm, clearly point to the presence of microbial products and residues in this fraction.

Soils, time, and primate paleoenvironments

USGS Publications Warehouse

Bown, T.M.; Kraus, M.J.

1993-01-01

Soils are the skin of the earth. From both poles to the equator, wherever rocks or sediment are exposed at the surface, soils are forming through the physical and chemical action of climate and living organisms. The physical attributes (color, texture, thickness) and chemical makeup of soils vary considerably, depending on the composition of the parent material and other variables: temperature, rainfall and soil moisture, vegetation, soil fauna, and the length of time that soil-forming processes have been at work. United States soil scientists1 have classified modern soils into ten major groups and numerous subgroups, each reflecting the composition and architecture of the soils and, to some extent, the processes that led to their formation. The physical and chemical processes of soil formation have been active throughout geologic time; the organic processes have been active at least since the Ordovician.2 Consequently, nearly all sedimentary rocks that were deposited in nonmarine settings and exposed to the elements contain a record of ancient, buried soils or paleosols. A sequence of these rocks, such as most ancient fluvial (stream) deposits, provides a record of soil paleoenvironments through time. Paleosols are also repositories of the fossils of organisms (body fossils) and the traces of those organisms burrowing, food-seeking, and dwelling activities (ichnofossils). Indeed, most fossil primates are found in paleosols. Careful study of ancient soils gives new, valuable insights into the correct temporal reconstruction of the primate fossil record and the nature of primate paleoenvironments. ?? 1993 Wiley-Liss, Inc.

[Variations of soil microbial community composition and enzyme activities with different salinities on Yuyao coast, Zhejiang, China].

PubMed

Sun, Hui; Zhang, Jian Feng; Xu, Hua Sen; Chen, Guang Cai; Wang, Li Ping

2016-10-01

In October 2015, soil samples with different salinity were collected in a coast area in Yuyao, Zhejiang, and soil microbial community composition, soil catalase, urease activities, as well as soil physical and chemical properties were studied. The results showed that Nitrospira took absolute advantage in the bacterial community, and showed good correlations to total potassium. Cladosporium and Fusarium were predominant in the fungal community. Meanwhile, Cladosporium was related to soil urease and total nitrogen, and same correlation was found between Fusarium and soil urease. Catalase activity ranged from 3.52 to 4.56 mL·g -1 , 3.08 to 4.61 mL·g -1 and 5.81 to 6.91 mL·g -1 for soils with heavy, medium and weak salinity, respectively. Catalase activity increased with the soil layer deepening, which was directly related to soil total potassium, and indirectly related to pH, organic matter, total nitrogen and total phosphorus through total potassium. Soil urease activity ranged among 0.04 to 0.52 mg·g -1 , 0.08 to 1.07 mg·g -1 and 0.27 to 8.21 mg·g -1 for each saline soil, respectively. Urease activity decreased with soil layer deepening which was directly related to soil total nitrogen, and was indirectly related to pH, organic matter and total potassium through total nitrogen. The total phosphorus was the largest effect factor on the bacterial community CCA ordination, and the urease was on fungal community.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erel, Y.

The isotopic composition of Pb measured in soil samples was used to determine rates and mechanisms of anthropogenic Pb migration in the soil. Petrol-Pb found in soluble halogenated aerosols migrates into the soil and is retained in the soil by the stationary soil particles. Lead infiltration velocity is approximately 5 {times} 10{sup {minus}1} cm/year, and its retardation factor is estimated to be on the order of 1 {times} 10{sup 3}. The infiltration of Pb into the soil is best described by the advection-dispersion equation under the assumption that the time scale of the longitudinal dispersion is much longer than themore » time scale of advection. Therefore, the contribution of dispersion to the solution of the advection-dispersion equation is negligible. As a result, the soil profile of petrol-Pb resembles the time-dependent input function of petrol-Pb. The estimated petrol-Pb penetration velocity and the isotopic composition profile of Pb in off-road soil are used for the computation of the fraction of anthropogenic Pb in this soil. It is calculated that the fraction of anthropogenic Pb in the acid-leached soil samples and in the soil residue of this soil profile drops from 60 and 22% near the surface to 6 and 0% at a depth of 33 cm, respectively. The downward migration velocity of Pb in soils of the studied area, which are typically 50 to 100 cm deep, implies a residence time of Pb in the soil of 100 to 200 years.« less

Ecological-floristic analysis of soil algae and cyanobacteria on the Tra-Tau and Yurak-Tau Mounts, Bashkiria

NASA Astrophysics Data System (ADS)

Bakieva, G. R.; Khaibullina, L. S.; Gaisina, L. A.; Kabirov, R. R.

2012-09-01

The species composition of the soil algae and cyanobacteria in the Tra-Tau and Yurak-Tau mountains is represented by 136 species belonging to five phyla: Cyanobacteria (56 species), Chlorophyta (52 species), Xanthophyta (13 species), Bacillariophyta (12 species), and Eustigmatophyta (3 species). Hantzschia amphioxys var. amphioxys, Hantzschia amphioxys var. constricta, Klebsormidium flaccidum, Leptolyngbya foveolarum, Luticola mutica, Navicula minima var. minima, Nostoc punctiforme, Phormidium jadinianum, Phormidium autumnale, and Pinnularia borealis were identified more often than other species. The composition of the algal flora depended on the soil properties; the higher plants also had a significant influence on the species composition of the soil algae.

Basaltic Soil of Gale Crater: Crystalline Component Compared to Martian Basalts and Meteorites

NASA Technical Reports Server (NTRS)

Treiman, A. H.; Bish, D. L.; Ming, D. W.; Morris, R. V.; Schmidt, M.; Downs, R. T.; Stolper, E. M.; Blake, D. F.; Vaniman, D. T.; Achilles, C. N.;

Soil Bacterial Community Shift Correlated with Change from Forest to Pasture Vegetation in a Tropical Soil

PubMed Central

Nüsslein, Klaus; Tiedje, James M.

1999-01-01

The change in vegetative cover of a Hawaiian soil from forest to pasture led to significant changes in the composition of the soil bacterial community. DNAs were extracted from both soil habitats and compared for the abundance of guanine-plus-cytosine (G+C) content, by analysis of abundance of phylotypes of small-subunit ribosomal DNA (SSU rDNA) amplified from fractions with 63 and 35% G+C contents, and by phylogenetic analysis of the dominant rDNA clones in the 63% G+C content fraction. All three methods showed differences between the forest and pasture habitats, providing evidence that vegetation had a strong influence on microbial community composition at three levels of taxon resolution. The forest soil DNA had a peak in G+C content of 61%, while the DNA of the pasture soil had a peak in G+C content of 67%. None of the dominant phylotypes found in the forest soil were detected in the pasture soil. For the 63% G+C fraction SSU rDNA sequence analysis of the three most dominant members revealed that their phyla changed from Fibrobacter and Syntrophomonas assemblages in the forest soil to Burkholderia and Rhizobium–Agrobacterium assemblages in the pasture soil. PMID:10427058

Legacy effects of drought on plant-soil feedbacks and plant-plant interactions.

PubMed

Kaisermann, Aurore; de Vries, Franciska T; Griffiths, Robert I; Bardgett, Richard D

2017-09-01

Interactions between aboveground and belowground biota have the potential to modify ecosystem responses to climate change, yet little is known about how drought influences plant-soil feedbacks with respect to microbial mediation of plant community dynamics. We tested the hypothesis that drought modifies plant-soil feedback with consequences for plant competition. We measured net pairwise plant-soil feedbacks for two grassland plant species grown in monoculture and competition in soils that had or had not been subjected to a previous drought; these were then exposed to a subsequent drought. To investigate the mechanisms involved, we assessed treatment responses of soil microbial communities and nutrient availability. We found that previous drought had a legacy effect on bacterial and fungal community composition that decreased plant growth in conspecific soils and had knock-on effects for plant competitive interactions. Moreover, plant and microbial responses to subsequent drought were dependent on a legacy effect of the previous drought on plant-soil interactions. We show that drought has lasting effects on belowground communities with consequences for plant-soil feedbacks and plant-plant interactions. This suggests that drought, which is predicted to increase in frequency with climate change, may change soil functioning and plant community composition via the modification of plant-soil feedbacks. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Effects of reclamation years on composition and diversity of soil bacterial communities in Northwest China.

PubMed

Cheng, Zhibo; Zhang, Fenghua; Gale, William Jeffrey; Wang, Weichao; Sang, Wen; Yang, Haichang

2018-01-01

The objective of this study was to evaluate bacterial community structure and diversity in soil aggregate fractions when salinized farmland was reclaimed after >27 years of abandonment and then farmed again for 1, 5, 10, and 15 years. Illumina MiSeq high-throughput sequencing was performed to characterize the soil bacterial communities in 5 aggregate size classes in each treatment. The results indicated that reclamation significantly increased macro-aggregation (>0.25 mm), as well as soil organic C, available N, and available P. The 10-year field had the largest proportion (93.9%) of soil in the macro-aggregate size classes (i.e., >0.25 mm) and the highest soil electrical conductivity. The 5 most dominant phyla in the soil samples were Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria, and Bacteroidetes. The phylogenetic diversity, Chao1, and Shannon indices increased after the abandoned land was reclaimed for farming, reaching maximums in the 15-year field. Among aggregate size classes, the 1-0.25 mm aggregates generally had the highest phylogenetic diversity, Chao1, and Shannon indices. Soil organic C and soil electrical conductivity were the main environmental factors affecting the soil bacterial communities. The composition and structure of the bacterial communities also varied significantly depending on soil aggregate size and time since reclamation.

Membrane inlet laser spectroscopy to measure H and O stable isotope compositions of soil and sediment pore water with high sample throughput

DOE PAGES

Oerter, Erik J.; Perelet, Alexei; Pardyjak, Eric; ...

2016-10-20

Here, the fast and accurate measurement of H and O stable isotope compositions (δ 2H and δ 18O values) of soil and sediment pore water remains an impediment to scaling-up the application of these isotopes in soil and vadose hydrology. Here we describe a method and its calibration to measuring soil and sediment pore water δ 2H and δ 18O values using a water vapor-permeable probe coupled to an isotope ratio infrared spectroscopy analyzer.

Degradation of Biofumigant Isothiocyanates and Allyl Glucosinolate in Soil and Their Effects on the Microbial Community Composition

PubMed Central

Hanschen, Franziska S.; Yim, Bunlong; Winkelmann, Traud; Smalla, Kornelia; Schreiner, Monika

2015-01-01

Brassicales species rich in glucosinolates are used for biofumigation, a process based on releasing enzymatically toxic isothiocyanates into the soil. These hydrolysis products are volatile and often reactive compounds. Moreover, glucosinolates can be degraded also without the presence of the hydrolytic enzyme myrosinase which might contribute to bioactive effects. Thus, in the present study the stability of Brassicaceae plant-derived and pure glucosinolates hydrolysis products was studied using three different soils (model biofumigation). In addition, the degradation of pure 2-propenyl glucosinolate was investigated with special regard to the formation of volatile breakdown products. Finally, the influence of pure glucosinolate degradation on the bacterial community composition was evaluated using denaturing gradient gel electrophoresis of 16S rRNA gene amplified from total community DNA. The model biofumigation study revealed that the structure of the hydrolysis products had a significant impact on their stability in the soil but not the soil type. Following the degradation of pure 2-propenyl glucosinolate in the soils, the nitrile as well as the isothiocyanate can be the main degradation products, depending on the soil type. Furthermore, the degradation was shown to be both chemically as well as biologically mediated as autoclaving reduced degradation. The nitrile was the major product of the chemical degradation and its formation increased with iron content of the soil. Additionally, the bacterial community composition was significantly affected by adding pure 2-propenyl glucosinolate, the effect being more pronounced than in treatments with myrosinase added to the glucosinolate. Therefore, glucosinolates can have a greater effect on soil bacterial community composition than their hydrolysis products. PMID:26186695

Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil.

PubMed

Val-Moraes, Silvana Pompeia; de Macedo, Helena Suleiman; Kishi, Luciano Takeshi; Pereira, Rodrigo Matheus; Navarrete, Acacio Aparecido; Mendes, Lucas William; de Figueiredo, Eduardo Barretto; La Scala, Newton; Tsai, Siu Mui; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

2016-12-01

Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.

Microbial Ecology of Soil Aggregation in Agroecosystems

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences in the abundance of chemical classes in clay loams compared to sandy loams. Together our data demonstrate that the potential for aggregation and C storage is strongly influenced by soil mineralogy with important implications for plant-microbe interactions that mediate C biogeochemistry.

Changes in bacterial diversity associated with bioremediation of used lubricating oil in tropical soils.

PubMed

Meeboon, Naruemon; Leewis, Mary-Cathrine; Kaewsuwan, Sireewan; Maneerat, Suppasil; Leigh, Mary Beth

2017-08-01

Used lubricating oil (ULO) is a widespread contaminant, particularly throughout tropical regions, and may be a candidate for bioremediation. However, little is known about the biodegradation potential or basic microbial ecology of ULO-contaminated soils. This study aims to determine the effects of used ULO on bacterial community structure and diversity. Using a combination of culture-based (agar plate counts) and molecular techniques (16S rRNA gene sequencing and DGGE), we investigated changes in soil bacterial communities from three different ULO-contaminated soils collected from motorcycle mechanical workshops (soil A, B, and C). We further explored the relationship between bacterial community structure, physiochemical soil parameters, and ULO composition in three ULO-contaminated soils. Results indicated that the three investigated soils had different community structures, which may be a result of the different ULO characteristics and physiochemical soil parameters of each site. Soil C had the highest ULO concentration and also the greatest diversity and richness of bacteria, which may be a result of higher nutrient retention, organic matter and cation exchange capacity, as well as freshness of oil compared to the other soils. In soils A and B, Proteobacteria (esp. Gammaproteobacteria) dominated the bacterial community, and in soil C, Actinobacteria and Firmicutes dominated. The genus Enterobacter, a member of the class Gammaproteobacteria, is known to include ULO-degraders, and this genus was the only one found in all three soils, suggesting that it could play a key role in the in situ degradation of ULO-contaminated tropical Thai soils. This study provides insights into our understanding of soil microbial richness, diversity, composition, and structure in tropical ULO-contaminated soils, and may be useful for the development of strategies to improve bioremediation.

Rock and Soil Types at Pathfinder Landing Site

NASA Technical Reports Server (NTRS)

1997-01-01

Type areas of rocks and soils. (A) Dark rock type and bright soil type: Shown is the dark rock Barnacle Bill. Reflectance spectra typical of fresh basalt and APXS spectra indicating more silica-rich basaltic andesite compositions characterize this type. These rocks are typically the small boulders and intermediate-sized cobbles at the Pathfinder site. The bright soil type is very common and in this case comprises Barnacle Bill's wind tail and much of the surround soil area. This soil has a high reflectance and a strongly reddened spectrum indicative of oxidized ferric minerals. (B) Bright rock type: Shown is the bright rock Wedge. Reflectance spectra typical of weathered basalt and APXS spectra indicating basaltic compositions characterize this type. These rocks are typically larger than 1 meter in diameter and many display morphologies indicating flood deposition. (C) Pink rock type: Shown is the pink rock Scooby Doo. APXS and reflectance spectra indicate a composition and optical characteristics similar to the drift soil. However, the morphology of the pink rock type indicates a cemented or rocklike structure. This material may be a chemically cemented hardpan that underlies much of the Pathfinder site. (D) Dark soil type: The dark soil type is typically found on the windward sides of rocks or in rock-free areas like Photometry Flats (shown here) where the bright soil has been striped away by aeolian action or in open areas. Other locations include the Mermaid Dune. (E) Disturbed soil type: The darkening of disturbed soil relative to its parent material, bright soil, as a result of changes in soil texture and compaction caused by movement of the rover and retraction of the lander airbag. (F) Lamb-like soil type: This soil type shows reflectance and spectral characteristics intermediate between the bright and dark soils. Its distinguishing feature is a weak spectral absorption near 900 nanometers not seen in either the bright or dark soils.

NOTE: original caption as published in Science Magazine

Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is a division of the California Institute of Technology (Caltech).

Population and community structure shifts of ammonia oxidizers after four-year successive biochar application to agricultural acidic and alkaline soils.

PubMed

He, Lili; Bi, Yucui; Zhao, Jin; Pittelkow, Cameron M; Zhao, Xu; Wang, Shenqiang; Xing, Guangxi

2018-04-01

Long-term studies that advance our mechanistic understanding of biochar (BC)‑nitrogen (N) interactions in agricultural soils are lacking. In this study, soil potential nitrification rates (PNR), the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities following 4-year of BC application were investigated using the shaken-slurry procedure and molecular sequencing techniques for an acidic Oxisol (QU) and an alkaline Cambisol (YU). Soils were obtained from an outdoor soil column experiment with straw-BC application rates of 0 (BC0), 2.25 (BC2.25) and 11.3 (BC11.3) Mgha -1 per cropping season for eight consecutive wheat/millet seasons. Quantitative polymerase chain reaction (qPCR) and 454 high-throughput pyrosequencing techniques were performed to quantify and sequence amoA gene copies and composition of AOA and AOB. Results showed that QU had lower PNR and a higher ratio of amoA gene copies of AOA to AOB than YU, PNR of QU with BC application was significantly associated with the amoA gene of AOB. Similar to previous short-term findings, BC application enhanced QU soil nitrification, which may be explained by the significant increase in AOB abundance and a shift in AOB community structure from Nitrosospira cluster 2 toward cluster 3, along with the disappearance of some obligate acidophile AOA groups, leading to the appearance of ammonia-oxidizers from neutral-alkaline soils in BC-amended acid soils. Canonical correspondence analysis (CCA) showed that soil pH was the most important factor driving shifts in ammonia-oxidizers composition. Although BC application did not have significant effects on PNR in YU, BC11.3 decreased AOA and AOB gene copies and influenced the relative abundance of community structure. Our findings represent the first investigation of long-term BC effects on AOA and AOB communities in agricultural soils using 454 high-throughput pyrosequencing, showing that BC application can alter soil characteristics and influence ammonia oxidizer community composition, abundance, especially in acid soils. Copyright © 2017 Elsevier B.V. All rights reserved.

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient.

PubMed

Eldridge, David J; Delgado-Baquerizo, Manuel; Woodhouse, Jason N; Neilan, Brett A

2016-11-01

The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative effects of grazing-induced disturbance on soil function. Further, our results suggest that most of this effect will be derived from echidnas, with little positive effects due to rabbits. Activities that enhance the habitat for echidnas or reduce rabbit populations are likely to have a positive effect on soil function in these systems. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

A Comparative Study of Sediment Quality in Four Reservoirs.

DTIC Science & Technology

1984-02-01

same time as the reservoir samples. Precision for interstitial water samples was initially measured using soil - solution samples. As interstitial...Variable Composite Sample hean, ma&L Replicates Deviation, ma L Deviation. Ammonium nitrogen Soil solution 0.07 12 0.01 14 DeGray composite 2.00 10 0.01...0.5 Nitrate nitrite Filtered wastewater 0.04 10 0.01 25 nitrogen Soluble reactive Soil solution 0.04 12 0.01 25 phosphorus DeGray composite 0.16 10 0.01

Predicting the Mineral Composition of Dust Aerosols. Part 1; Representing Key Processes

NASA Technical Reports Server (NTRS)

Perlwitz, J. P.; Garcia-Pando, C. Perez; Miller, R. L.

2015-01-01

Soil dust aerosols created by wind erosion are typically assigned globally uniform physical and chemical properties within Earth system models, despite known regional variations in the mineral content of the parent soil. Mineral composition of the aerosol particles is important to their interaction with climate, including shortwave absorption and radiative forcing, nucleation of cloud droplets and ice crystals, heterogeneous formation of sulfates and nitrates, and atmospheric processing of iron into bioavailable forms that increase the productivity of marine phytoplankton. Here, aerosol mineral composition is derived by extending a method that provides the composition of a wet-sieved soil. The extension accounts for measurements showing significant differences between the mineral fractions of the wetsieved soil and the emitted aerosol concentration. For example, some phyllosilicate aerosols are more prevalent at silt sizes, even though they are nearly absent at these diameters in a soil whose aggregates are dispersed by wet sieving. We calculate the emitted mass of each mineral with respect to size by accounting for the disintegration of soil aggregates during wet sieving. These aggregates are emitted during mobilization and fragmentation of the original undispersed soil that is subject to wind erosion. The emitted aggregates are carried far downwind from their parent soil. The soil mineral fractions used to calculate the aggregates also include larger particles that are suspended only in the vicinity of the source. We calculate the emitted size distribution of these particles using a normalized distribution derived from aerosol measurements. In addition, a method is proposed for mixing minerals with small impurities composed of iron oxides. These mixtures are important for transporting iron far from the dust source, because pure iron oxides are more dense and vulnerable to gravitational removal than most minerals comprising dust aerosols. A limited comparison to measurements from North Africa shows that the model extensions result in better agreement, consistent with a more extensive comparison to global observations as well as measurements of elemental composition downwind of the Sahara, as described in companion articles.

Predicting the mineral composition of dust aerosols - Part 1: Representing key processes

NASA Astrophysics Data System (ADS)

Perlwitz, J. P.; Pérez García-Pando, C.; Miller, R. L.

2015-10-01

Soil dust aerosols created by wind erosion are typically assigned globally uniform physical and chemical properties within Earth system models, despite known regional variations in the mineral content of the parent soil. Mineral composition of the aerosol particles is important to their interaction with climate, including shortwave absorption and radiative forcing, nucleation of cloud droplets and ice crystals, heterogeneous formation of sulfates and nitrates, and atmospheric processing of iron into bioavailable forms that increase the productivity of marine phytoplankton. Here, aerosol mineral composition is derived by extending a method that provides the composition of a wet-sieved soil. The extension accounts for measurements showing significant differences between the mineral fractions of the wet-sieved soil and the emitted aerosol concentration. For example, some phyllosilicate aerosols are more prevalent at silt sizes, even though they are nearly absent at these diameters in a soil whose aggregates are dispersed by wet sieving. We calculate the emitted mass of each mineral with respect to size by accounting for the disintegration of soil aggregates during wet sieving. These aggregates are emitted during mobilization and fragmentation of the original undispersed soil that is subject to wind erosion. The emitted aggregates are carried far downwind from their parent soil. The soil mineral fractions used to calculate the aggregates also include larger particles that are suspended only in the vicinity of the source. We calculate the emitted size distribution of these particles using a normalized distribution derived from aerosol measurements. In addition, a method is proposed for mixing minerals with small impurities composed of iron oxides. These mixtures are important for transporting iron far from the dust source, because pure iron oxides are more dense and vulnerable to gravitational removal than most minerals comprising dust aerosols. A limited comparison to measurements from North Africa shows that the model extensions result in better agreement, consistent with a more extensive comparison to global observations as well as measurements of elemental composition downwind of the Sahara, as described in companion articles.

Limitations and potential of spectral subtractions in fourier-transform infrared (FTIR) spectroscopy of soil samples

USDA-ARS?s Scientific Manuscript database

Soil science research is increasingly applying Fourier transform infrared (FTIR) spectroscopy for analysis of soil organic matter (SOM). However, the compositional complexity of soils and the dominance of the mineral component can limit spectroscopic resolution of SOM and other minor components. The...

On quantifying active soil carbon using mid-infrared spectroscopy

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) is derived from plant or animal residues deposited on or in soil and is in various stages of decomposition and mineralization. Total SOM is a common measure of soil quality, although due to its heterogeneous composition SOM can vary dramatically in terms of its biochemical...

Glomalin and soil aggregation under six management systems in the Northern Great Plains, USA

USDA-ARS?s Scientific Manuscript database

The soil environment is linked to aboveground management including plant species composition, grazing intensity, lev-els of soil disturbance, residue management, and the length of time of a living plant is growing. Soil samples were col-lected under rangeland [native grass, rotational grazing (NGRG)...

RESPONSE OF SOIL MICROBIAL BIOMASS AND COMMUNITY COMPOSITION TO CHRONIC NITROGEN ADDITIONS AT HARVARD FOREST

EPA Science Inventory

Soil microbial communities may respond to anthropogenic increases in ecosystem nitrogen (N) availability, and their response may ultimately feedback on ecosystem carbon and N dynamics. We examined the long-term effects of chronic N additions on soil microbes by measuring soil mi...

Scale-dependent variation in nitrogen cycling and soil fungal communities along gradients of forest composition and age in regenerating tropical dry forests.

PubMed

Waring, Bonnie G; Adams, Rachel; Branco, Sara; Powers, Jennifer S

2016-01-01

Rates of ecosystem nitrogen (N) cycling may be mediated by the presence of ectomycorrhizal fungi, which compete directly with free-living microbes for N. In the regenerating tropical dry forests of Central America, the distribution of ectomycorrhizal trees is affected by succession and soil parent material, both of which may exert independent influence over soil N fluxes. In order to quantify these interacting controls, we used a scale-explicit sampling strategy to examine soil N cycling at scales ranging from the microsite to ecosystem level. We measured fungal community composition, total and inorganic N pools, gross proteolytic rate, net N mineralization and microbial extracellular enzyme activity at multiple locations within 18 permanent plots that span dramatic gradients of soil N concentration, stand age and forest composition. The ratio of inorganic to organic N cycling was correlated with variation in fungal community structure, consistent with a strong influence of ectomycorrhiza on ecosystem-scale N cycling. However, on average, > 61% of the variation in soil biogeochemistry occurred within plots, and the effects of forest composition were mediated by this local-scale heterogeneity in total soil N concentrations. These cross-scale interactions demonstrate the importance of a spatially explicit approach towards an understanding of controls on element cycling. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Soil and foliar nutrient and nitrogen isotope composition (δ(15)N) at 5 years after poultry litter and green waste biochar amendment in a macadamia orchard.

PubMed

Bai, Shahla Hosseini; Xu, Cheng-Yuan; Xu, Zhihong; Blumfield, Timothy J; Zhao, Haitao; Wallace, Helen; Reverchon, Frédérique; Van Zwieten, Lukas

2015-03-01

This study aimed to evaluate the improvement in soil fertility and plant nutrient use in a macadamia orchard following biochar application. The main objectives of this study were to assess the effects of poultry litter and green waste biochar applications on nitrogen (N) cycling using N isotope composition (δ(15)N) and nutrient availability in a soil-plant system at a macadamia orchard, 5 years following application. Biochar was applied at 10 t ha(-1) dry weight but concentrated within a 3-m diameter zone when trees were planted in 2007. Soil and leaf samples were collected in 2012, and both soil and foliar N isotope composition (δ(15)N) and nutrient concentrations were assessed. Both soil and foliar δ(15)N increased significantly in the poultry litter biochar plots compared to the green waste biochar and control plots. A significant relationship was observed between soil and plant δ(15)N. There was no influence of either biochars on foliar total N concentrations or soil NH4 (+)-N and NO3 (-)-N, which suggested that biochar application did not pose any restriction for plant N uptake. Plant bioavailable phosphorus (P) was significantly higher in the poultry litter biochar treatment compared to the green waste biochar treatment and control. We hypothesised that the bioavailability of N and P content of poultry litter biochar may play an important role in increasing soil and plant δ(15)N and P concentrations. Biochar application affected soil-plant N cycling and there is potential to use soil and plant δ(15)N to investigate N cycling in a soil-biochar-tree crop system. The poultry litter biochar significantly increased soil fertility compared to the green waste biochar at 5 years following biochar application which makes the poultry litter a better feedstock to produce biochar compared to green waste for the tree crops.

Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics.

PubMed

Ren, Chengjie; Zhang, Wei; Zhong, ZeKun; Han, Xinhui; Yang, Gaihe; Feng, Yongzhong; Ren, Guangxin

2018-01-01

Alt'itudinal gradients strongly affect plant biodiversity, but the effects on microbial patterns remain unclear, especially in the large scale. We therefore designed an altitudinal gradient experiment that covered three climate zones to monitor soil microbial community dynamics and to compare those with plant and soil characteristics. Illumina sequencing of the 16S rRNA gene and ITS gene was used to analyze soil microbial (bacterial and fungal) diversity and composition, and fumigation-extraction was used to determine microbial biomass; the plant community metrics (i.e., percent cover, Shannon-Wiener, grass biomass, and carbon/nitrogen in leaf and biomass) and soil properties (i.e., soil moisture, soil temperature, bulk density, organic carbon, total nitrogen, and available nitrogen) were determined. The results showed that carbon/nitrogen in microbial biomass was higher at medium altitude and was positively related to carbon and nitrogen in both soil and grass biomass along the altitudinal gradients. Soil bacterial alpha diversity was significantly higher at medium altitude but fungal alpha diversity did not affected by altitudinal gradients; the effect of altitudinal gradients on bacterial beta diversity was larger than that on fungal beta diversity, although both groups were significantly affected by altitudinal gradients. Moreover, Alpha-proteobacteria, Beta-proteobacteria, and Gemmatimonadetes were significantly more abundant in higher altitude than in lower altitude, both Acidobacteria and Actinobacteria significantly declined with increasing altitude; other bacterial taxa such as Chloroflexi, Nitrospirae, Gamma-proteobacteria, and Delta-proteobacteria were significantly higher at medium altitudes. For fungal taxa, Basidiomycota and Ascomycota were the dominant phyla and responded insignificantly to the altitudinal gradients. The responses of microbial alpha diversity were mostly associated with plant Shannon index, organic carbon, and total nitrogen, whereas microbial beta diversity and composition mainly depended on soil moisture and temperature. Overall, these results suggest that soil bacteria rather than fungi can reflect changes in plant and soil characteristics along altitudinal gradients. Copyright © 2017 Elsevier B.V. All rights reserved.

A Comparative Analyses of Granulometry, Mineral Composition and Major and Trace Element Concentrations in Soils Commonly Ingested by Humans

PubMed Central

Ngole-Jeme, Veronica M.; Ekosse, Georges-Ivo E.

2015-01-01

This study compared the granulometric properties, mineralogical composition and concentrations of major and trace element oxides of commonly ingested soils (geophagic soil) collected from different countries with a view of understanding how varied they may be in these properties and to understand the possible health implications of ingesting them. Soil samples were collected from three different countries (South Africa, Swaziland and Democratic Republic of Congo (DRC)) and their granulometric properties, concentrations of major and trace element oxides as well as mineralogical composition determined. Differences were observed in the granulometric properties of geophagic soil from the three different countries with most of them having <20% clay content. The soils also showed varied degrees of weathering with values of Chemical Index of Alteration (CIA) and Chemical Index of Weathering (CIW) being between 60% and 99.9% respectively. The mineral assemblages of the soils from South Africa and Swaziland were dominated by the primary minerals quartz and feldspar whereas soils from DRC had more of kaolinite, a secondary mineral than primary minerals. Soils from DRC were associated with silt, clay, Al2O3, and CIA unlike most samples from South Africa which were associated with SiO2, sand, K2O, CaO, and MgO. The soils from Swaziland were closely associated with silt, H2O and Fe2O3(t). These associations reflect the mineralogy of the samples. These soils are not likely to serve as nutrient supplements because of the low concentrations of the nutrient elements contained. The coarse texture of the samples may also result in dental destruction during mastication. Sieving of the soils before ingestion to remove coarse particles is recommended to reduce the potential health threat associated with the ingestion of coarse-textured soils. PMID:26264010

Combinational effects of sulfomethoxazole and copper on soil microbial community and function.

PubMed

Liu, Aiju; Cao, Huansheng; Yang, Yan; Ma, Xiaoxuan; Liu, Xiao

2016-03-01

Sulfonamides and Cu are largely used feed additives in poultry farm. Subsequently, they are spread onto agricultural soils together with contaminated manure used as fertilizer. Both sulfonamides and Cu affect the soil microbial community. However, an interactive effect of sulfonamides and Cu on soil microorganisms is not well understood. Therefore, a short-time microcosm experiment was conducted to investigate the interaction of veterinary antibiotic sulfomethoxazole (SMX) and Cu on soil microbial structure composition and functions. To this end, selected concentrations of SMX (0, 5, and 50 mg kg(-1)) and Cu (0, 300, and 500 mg kg(-1)) were combined, respectively. Clear dose-dependent effects of SMX on microbial biomass and basal respiration were determined, and these effects were amplified in the presence of additional Cu. For activities of soil enzymes including β-glucosidase, urease, and protease, clear reducing effects were determined in soil samples containing 5 or 50 mg kg(-1) of SMX, and the interaction of SMX and Cu was significant, particularly in soil samples containing 50 mg kg(-1) SMX or 500 mg kg(-1) Cu. SMX amendments, particularly in combination with Cu, significantly reduced amounts of the total, bacterial, and fungal phospholipid fatty acids (PLFAs) in soil. Moreover, the derived ratio of bacteria to fungi decreased significantly with incremental SMX and Cu, and principal component analysis of the PLFAs showed that soil microbial composition was significantly affected by SMX interacted with Cu at 500 mg kg(-1). All of these results indicated that the interaction of SMX and Cu was synergistic to amplify the negative effect of SMX on soil microbial biomass, structural composition, and even the enzymatic function.

Effects of organic matter fraction and compositional changes on distribution of cadmium and zinc in long-term polluted paddy soils.

PubMed

Zhou, Tong; Wu, Longhua; Luo, Yongming; Christie, Peter

2018-01-01

Soil particulate organic matter (POM) has rapid turnover and metal enrichment, but the interactions between organic matter (OM) and metals have not been well studied. The present study aimed to investigate changes in the OM concentration and composition of the POM fraction and their corresponding effects on metal distribution and extractability in long-term polluted paddy soils. Soil 2000-53 μm POM size fractions had higher contents of C-H and C=O bonds, C-H/C=O ratios and concentrations of fulvic acid (FA), humic acid (HA), cadmium (Cd) and zinc (Zn) than the bulk soils. Cadmium and Zn stocks in soil POM fractions were 24.5-27.9% and 7.12-16.7%, respectively, and were more readily EDTA-extractable. Compared with the control soil, the 2000-250 μm POM size fractions had higher organic carbon concentrations and C/N ratios in the polluted soils. However, there were no significant differences in the contents in C-H and C=O bonds or C-H/C=O ratios of POM fractions among the control, slightly and highly polluted soils. In accordance with the lower contents of C=O bonds and FA and HA concentrations, the Cd and Zn concentrations in 250-53 μm POM size fractions were lower than those in 2000-250 μm POM size fractions. Enrichment of Cd in POM fractions increased with increasing soil pollution level. These results support the view that changes in the OM concentration and the size and composition of POM fractions play a key role in determining the distribution of Cd and Zn in paddy soils. Copyright © 2017. Published by Elsevier Ltd.

Deep Soil Carbon in the Critical Zone: Amount and Nature of Carbon in Weathered Bedrock, and its Implication for Soil Carbon Inventory

NASA Astrophysics Data System (ADS)

Moreland, K. C.; Tian, Z.; Berhe, A. A.; O'Geen, A. T.

2017-12-01

Globally, soils store more carbon (C) than the vegetation and the atmosphere combined. Up to 60-80% of the C stored in soils is found in below 30cm soil depth, but there is little data on C storage in weathered bedrock or saprolite. Deep soil organic matter (SOM) can be a mixture of new and old SOM; that is rendered relatively stable due to burial, aggregation, its disconnection from decomposers, and chemical association that organic matter forms with soil minerals. The limited data available on deep SOM dynamics suggests that stock, distribution, and composition of deep SOM are strongly correlated to climate. The overall objective of this research is to investigate how climate regulates OM storage, composition, stability, and stabilization mechanisms. Expecting that the amount of OM stored in deep soil and the stability are a function of soil thickness and availability of weathering products (i.e. reactive minerals), the stock and stability of deep SOM is expected to follow a similar relationship with climate, as does the intensity of weathering. This research is conducted in the NSF funded Southern Sierra Critical Zone Observatories that is located along a climosequence, the western slopes of the Sierra Naevada Mountains of California. Here we will present results derived from characterization of soils and weathered bedrock using elemental and stable isotope elemental analysis, and Fourier Transformed Infrared Spectroscopy to determine OM concentration and functional group level composition of bulk SOM. Our findings show that adding in subsoil and weathered bedrock C stocks increases estimates of soil C stock by 1/3rd to 2/3rd.

Chemical features of soils in a natural forest of West Hungary

NASA Astrophysics Data System (ADS)

Hofmann, Eszter; Bidló, András

2015-04-01

The present research focuses on the chemical results of soils formed on miocene carbonate rocks in a natural forest of West Hungary. Soil profiles derived from the Szárhalom Forest, located near the Lake Fertő, next to the city of Sopron. Six soil profiles were opened and analysed in this area. In the field the following physical parameters were evaluated from the soil profiles: transition, structure, compactness, roots, skeletal percent, colour, physical assortment, concretion and soil defect. Laboratory analysis involved the measurement of acidity, particle distribution, carbonated lime content, humus content, ammonium lactate-acetic acid soluble phosphorus- and potassium content, potassium chloride soluble calcium- and magnesium content, ethylene-diamine-tetraacetic-acid (EDTA) and diethylene-triamine-pentaacetic-acid (DTPA) soluble copper-, iron-, manganese- and zinc contents. These soils formed under a hornbeam-oak forest climate mainly and under a beech forest climate diffusely. The location and climate of the sites forms a basis of the comparison of the soils with similar base rock. The formation of the acidic and humus-rich upper layer of the soil profiles is influenced by the mineral composition and the weathering of the rocks. X-ray diffraction (Philips P W3710/PW1050 type X-ray diffractometer), thermoanalytical measurements (Mettler Toledo TGA/DSC 1 type thermogravimeter) and ICP-OES (Thermo Scientific iCAP 7000 Series) were also carried out to determine the mineral composition of the soils and the content of heavy metals. The soil samples were collected with both traditional and undisturbed (using the Kubiena box) sampling methods to enable further micromorphological investigations as well. The research is supported by the "Agroclimate-2" (VKSZ_12-1-2013-0034) joint EU-national research project. Key words: Natural forest, Miocene limestone, Mineral composition, Thermal analysis, Micromorphology

Below-ground attributes on reclaimed surface minelands over a 40-year chronosequence

NASA Astrophysics Data System (ADS)

Limb, Ryan; Bohrer, Stefanie; Volk, Jay

2017-04-01

Reclamation following mining activities often aims to restore stable soils that support productive and diverse native plant communities. The soil re-spread process increases soil compaction, which may alter soil water, plant composition, rooting depths and soil organic matter. This may have a direct impact on vegetation establishment and species recruitment. Seasonal wet/dry and freeze/thaw patterns are thought to alleviate soil compaction over time. However, this has not been formally evaluated on reclaimed landscapes at large scales. Our objectives were to (1) determine soil compaction alleviation, (2) rooting depth and (3) spatial patterns of soil water content over a time-since-reclamation gradient. Soil resistance to penetration varied by depth, with shallow compaction remaining unchanged, but deeper compaction increased over time rather than being alleviated. Root biomass and depth did not increase with time and was consistently less than reference locations. Plant communities initially had a strong native component, but quickly became dominated by invasive species following reclamation and soil water content became increasingly homogeneous over the 40-year chronosequence. Seasonal weather patterns and soil organic matter additions can reduce soil compaction if water infiltration is not limited. Shallow and strongly fibrous-rooted grasses present in reclaimed sites added organic matter to shallow soil layers, but did not penetrate the compacted layers and allow water infiltration. Strong linkages between land management strategies, soil properties and vegetation composition can advance reclamation efforts and promote heterogeneous landscapes. However, current post-reclamation management strategies are not facilitating natural seasonal weather patterns to reducing soil compaction.

[Research on characteristics of soil clay mineral evolution in paddy field and dry land by XRD spectrum].

PubMed

Zhang, Zhi-dan; Li, Qiao; Luo, Xiang-li; Jiang, Hai-chao; Zheng, Qing-fu; Zhao, Lan-po; Wang, Ji-hong

2014-08-01

The present paper took the typical saline-alkali soil in Jilin province as study object, and determinated the soil clay mineral composition characteristics of soil in paddy field and dry land. Then XRD spectrum was used to analyze the evolutionary mechanism of clay mineral in the two kinds of soil. The results showed that the physical and chemical properties of soil in paddy field were better than those in dry land, and paddy field would promote the weathering of mineral particles in saline-alkali soil and enhance the silt content. Paddy field soil showed a strong potassium-removal process, with a higher degree of clay mineral hydration and lower degree of illite crystallinity. Analysis of XRD spectrum showed that the clay mineral composition was similar in two kinds of soil, while the intensity and position of diffraction peak showed difference. The evolution process of clay mineral in dry land was S/I mixture-->vermiculite, while in paddy field it was S/I mixture-->vermiculite-->kaolinite. One kind of hydroxylated 'chlorite' mineral would appear in saline-alkali soil in long-term cultivated paddy field. Taking into account that the physical and chemical properties of soil in paddy field were better then those in dry land, we could know that paddy field could help much improve soil structure, cultivate high-fertility soil and improve saline-alkali soil. This paper used XRD spectrum to determine the characteristics of clay minerals comprehensively, and analyzed two'kinds of land use comparatively, and was a new perspective of soil minerals study.

Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest.

PubMed

Du, Can; Geng, Zengchao; Wang, Qiang; Zhang, Tongtong; He, Wenxiang; Hou, Lin; Wang, Yueling

2017-09-01

Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0-10, 10-20, 20-40, and 40-60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40-60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40-60 cm (62.88%). In particular, the 40-60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

DOE PAGES

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; ...

2016-04-29

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterialmore » community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. As a result, we identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.« less

Organic amendments to avocado crops induce suppressiveness and influence the composition and activity of soil microbial communities.

PubMed

Bonilla, Nuria; Vida, Carmen; Martínez-Alonso, Maira; Landa, Blanca B; Gaju, Nuria; Cazorla, Francisco M; de Vicente, Antonio

2015-05-15

One of the main avocado diseases in southern Spain is white root rot caused by the fungus Rosellinia necatrix Prill. The use of organic soil amendments to enhance the suppressiveness of natural soil is an inviting approach that has successfully controlled other soilborne pathogens. This study tested the suppressive capacity of different organic amendments against R. necatrix and analyzed their effects on soil microbial communities and enzymatic activities. Two-year-old avocado trees were grown in soil treated with composted organic amendments and then used for inoculation assays. All of the organic treatments reduced disease development in comparison to unamended control soil, especially yard waste (YW) and almond shells (AS). The YW had a strong effect on microbial communities in bulk soil and produced larger population levels and diversity, higher hydrolytic activity and strong changes in the bacterial community composition of bulk soil, suggesting a mechanism of general suppression. Amendment with AS induced more subtle changes in bacterial community composition and specific enzymatic activities, with the strongest effects observed in the rhizosphere. Even if the effect was not strong, the changes caused by AS in bulk soil microbiota were related to the direct inhibition of R. necatrix by this amendment, most likely being connected to specific populations able to recolonize conducive soil after pasteurization. All of the organic amendments assayed in this study were able to suppress white root rot, although their suppressiveness appears to be mediated differentially. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

PubMed Central

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio; Koechli, Chantal; Campbell, Ashley; Buckley, Daniel H; Lehmann, Johannes

2016-01-01

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO2 fluxes (up to 6x), and caused rapid and persistent changes in bacterial community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. We identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil. PMID:27128990

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitman, Thea; Pepe-Ranney, Charles; Enders, Akio

Pyrogenic organic matter (PyOM) additions to soils can have large impacts on soil organic carbon (SOC) cycling. As the soil microbial community drives SOC fluxes, understanding how PyOM additions affect soil microbes is essential to understanding how PyOM affects SOC. We studied SOC dynamics and surveyed soil bacterial communities after OM additions in a field experiment. We produced and mixed in either 350 °C corn stover PyOM or an equivalent initial amount of dried corn stover to a Typic Fragiudept soil. Stover increased SOC-derived and total CO 2 fluxes (up to 6x), and caused rapid and persistent changes in bacterialmore » community composition over 82 days. In contrast, PyOM only temporarily increased total soil CO 2 fluxes (up to 2x) and caused fewer changes in bacterial community composition. Of the operational taxonomic units (OTUs) that increased in response to PyOM additions, 70% also responded to stover additions. These OTUs likely thrive on easily mineralizable carbon (C) that is found both in stover and, to a lesser extent, in PyOM. In contrast, we also identified unique PyOM responders, which may respond to substrates such as polyaromatic C. In particular, members of Gemmatimonadetes tended to increase in relative abundance in response to PyOM but not to fresh organic matter. As a result, we identify taxa to target for future investigations of the mechanistic underpinnings of ecological phenomena associated with PyOM additions to soil.« less

Soil Physical, Chemical, and Thermal Characterization, Council Road Site, Seward Peninsula, Alaska, 2016

DOE Data Explorer

Alexander Kholodov; David Graham; Ji-Won Moon

2018-01-22

This dataset provides the results of physical, chemical, and thermal characterization of soils at the Council Road Site at MM71, Seward Peninsula, Alaska. Soil pits were dug on 11 September 2016 at three sites. This dataset includes field observations and descriptions of soil layers or horizons, field measurements of soil volumetric water content, soil temperature, thermal conductivity, and heat capacity. Laboratory measurements of soil properties include gravimetric water content, bulk density, volumetric water content, total carbon and nitrogen, and elemental composition from X-ray fluorescence for some elements.

Separate effects of flooding and anaerobiosis on soil greenhouse gas emissions and redox sensitive biogeochemistry

Treesearch

Gavin McNicol; Whendee L. Silver

2014-01-01

Soils are large sources of atmospheric greenhouse gases, and both the magnitude and composition of soil gas emissions are strongly controlled by redox conditions. Though the effect of redox dynamics on greenhouse gas emissions has been well studied in flooded soils, less research has focused on redox dynamics without total soil inundation. For the latter, all that is...

Structural composition of organic matter in particle-size fractions of soils along a climo-biosequence in the main range of Peninsular Malaysia

NASA Astrophysics Data System (ADS)

Jafarzadeh-Haghighi, Amir Hossein; Shamshuddin, Jusop; Hamdan, Jol; Zainuddin, Norhazlin

2016-09-01

Information on structural composition of organic matter (OM) in particle-size fractions of soils along a climo-biosequence is sparse. The objective of this study was to examine structural composition and morphological characteristics of OM in particle-size fractions of soils along a climo-biosequence in order to better understand the factors and processes affecting structural composition of soil organic matter. To explore changes in structural composition of OM in soils with different pedogenesis, the A-horizon was considered for further analyses including particle-size fractionation, solid-state 13C nuclear magnetic resonance (NMR) spectroscopy and scanning electron microscopy (SEM). Due to the increase in the thickness of organic layer with increasing elevation, the A-horizon was situated at greater depth in soils of higher elevation. The relationship between relative abundances of carbon (C) structures and particle-size fractions was examined using principal component analysis (PCA). It was found that alkyl C (20.1-73.4%) and O-alkyl C (16.8-67.7%) dominated particle-size fractions. The proportion of alkyl C increased with increasing elevation, while O-alkyl C showed an opposite trend. Results of PCA confirmed this finding and showed the relative enrichment of alkyl C in soils of higher elevation. Increase in the proportion of alkyl C in 250-2000 μm fraction is linked to selective preservation of aliphatic compounds derived from root litter. SEM results showed an increase in root contribution to the 250-2000 μm fraction with increasing elevation. For the <53 μm fraction, pedogenic process of podzolization is responsible for the relative enrichment of alkyl C. This study demonstrates that changes in structural composition of OM in particle-size fractions of soils along the studied climo-biosequence are attributed to site-specific differences in pedogenesis as a function of climate and vegetation.

Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition.

PubMed

Castaño, Carles; Parladé, Javier; Pera, Joan; Martínez de Aragón, Juan; Alday, Josu G; Bonet, José Antonio

2016-11-01

Drying soil samples before DNA extraction is commonly used for specific fungal DNA quantification and metabarcoding studies, but the impact of different drying procedures on both the specific fungal DNA quantity and the fungal community composition has not been analyzed. We tested three different drying procedures (freeze-drying, oven-drying, and room temperature) on 12 different soil samples to determine (a) the soil mycelium biomass of the ectomycorrhizal species Lactarius vinosus using qPCR with a specifically designed TaqMan® probe and (b) the fungal community composition and diversity using the PacBio® RS II sequencing platform. Mycelium biomass of L. vinosus was significantly greater in the freeze-dried soil samples than in samples dried at oven and room temperature. However, drying procedures had no effect on fungal community composition or on fungal diversity. In addition, there were no significant differences in the proportions of fungi according to their functional roles (moulds vs. mycorrhizal species) in response to drying procedures. Only six out of 1139 operational taxonomic units (OTUs) had increased their relative proportions after soil drying at room temperature, with five of these OTUs classified as mould or yeast species. However, the magnitude of these changes was small, with an overall increase in relative abundance of these OTUs of approximately 2 %. These results suggest that DNA degradation may occur especially after drying soil samples at room temperature, but affecting equally nearly all fungi and therefore causing no significant differences in diversity and community composition. Despite the minimal effects caused by the drying procedures at the fungal community composition, freeze-drying resulted in higher concentrations of L. vinosus DNA and prevented potential colonization from opportunistic species.

The phylogenetic composition and structure of soil microbial communities shifts in response to elevated carbon dioxide.

PubMed

He, Zhili; Piceno, Yvette; Deng, Ye; Xu, Meiying; Lu, Zhenmei; Desantis, Todd; Andersen, Gary; Hobbie, Sarah E; Reich, Peter B; Zhou, Jizhong

2012-02-01

One of the major factors associated with global change is the ever-increasing concentration of atmospheric CO(2). Although the stimulating effects of elevated CO(2) (eCO(2)) on plant growth and primary productivity have been established, its impacts on the diversity and function of soil microbial communities are poorly understood. In this study, phylogenetic microarrays (PhyloChip) were used to comprehensively survey the richness, composition and structure of soil microbial communities in a grassland experiment subjected to two CO(2) conditions (ambient, 368 p.p.m., versus elevated, 560 p.p.m.) for 10 years. The richness based on the detected number of operational taxonomic units (OTUs) significantly decreased under eCO(2). PhyloChip detected 2269 OTUs derived from 45 phyla (including two from Archaea), 55 classes, 99 orders, 164 families and 190 subfamilies. Also, the signal intensity of five phyla (Crenarchaeota, Chloroflexi, OP10, OP9/JS1, Verrucomicrobia) significantly decreased at eCO(2), and such significant effects of eCO(2) on microbial composition were also observed at the class or lower taxonomic levels for most abundant phyla, such as Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Acidobacteria, suggesting a shift in microbial community composition at eCO(2). Additionally, statistical analyses showed that the overall taxonomic structure of soil microbial communities was altered at eCO(2). Mantel tests indicated that such changes in species richness, composition and structure of soil microbial communities were closely correlated with soil and plant properties. This study provides insights into our understanding of shifts in the richness, composition and structure of soil microbial communities under eCO(2) and environmental factors shaping the microbial community structure.

Predicting the mineral composition of dust aerosols - Part 1: Representing key processes

NASA Astrophysics Data System (ADS)

Perlwitz, J. P.; Pérez García-Pando, C.; Miller, R. L.

2015-02-01

Soil dust aerosols created by wind erosion are typically assigned globally uniform physical and chemical properties within Earth system models, despite known regional variations in the mineral content of the parent soil. Mineral composition of the aerosol particles is important to their interaction with climate, including shortwave absorption and radiative forcing, nucleation of cloud droplets and ice crystals, coating by heterogeneous uptake of sulfates and nitrates, and atmospheric processing of iron into bioavailable forms that increase the productivity of marine phytoplankton. Here, aerosol mineral composition is derived by extending a method that provides the composition of a wet-sieved soil. The extension accounts for measurements showing significant differences between the mineral fractions of the wet-sieved soil and the resulting aerosol concentration. For example, some phyllosilicate aerosols are more prevalent at silt sizes, even though they are nearly absent in a soil whose aggregates are dispersed by wet sieving during analysis. We reconstruct the undispersed size distribution of the original soil that is subject to wind erosion. An empirical constraint upon the relative emission of clay and silt is applied that further differentiates the soil and aerosol mineral composition. In addition, a method is proposed for mixing minerals with small impurities composed of iron oxides. These mixtures are important for transporting iron far from the dust source, because pure iron oxides are more dense and vulnerable to gravitational removal than most minerals comprising dust aerosols. A limited comparison to measurements from North Africa shows that the extension brings the model into better agreement, consistent with a more extensive comparison to global observations as well as measurements of elemental composition downwind of the Sahara, as described in companion articles.

Apollo 14 - Nature and origin of rock types in soil from the Fra Mauro formation.

NASA Technical Reports Server (NTRS)

Aitken, F. K.; Anderson, D. H.; Bass, M. N.; Brown, R. W.; Butler, P., Jr.; Heiken, G.; Jakes, P.; Reid, A. M.; Ridley, W. I.; Takeda, H.

1971-01-01

Compositions of glasses in the Apollo 14 soil correspond to four types of Fra Mauro basalts, to mare basalts and soils, and, in minor amounts, to gabbroic anorthosite and potash granite. The Fra Mauro basalts can be related by simple low pressure crystal-liquid fractionation that implies a parent composition like that of Apollo 14 sample 14310.

Soil organic matter composition and quality across fire severity gradients in coniferous and deciduous forests of the southern boreal region

Treesearch

Jessica R. Miesel; William C. Hockaday; Randy Kolka; Philip A. Townsend

2015-01-01

Recent patterns of prolonged regional drought in southern boreal forests of the Great Lakes region, USA, suggest that the ecological effects of disturbance by wildfire may become increasingly severe. Losses of forest soil organic matter (SOM) during fire can limit soil nutrient availability and forest regeneration. These processes are also influenced by the composition...

Soil Components in Heterogeneous Impact Glass in Martian Meteorite EETA79001

NASA Technical Reports Server (NTRS)

Schrader, C. M.; Cohen, B. A.; Donovan, J. J.; Vicenzi, E. P.

2010-01-01

Martian soil composition can illuminate past and ongoing near-surface processes such as impact gardening [2] and hydrothermal and volcanic activity [3,4]. Though the Mars Exploration Rovers (MER) have analyzed the major-element composition of Martian soils, no soil samples have been returned to Earth for detailed chemical analysis. Rao et al. [1] suggested that Martian meteorite EETA79001 contains melted Martian soil in its impact glass (Lithology C) based on sulfur enrichment of Lithology C relative to the meteorite s basaltic lithologies (A and B) [1,2]. If true, it may be possible to extract detailed soil chemical analyses using this meteoritic sample. We conducted high-resolution (0.3 m/pixel) element mapping of Lithology C in thin section EETA79001,18 by energy dispersive spectrometry (EDS). We use these data for principal component analysis (PCA).

The Study Of Soil And Agrochemical Features Of Zonal Soils Of Coal Mining Enterprises In Kemerovo Region

NASA Astrophysics Data System (ADS)

Yakovchenko, M. A.; Kosolapova, A. A.; Ermolaev, V. A.

2017-01-01

The paper represents the results of the study of soil and agrochemical features of zonal soils: the grain-size composition, the content of humus, phosphorus and potassium, and heavy metals, the reaction of soil solution of the territory of the open-pit coal mine No12 of Kemerovo region in the areas of the working enterprise. The species composition of the lignose and herbaceous vegetation of the undisturbed territories has been studied. It has been revealed that the fertile soil layer of the studied areas of the open-pit coal mine is characterized as fertile but can’t be removed and stored because the surface of the whole area under study is forest-covered very much, rumpled, there are gullies and a lot of wind-fallen trees.

Influence of soil development on the geomorphic evolution of landscapes: An example from the Transverse Ranges of California

NASA Astrophysics Data System (ADS)

Eppes, M. C.; McFadden, L. D.; Matti, J.; Powell, R.

2002-03-01

Soil development can significantly influence the topographic evolution of a tectonically deforming mountain piedmont. Faults and folds associated with the North Frontal thrust system deform piedmont sediments of variable compositions along the north flank of the San Bernardino Mountains. The topographic expressions of folds with similar structural characteristics diverge appreciably, primarily as a function of differences in sediment composition and associated soil development. Soils with petrocalcic horizons in limestone- rich deposits are resistant to erosion, and anticlinal folds form prominent ridges. Folds forming in granite-derived deposits with argillic soil horizons are eroded and/or buried and are therefore topographically less pronounced. We propose that these landform contrasts can be explained by differences in soil-controlled hydrologic and erosion characteristics of deposits without calling upon changes in tectonic style along the mountain front.

Soil Aggregate Stability and Grassland Productivity Associations in a Northern Mixed-Grass Prairie

PubMed Central

Reinhart, Kurt O.; Vermeire, Lance T.

2016-01-01

Soil aggregate stability data are often predicted to be positively associated with measures of plant productivity, rangeland health, and ecosystem functioning. Here we revisit the hypothesis that soil aggregate stability is positively associated with plant productivity. We measured local (plot-to-plot) variation in grassland community composition, plant (aboveground) biomass, root biomass, % water-stable soil aggregates, and topography. After accounting for spatial autocorrelation, we observed a negative association between % water-stable soil aggregates (0.25–1 and 1–2 mm size classes of macroaggregates) and dominant graminoid biomass, and negative associations between the % water-stable aggregates and the root biomass of a dominant sedge (Carex filifolia). However, variation in total root biomass (0–10 or 0–30 cm depths) was either negatively or not appreciably associated with soil aggregate stabilities. Overall, regression slope coefficients were consistently negative thereby indicating the general absence of a positive association between measures of plant productivity and soil aggregate stability for the study area. The predicted positive association between factors was likely confounded by variation in plant species composition. Specifically, sampling spanned a local gradient in plant community composition which was likely driven by niche partitioning along a subtle gradient in elevation. Our results suggest an apparent trade-off between some measures of plant biomass production and soil aggregate stability, both known to affect the land’s capacity to resist erosion. These findings further highlight the uncertainty of plant biomass-soil stability associations. PMID:27467598

Soil Aggregate Stability and Grassland Productivity Associations in a Northern Mixed-Grass Prairie.

PubMed

Reinhart, Kurt O; Vermeire, Lance T

2016-01-01

Soil aggregate stability data are often predicted to be positively associated with measures of plant productivity, rangeland health, and ecosystem functioning. Here we revisit the hypothesis that soil aggregate stability is positively associated with plant productivity. We measured local (plot-to-plot) variation in grassland community composition, plant (aboveground) biomass, root biomass, % water-stable soil aggregates, and topography. After accounting for spatial autocorrelation, we observed a negative association between % water-stable soil aggregates (0.25-1 and 1-2 mm size classes of macroaggregates) and dominant graminoid biomass, and negative associations between the % water-stable aggregates and the root biomass of a dominant sedge (Carex filifolia). However, variation in total root biomass (0-10 or 0-30 cm depths) was either negatively or not appreciably associated with soil aggregate stabilities. Overall, regression slope coefficients were consistently negative thereby indicating the general absence of a positive association between measures of plant productivity and soil aggregate stability for the study area. The predicted positive association between factors was likely confounded by variation in plant species composition. Specifically, sampling spanned a local gradient in plant community composition which was likely driven by niche partitioning along a subtle gradient in elevation. Our results suggest an apparent trade-off between some measures of plant biomass production and soil aggregate stability, both known to affect the land's capacity to resist erosion. These findings further highlight the uncertainty of plant biomass-soil stability associations.

Agrophysical assessment of alluvial calcareous soils of the Çumra region of Central Anatolia in Turkey

NASA Astrophysics Data System (ADS)

Shein, E. V.; Erol, S. A.; Milanovskii, E. Yu.; Verkhovtseva, N. V.; Mikayilov, F. D.; Er, F.; Ersahin, S.

2014-07-01

Some physical (density, coefficient of filtration, particle-size composition, etc.) and chemical (contents of carbonates, organic carbon, nitrogen, etc.) properties of an alluvial calcareous soil were studied in Central Anatolia (Konya province, Çumra region). These heavy-textured (medium clay) soils with a low content of organic carbon (less than 1%) have favorable agrophysical properties due to the stable structure of the pore space. The studies of the water regime of soils under drop irrigation confirm the favorable hydrological properties of these soils. The use of the known agrophysical estimates (after Medvedev, the index of the optimal water regime, etc.) has revealed the high dispersal of the data related to the low humus content in these heavy-textured soils. The favorable structure of the pore space is suggested to be stipulated by the active activity of the numerous and diverse representatives of soil biota. Four phyla predominate in the microbio-logical composition of the soils studied; among them, Actinobacteria is the dominant. The composition of this phylum is dominated by the elevated number of both higher ( Streptomyces) and lower (three species of Rhodococcus) actinobacteria. The high biodiversity of bacteria against the background of their great total number and the developed trophic interactions in the microbial community promote the well-balanced production of specific metabolites, including gaseous ones (CO2, H2). This circumstance allows this clayey soil to function rather actively while protecting the pore space against compaction and maintaining the optimal density, porosity, and hydrological properties.

Changes in soil bacterial community structure with increasing disturbance frequency.

PubMed

Kim, Mincheol; Heo, Eunjung; Kang, Hojeong; Adams, Jonathan

2013-07-01

Little is known of the responsiveness of soil bacterial community structure to disturbance. In this study, we subjected a soil microcosm to physical disturbance, sterilizing 90 % of the soil volume each time, at a range of frequencies. We analysed the bacterial community structure using 454 pyrosequencing of the 16S rRNA gene. Bacterial diversity was found to decline with the increasing disturbance frequencies. Total bacterial abundance was, however, higher at intermediate and high disturbance frequencies, compared to low and no-disturbance treatments. Changing disturbance frequency also led to changes in community composition, with changes in overall species composition and some groups becoming abundant at the expense of others. Some phylogenetic groups were found to be relatively more disturbance-sensitive or tolerant than others. With increasing disturbance frequency, phylogenetic species variability (an index of community composition) itself became more variable from one sample to another, suggesting a greater role of chance in community composition. Compared to the tightly clustered community of the original undisturbed soil, in all the aged disturbed soils the lists of most abundant operational taxonomic units (OTUs) in each replicate were very different, suggesting a possible role of stochasticity in resource colonization and exploitation in the aged and disturbed soils. For example, colonization may be affected by whichever localized concentrations of bacterial populations happen to survive the last disturbance and be reincorporated in abundance into each pot. Overall, it appears that the soil bacterial community is very sensitive to physical disturbance, losing diversity, and that certain groups have identifiable 'high disturbance' vs. 'low disturbance' niches.

Using a trait-based approach to link microbial community composition and functioning to soil salinity

NASA Astrophysics Data System (ADS)

Rath, Kristin; Fierer, Noah; Rousk, Johannes

2017-04-01

Our knowledge of the dynamics structuring microbial communities and the consequences this has for soil functions is rudimentary. In particular, predictions of the response of microbial communities to environmental change and the implications for associated ecosystem processes remain elusive. Understanding how environmental factors structure microbial communities and regulate the functions they perform is key to a mechanistic understanding of how biogeochemical cycles respond to environmental change. Soil salinization is an agricultural problem in many parts of the world. The activity of soil microorganisms is reduced in saline soils compared to non-saline soil. However, soil salinity often co-varies with other factors, making it difficult to assign responses of microbial communities to direct effects of salinity. A trait-based approach allows us to connect the environmental factor salinity with the responses of microbial community composition and functioning. Salinity along a salinity gradient serves as a filter for the community trait distribution of salt tolerance, selecting for higher salt tolerance at more saline sites. This trait-environment relationship can be used to predict responses of microbial communities to environmental change. Our aims were to (i) use salinity along natural salinity gradients as an environmental filter, and (ii) link the resulting filtered trait-distributions of the communities (the trait being salt tolerance) to the community composition. Soil samples were obtained from two replicated salinity gradients along an Australian salt lake, spanning a wide range of soil salinities (0.1 dS m-1 to >50 dS m-1). In one of the two gradients salinity was correlated with pH. Community trait distributions for salt tolerance were assessed by establishing dose-dependences for extracted bacterial communities using growth rate assays. In addition, functional parameters were measured along the salt gradients. Community composition of sites was compared through 16S rRNA gene amplicon sequencing. Microbial community composition changed greatly along the salinity gradients. Using the salt-tolerance assessments to estimate bacterial trait-distributions we could determine substantial differences in tolerance to salt revealing a strong causal connection between environment and trait distributions. By constraining the community composition with salinity tolerance in ordinations, we could assign which community differences were directly due to a shift in community trait distributions. These analyses revealed that a substantial part (up to 30%) of the community composition differences were directly driven by environmental salt concentrations.. Even though communities in saline soils had trait-distributions aligned to their environment, their performance (respiration, growth rates) was lower than those in non-saline soils and remained low even after input of organic material. Using a trait-based approach we could connect filtered trait distributions along environmental gradients, to the composition of the microbial community. We show that soil salinity played an important role in shaping microbial community composition by selecting for communities with higher salt tolerance. The shift toward bacterial communities with trait distributions matched to salt environments probably compensated for much of the potential loss of function induced by salinity, resulting in a degree of apparent functional redundancy for decomposition. However, more tolerant communities still showed reduced functioning, suggesting a trade-off between salt tolerance and performance.

Impervious Surfaces Alter Soil Bacterial Communities in Urban Areas: A Case Study in Beijing, China

PubMed Central

Hu, Yinhong; Dou, Xiaolin; Li, Juanyong; Li, Feng

2018-01-01

The rapid expansion of urbanization has caused land cover change, especially the increasing area of impervious surfaces. Such alterations have significant effects on the soil ecosystem by impeding the exchange of gasses, water, and materials between soil and the atmosphere. It is unclear whether impervious surfaces have any effects on soil bacterial diversity and community composition. In the present study, we conducted an investigation of bacterial communities across five typical land cover types, including impervious surfaces (concrete), permeable pavement (bricks with round holes), shrub coverage (Buxus megistophylla Levl.), lawns (Festuca elata Keng ex E. Alexeev), and roadside trees (Sophora japonica Linn.) in Beijing, to explore the response of bacteria to impervious surfaces. The soil bacterial communities were addressed by high-throughput sequencing of the bacterial 16S rRNA gene. We found that Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, and Firmicutes were the predominant phyla in urban soils. Soil from impervious surfaces presented a lower bacterial diversity, and differed greatly from other types of land cover. Soil bacterial diversity was predominantly affected by Zn, dissolved organic carbon (DOC), and soil moisture content (SMC). The composition of the bacterial community was similar under shrub coverage, roadside trees, and lawns, but different from beneath impervious surfaces and permeable pavement. Variance partitioning analysis showed that edaphic properties contributed to 12% of the bacterial community variation, heavy metal pollution explained 3.6% of the variation, and interaction between the two explained 33% of the variance. Together, our data indicate that impervious surfaces induced changes in bacterial community composition and decrease of bacterial diversity. Interactions between edaphic properties and heavy metals were here found to change the composition of the bacterial community and diversity across areas with different types of land cover, and soil properties play a more important role than heavy metals. PMID:29545776

Elevational Variation in Soil Amino Acid and Inorganic Nitrogen Concentrations in Taibai Mountain, China.

PubMed

Cao, Xiaochuang; Ma, Qingxu; Zhong, Chu; Yang, Xin; Zhu, Lianfeng; Zhang, Junhua; Jin, Qianyu; Wu, Lianghuan

2016-01-01

Amino acids are important sources of soil organic nitrogen (N), which is essential for plant nutrition, but detailed information about which amino acids predominant and whether amino acid composition varies with elevation is lacking. In this study, we hypothesized that the concentrations of amino acids in soil would increase and their composition would vary along the elevational gradient of Taibai Mountain, as plant-derived organic matter accumulated and N mineralization and microbial immobilization of amino acids slowed with reduced soil temperature. Results showed that the concentrations of soil extractable total N, extractable organic N and amino acids significantly increased with elevation due to the accumulation of soil organic matter and the greater N content. Soil extractable organic N concentration was significantly greater than that of the extractable inorganic N (NO3--N + NH4+-N). On average, soil adsorbed amino acid concentration was approximately 5-fold greater than that of the free amino acids, which indicates that adsorbed amino acids extracted with the strong salt solution likely represent a potential source for the replenishment of free amino acids. We found no appreciable evidence to suggest that amino acids with simple molecular structure were dominant at low elevations, whereas amino acids with high molecular weight and complex aromatic structure dominated the high elevations. Across the elevational gradient, the amino acid pool was dominated by alanine, aspartic acid, glycine, glutamic acid, histidine, serine and threonine. These seven amino acids accounted for approximately 68.9% of the total hydrolyzable amino acid pool. The proportions of isoleucine, tyrosine and methionine varied with elevation, while soil major amino acid composition (including alanine, arginine, aspartic acid, glycine, histidine, leucine, phenylalanine, serine, threonine and valine) did not vary appreciably with elevation (p>0.10). The compositional similarity of many amino acids across the elevational gradient suggests that soil amino acids likely originate from a common source or through similar biochemical processes.

Grassland Soil Carbon Responses to Nitrogen Additions

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Tfailly, M.; Callister, S.; Bramer, L.; Thompson, A.

2017-12-01

Using a long-term continental scale experiment, we tested if increases in nitrogen (N) inputs augment the accumulation of plant and microbial residues onto mineral soil surfaces. This research investigates N effects on molecular biogeochemistry across six sites from the Nutrient Network (NutNet) experiment. The coupling between concurrently changing carbon (C) and N cycles remains a key uncertainty in understanding feedbacks between the terrestrial C cycle and climate change. Existing models do not consider the full suite of linked C-N processes, particularly belowground, that could drive future C-climate feedbacks. Soil harbors a wealth of diverse organic molecules, most of which have not been measured in hypothesis driven field research. For the first time we systematically assess the chemical composition of soil organic matter (SOM) and functional characteristics of the soil microbiome, to enhance our understanding of the molecular underpinnings of ecosystem C and N cycling. We have acquired soils from 5 ecosystem experiments across the US that have been subjected to 8 years of N addition treatments. These soils have been analyzed for chemical composition to identify how the soil fertility and stability is altered by N fertilization. We found distinct SOM signatures from our field experiments and shifts in soil chemistry in response to 8 years of N fertilization. Across all sites, we found the molecular composition of SOM varied with clay content, supporting the importance of soil mineralogy in the accumulation of specific chemical classes of SOM. While many molecules were common across sites, we discovered a suite of molecules that were site specific. N fertilization had a significant effect on SOM composition. Differences between control and N amended plots were greater in sites rich in lipids and more complex molecules, compared to sites with SOM rich in amino-sugar and protein like substances. Our results have important implications for how SOM is represented in models and the possibility for incorporating molecular understanding to advance ecosystem predictions.

Elevational Variation in Soil Amino Acid and Inorganic Nitrogen Concentrations in Taibai Mountain, China

PubMed Central

Yang, Xin; Zhu, Lianfeng; Zhang, Junhua; Jin, Qianyu; Wu, Lianghuan

2016-01-01

Amino acids are important sources of soil organic nitrogen (N), which is essential for plant nutrition, but detailed information about which amino acids predominant and whether amino acid composition varies with elevation is lacking. In this study, we hypothesized that the concentrations of amino acids in soil would increase and their composition would vary along the elevational gradient of Taibai Mountain, as plant-derived organic matter accumulated and N mineralization and microbial immobilization of amino acids slowed with reduced soil temperature. Results showed that the concentrations of soil extractable total N, extractable organic N and amino acids significantly increased with elevation due to the accumulation of soil organic matter and the greater N content. Soil extractable organic N concentration was significantly greater than that of the extractable inorganic N (NO3−-N + NH4+-N). On average, soil adsorbed amino acid concentration was approximately 5-fold greater than that of the free amino acids, which indicates that adsorbed amino acids extracted with the strong salt solution likely represent a potential source for the replenishment of free amino acids. We found no appreciable evidence to suggest that amino acids with simple molecular structure were dominant at low elevations, whereas amino acids with high molecular weight and complex aromatic structure dominated the high elevations. Across the elevational gradient, the amino acid pool was dominated by alanine, aspartic acid, glycine, glutamic acid, histidine, serine and threonine. These seven amino acids accounted for approximately 68.9% of the total hydrolyzable amino acid pool. The proportions of isoleucine, tyrosine and methionine varied with elevation, while soil major amino acid composition (including alanine, arginine, aspartic acid, glycine, histidine, leucine, phenylalanine, serine, threonine and valine) did not vary appreciably with elevation (p>0.10). The compositional similarity of many amino acids across the elevational gradient suggests that soil amino acids likely originate from a common source or through similar biochemical processes. PMID:27337100

Examining the effect of altered redox conditions on deep soil organic matter stability

NASA Astrophysics Data System (ADS)

Gabriel, C.; Kellman, L. M.; Ziegler, S. E.

2013-12-01

Since subsoil horizons contribute significantly to terrestrial carbon (C) budgets, understanding the influence of disturbances such as forest harvesting on subsoil C stability is critical. Clearcut harvesting leads to changes in the soil physico-chemical environment, including altering redox conditions arising from changes in soil hydrology that increase soil saturation, soil temperature, and pH. These physico-chemical changes have the potential to alter the adsorption of soil organic matter (SOM) to minerals, particularly at depth where SOM is primarily associated with mineral phases. The objective of this study was to determine the effect of differing redox states (aerobic vs. anaerobic) and temperature upon SOM stability of forested soils representative of the Acadian Forest Region of Eastern North America. Composite soil samples through depth (0-10, 10-20, 20-35, and 35-50 cm) from a mature red spruce forest (110 years) were incubated under optimum (aerobic) or saturated (anaerobic) conditions for 1 or 4 months at two temperatures (5 and 15 C). Following incubation, soil leachate was analyzed for dissolved organic carbon (DOC), and UV-vis absorbance in order to determine soil C losses and its optical character. Specific UV-vis absorbance SUVA (254 nm) and spectral slope ratios were calculated in order to assess the composition of chromophoric dissolved organic matter (CDOM). Preliminary results from the 1 month incubation indicate that under anaerobic conditions, all depths released DOC with a higher SUVA than under aerobic conditions, with the largest change observed in the 0-10 cm depth increment. Soil incubated at 5 C produced leachate with significantly less DOC and with a lower absorbance compared to 15 C under both redox conditions. These results suggest that both temperature and redox state are important in determining the aromaticity of DOC released from soils. Spectral slope ratios revealed that a greater proportion of CDOM of lower molecular weight (MW) compounds were released from deep mineral podzolic soils when saturated (high SUVA, low spectral slope), while higher MW CDOM were released from shallow soil strata (low SUVA, high spectral slope). This is consistent with research that indicates plant-derived SOM and microbial products each dominate in shallow and deep mineral soils, respectively. These preliminary results suggest that alterations to the redox state of a forested podzolic soil may have the potential to alter the mobilization of SOM, its composition and associated soil carbon stores.

Monitoring water stable isotope composition in soils using gas-permeable tubing and infrared laser absorption spectroscopy

NASA Astrophysics Data System (ADS)

Rothfuss, Youri; Vereecken, Harry; Brüggemann, Nicolas

2013-04-01

The water stable isotopologues 1H2H16O and 1H218O are powerful tracers of processes occurring in nature. Their slightly different masses as compared to the most abundant water isotopologue (1H216O) affect their thermodynamic (e.g. during chemical equilibrium reactions or physical phase transitions with equilibration) and kinetic (liquid and vapor phases transport processes and chemical reactions without equilibration) properties. This results in measurable differences of the isotopic composition of water within or between the different terrestrial ecosystem compartments (i.e. sub-soil, soil, surface waters, plant, and atmosphere). These differences can help addressing a number of issues, among them water balance closure and flux partitioning from the soil-plant-atmosphere continuum at the field to regional scales. In soils particularly, the isotopic composition of water (δ2H and δ18O) provides qualitative information about whether water has only infiltrated or already been re-evaporated since the last rainfall event or about the location of the evaporation front. From water stable isotope composition profiles measured in soils, it is also possible, under certain hypotheses, to derive quantitative information such as soil evaporation flux and the identification of root water uptake depths. In addition, water stable isotopologues have been well implemented into physically based Soil-Vegetation-Atmosphere Transfer models (e.g. SiSPAT-Isotope; Soil-Litter iso; TOUGHREACT) and have demonstrated their potential. However, the main disadvantage of the isotope methodology is that, contrary to other soil state variables that can be monitored over long time periods, δ2H and δ18O are typically analyzed following destructive sampling. Here, we present a non-destructive method for monitoring soil liquid water δ2H and δ18O over a wide range of water availability conditions and temperatures by sampling and measuring water vapor equilibrated with soil water using gas-permeable polypropylene tubing and a cavity ring-down laser absorption spectrometer. By analyzing water vapor δ2H and δ18O sampled with the tubing from a fine sand for temperatures ranging between 8-24° C, we demonstrate that (i) our new method is capable of monitoring δ2H and δ18O in soils online with high precision and, after calibration, also with high accuracy, (ii) our sampling protocol enabled detecting changes of δ2H and δ18O following non-fractionating addition and removal of liquid water and water vapor of different isotopic compositions, and (iii) the time needed for the tubing to monitor these changes is compatible with the observed variations of δ2H and δ18O in soils under natural conditions.

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

PubMed Central

Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts. PMID:28326062

Regional-Scale Drivers of Forest Structure and Function in Northwestern Amazonia

PubMed Central

Higgins, Mark A.; Asner, Gregory P.; Anderson, Christopher B.; Martin, Roberta E.; Knapp, David E.; Tupayachi, Raul; Perez, Eneas; Elespuru, Nydia; Alonso, Alfonso

2015-01-01

Field studies in Amazonia have found a relationship at continental scales between soil fertility and broad trends in forest structure and function. Little is known at regional scales, however, about how discrete patterns in forest structure or functional attributes map onto underlying edaphic or geological patterns. We collected airborne LiDAR (Light Detection and Ranging) data and VSWIR (Visible to Shortwave Infrared) imaging spectroscopy measurements over 600 km2 of northwestern Amazonian lowland forests. We also established 83 inventories of plant species composition and soil properties, distributed between two widespread geological formations. Using these data, we mapped forest structure and canopy reflectance, and compared them to patterns in plant species composition, soils, and underlying geology. We found that variations in soils and species composition explained up to 70% of variation in canopy height, and corresponded to profound changes in forest vertical profiles. We further found that soils and plant species composition explained more than 90% of the variation in canopy reflectance as measured by imaging spectroscopy, indicating edaphic and compositional control of canopy chemical properties. We last found that soils explained between 30% and 70% of the variation in gap frequency in these forests, depending on the height threshold used to define gaps. Our findings indicate that a relatively small number of edaphic and compositional variables, corresponding to underlying geology, may be responsible for variations in canopy structure and chemistry over large expanses of Amazonian forest. PMID:25793602

Remediation of cadmium- and lead-contaminated agricultural soil by composite washing with chlorides and citric acid.

PubMed

Li, Yu-jiao; Hu, Peng-jie; Zhao, Jie; Dong, Chang-xun

2015-04-01

Composite washing of cadmium (Cd)- and lead (Pb)-contaminated agricultural soil from Hunan province in China using mixtures of chlorides (FeCl3, CaCl2) and citric acid (CA) was investigated. The concentrations of composite washing agents for metal removal were optimized. Sequential extraction was conducted to study the changes in metal fractions after soil washing. The removal of two metals at optimum concentration was reached. Using FeCl3 mixed with CA, 44% of Cd and 23% of Pb were removed, and 49 and 32% by CaCl2 mixed with CA, respectively. The mechanism of composite washing was postulated. A mixture of chlorides and CA enhanced metal extraction from soil through the formation of metal-chloride and metal-citrate complexes. CA in extract solutions promoted the formation of metal-chloride complexes and reduced the solution pH. Composite washing reduced Cd and Pb in Fe-Mn oxide forms significantly. Chlorides and CA exerted a synergistic effect on metal extraction during composite washing.

Fire regime, not time-since-fire, affects soil fungal community diversity and composition in temperate grasslands.

PubMed

Egidi, Eleonora; McMullan-Fisher, Sapphire; Morgan, John W; May, Tom; Zeeman, Ben; Franks, Ashley E

2016-09-01

Frequent burning is commonly undertaken to maintain diversity in temperate grasslands of southern Australia. How burning affects below-ground fungal community diversity remains unknown. We show, using a fungal rDNA metabarcoding approach (Illumina MiSeq), that the fungal community composition was influenced by fire regime (frequency) but not time-since-fire. Fungal community composition was resilient to direct fire effects, most likely because grassland fires transfer little heat to the soil. Differences in the fungal community composition due to fire regime was likely due to associated changes that occur in vegetation with recurrent fire, via the break up of obligate symbiotic relationships. However, fire history only partially explains the observed dissimilarity in composition among the soil samples, suggesting a distinctiveness in composition in each grassland site. The importance of considering changes in soil microbe communities when managing vegetation with fire is highlighted. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Influence of fertilisation regimes on a nosZ-containing denitrifying community in a rice paddy soil.

PubMed

Chen, Zhe; Hou, Haijun; Zheng, Yan; Qin, Hongling; Zhu, Yijun; Wu, Jinshui; Wei, Wenxue

2012-03-30

Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17-year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ-denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR. Both the largest abundance of nosZ-denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation). This study shows that the addition of different fertilisers affects the size and composition of the nosZ-denitrifier community in paddy soil. Copyright © 2011 Society of Chemical Industry.

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

PubMed Central

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

PubMed

Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

2016-01-01

The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

Effect of long-term farming strategies on soil microbiota and soil health

NASA Astrophysics Data System (ADS)

Sommermann, Loreen; Babin, Doreen; Sandmann, Martin; Smalla, Kornelia; Schellenberg, Ingo; Grosch, Rita; Geistlinger, Joerg

2017-04-01

Increasing food and energy demands have resulted in considerable intensification of farming practices, which brought about severe consequences for agricultural soils, e.g. loss of fertility, erosion and enrichment of soil-borne plant diseases. In order to maintain soil quality and health for the future, the development of more extensive and sustainable farming strategies is urgently needed. The soil microbiome is regarded as a key player in soil ecosystem functions, particularly the natural ability of soils to suppress plant pathogens (suppressiveness). Recent studies showed that soil microbial communities are influenced by agricultural management. To further analyze the effects of farming strategies on soil suppressiveness and plant performance, agricultural soils from three long-term field trials in Thyrow, Bernburg (both in Germany) and Therwil (Switzerland) were sampled and subjected to molecular profiling of soil bacteria and fungi using marker genes and high-throughput amplicon sequencing. Significant effects on bacterial as well as fungal community composition, including plant pathogenic and beneficial taxa, were observed among variants of tillage and crop rotation. The least effect on both communities had fertilization, with no significance between variants. Subsequently, the same soils were subjected to growth chamber pot experiments with lettuce as a model (Lactuca sativa). After a growth period of six weeks significant differences in lettuce shoot and soil microbial biomass were observed among soil samples of the different long-term trials. Furthermore, the lettuce rhizosphere exhibited diverse bacterial community compositions as observed by DGGE (denaturing gradient gel electrophoresis). Using group-specific PCR-DGGE fingerprints, bacterial responders to fertilization, soil management and crop rotation were identified among different taxonomic groups. Currently, bacterial and fungal amplicon sequencing of rhizosphere and bulk soil from these pot experiments is ongoing in order to provide further insights into taxa potentially indicative for agricultural management and soil health. Presently, we are testing the potential of the different soil microbiomes to suppress the lettuce pathogen Rhizoctonia solani.

Advancing Analysis of Spatio-Temporal Variations of Soil Nutrients in the Water Level Fluctuation Zone of China’s Three Gorges Reservoir Using Self-Organizing Map

PubMed Central

Ye, Chen; Li, Siyue; Yang, Yuyi; Shu, Xiao; Zhang, Jiaquan; Zhang, Quanfa

2015-01-01

The ~350 km2 water level fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR) of China, situated at the intersection of terrestrial and aquatic ecosystems, experiences a great hydrological change with prolonged winter inundation. Soil samples were collected in 12 sites pre- (September 2008) and post submergence (June 2009) in the WLFZ and analyzed for soil nutrients. Self-organizing map (SOM) and statistical analysis including multi-way ANOVA, paired-T test, and stepwise least squares multiple regression were employed to determine the spatio-temporal variations of soil nutrients in relation to submergence, and their correlations with soil physical characteristics. Results showed significant spatial variability in nutrients along ~600 km long shoreline of the TGR before and after submergence. There were higher contents of organic matter, total nitrogen (TN), and nitrate (NO3-) in the lower reach and total phosphorus (TP) in the upper reach that were primarily due to the spatial variations in soil particle size composition and anthropogenic activities. Submergence enhanced soil available potassium (K), while significantly decreased soil N, possibly due to the alterations of soil particle size composition and increase in soil pH. In addition, SOM analysis determined important roles of soil pH value, bulk density, soil particle size (i.e., silt and sand) and nutrients (TP, TK, and AK) on the spatial and temporal variations in soil quality. Our results suggest that urban sewage and agricultural runoffs are primary pollutants that affect soil nutrients in the WLFZ of TGR. PMID:25789612

Environmental Factors Affect Acidobacterial Communities below the Subgroup Level in Grassland and Forest Soils

PubMed Central

Naether, Astrid; Foesel, Bärbel U.; Naegele, Verena; Wüst, Pia K.; Weinert, Jan; Bonkowski, Michael; Alt, Fabian; Oelmann, Yvonne; Polle, Andrea; Lohaus, Gertrud; Gockel, Sonja; Hemp, Andreas; Kalko, Elisabeth K. V.; Linsenmair, Karl Eduard; Pfeiffer, Simone; Renner, Swen; Schöning, Ingo; Weisser, Wolfgang W.; Wells, Konstans; Fischer, Markus; Overmann, Jörg

2012-01-01

In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered. PMID:22885760

Soil and geography are more important determinants of indigenous arbuscular mycorrhizal communities than management practices in Swiss agricultural soils.

PubMed

Jansa, Jan; Erb, Angela; Oberholzer, Hans-Rudolf; Smilauer, Petr; Egli, Simon

2014-04-01

Arbuscular mycorrhizal fungi (AMF) are ubiquitous soil fungi, forming mutualistic symbiosis with a majority of terrestrial plant species. They are abundant in nearly all soils, less diverse than soil prokaryotes and other intensively studied soil organisms and thus are promising candidates for universal indicators of land management legacies and soil quality degradation. However, insufficient data on how the composition of indigenous AMF varies along soil and landscape gradients have hampered the definition of baselines and effect thresholds to date. Here, indigenous AMF communities in 154 agricultural soils collected across Switzerland were profiled by quantitative real-time PCR with taxon-specific markers for six widespread AMF species. To identify the key determinants of AMF community composition, the profiles were related to soil properties, land management and site geography. Our results indicate a number of well-supported dependencies between abundances of certain AMF taxa and soil properties such as pH, soil fertility and texture, and a surprising lack of effect of available soil phosphorus on the AMF community profiles. Site geography, especially the altitude and large geographical distance, strongly affected AMF communities. Unexpected was the apparent lack of a strong land management effect on the AMF communities as compared to the other predictors, which could be due to the rarity of highly intensive and unsustainable land management in Swiss agriculture. In spite of the extensive coverage of large geographical and soil gradients, we did not identify any taxon suitable as an indicator of land use among the six taxa we studied. © 2014 John Wiley & Sons Ltd.

Elemental composition of Arctic soils and aerosols in Ny-Ålesund measured using laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Kim, Gibaek; Yoon, Young-Jun; Kim, Hyun-A.; Cho, Hee-joo; Park, Kihong

2017-08-01

Two laser-induced breakdown spectroscopy (LIBS) systems (soil LIBS and aerosol LIBS) were used to determine the elemental composition of soils and ambient aerosols less than 2.5 μm in Ny-Ålesund, Svalbard (the world's most northerly human settlement). For soil LIBS measurements, matrix effects such as moisture content, soil grain size, and surrounding gas on the LIBS response were minimized. When Ar gas was supplied onto the soil sample surfaces, a significant enhancement in LIBS emission lines was observed. Arctic soil samples were collected at 10 locations, and various elements (Al, Ba, C, Ca, Cu, Fe, H, K, Mg, Mn, N, Na, O, Pb, and Si) were detected in soils. The elemental distribution in arctic soils was clearly distinguishable from those in urban and abandoned mining soils in Korea. Moreover, the concentrations of most of anthropogenic metals were fairly low, and localized sources in extremely close proximity affected the elevated level of Cu in the soil samples derived from Ny-Ålesund. The number of elements detected in aerosols (C, Ca, H, K, Mg, Na, and O) was lower than those determined in soils. The elements in aerosols can mainly originate from minerals and sea salts. The elemental distribution in aerosols was also clearly distinguishable from that in soils, suggesting that the resuspension of local soil particles by wind erosion into aerosols was minimal. The daily variation of particle number concentration (RSD = 71%) and the elements in aerosols (RSD = 25%) varied substantially, possibly due to fluctuating air masses and meteorological conditions.

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

PubMed Central

Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. PMID:29538438

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields.

PubMed

Song, Xuhong; Pan, Yuan; Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

[Effects of continuous cropping of vegetables on ammonia oxidizers community structure].

PubMed

Meng, De-Long; Yang, Yang; Wu, Yan-Zheng; Wu, Min-Na; Qin, Hong-Ling; Zhu, Yi-Jun; Wei, Wen-Xue

2012-04-01

Investigations were conducted on the effects of intensive application of chemical fertilizers in crop production on soil nitrifier communities and the relationship between nitrifier communities and soil nitrification ability. Two series of vegetable soils were selected from Huangxing, Changsha, reflecting continuous vegetable cropping with about 20 years and new vegetable field with only about 2 years vegetable growing history. In each series five independent topsoils (0-20 cm) were sampled and each soil was a mixture of 10 cores randomly taken in the same field. Terminal restriction fragment length polymorphism (T-RFLP) and quantity PCR (Q-PCR) were used to determine the composition and abundance of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities. Results indicated that long-term and continuous vegetable cropping obviously changed the compositions of both AOB and AOA amoA gene, soil pH and Olsen-P content were the dominant factors affecting the composition of AOB amoA. In the vegetable soils, although the copy number of AOA amoA gene was about 5 times higher than AOB amoA gene, no significant correlation was detected between AOA amoA gene abundance and soil nitrification rate. It was not sure whether long-term and continuous vegetable cropping could shift the abundance of AOB and AOA, but it resulted in the enrichment of some dominant AOB species and increase of soil nitrification potential (PNF).

Linking biological soil crust diversity to ecological functions

NASA Astrophysics Data System (ADS)

Glaser, Karin; Borchhardt, Nadine; Schulz, Karoline; Mikhailyuk, Tatiana; Baumann, Karen; Leinweber, Peter; Ulf, Karsten

2016-04-01

Biological soil crusts (BSCs) are an association of different microorganisms and soil particles in the top millimeters of the soil. They are formed by algae, cyanobacteria, microfungi, bacteria, bryophytes and lichens in various compositions. Our aim was to determine and compare the biodiversity of all occurring organisms in biogeographically different habitats, ranging from polar (both Arctic and Antarctic), subpolar (Scandinavia), temperate (Germany) to dry regions (Chile). The combination of microscopy and molecular techniques (next-generation sequencing) revealed highly diverse crust communities, whose composition clustered by region and correlates with habitat characteristics such as water content. The BSC biodiversity was then linked to the ecological function of the crusts. The functional role of the BSCs in the biogeochemical cycles of carbon, nitrogen and phosphorous is evaluated using an array of state of the art soil chemistry methods including Py-FIMS (pyrolysis field ionization mass spectrometry) and XANES (x-ray absorbance near edge structure). Total P as well as P fractions were quantified in all BSCs, adjacent soil underneath and comparable nearby soil of BSC-free areas revealing a remarkable accumulation of total phosphorous and a distinct pattern of P fractions in the crust. Further, we observed an indication of a different P-speciation composition in the crust compared with BSC-free soil. The data allow answering the question whether BSCs act as sink or source for these compounds, and how biodiversity controls the biogeochemical function of BSCs.

Nestedness in Arbuscular Mycorrhizal Fungal Communities along Soil pH Gradients in Early Primary Succession: Acid-Tolerant Fungi Are pH Generalists

PubMed Central

Kawahara, Ai; An, Gi-Hong; Miyakawa, Sachie; Sonoda, Jun

2016-01-01

Soil acidity is a major constraint on plant productivity. Arbuscular mycorrhizal (AM) fungi support plant colonization in acidic soil, but soil acidity also constrains fungal growth and diversity. Fungi in extreme environments generally evolve towards specialists, suggesting that AM fungi in acidic soil are acidic-soil specialists. In our previous surveys, however, some AM fungi detected in strongly acidic soils could also be detected in a soil with moderate pH, which raised a hypothesis that the fungi in acidic soils are pH generalists. To test the hypothesis, we conducted a pH-manipulation experiment and also analyzed AM fungal distribution along a pH gradient in the field using a synthesized dataset of the previous and recent surveys. Rhizosphere soils of the generalist plant Miscanthus sinensis were collected both from a neutral soil and an acidic soil, and M. sinensis seedlings were grown at three different pH. For the analysis of field communities, rhizosphere soils of M. sinensis were collected from six field sites across Japan, which covered a soil pH range of 3.0–7.4, and subjected to soil trap culture. AM fungal community compositions were determined based on LSU rDNA sequences. In the pH-manipulation experiment the acidification of medium had a significant impact on the compositions of the community from the neutral soil, but the neutralization of the medium had no effect on those of the community from the acidic soil. Furthermore, the communities in lower -pH soils were subsets of (nested in) those in higher-pH soils. In the field communities a significant nestedness pattern was observed along the pH gradient. These observations suggest that the fungi in strongly acidic soils are pH generalists that occur not only in acidic soil but also in wide ranges of soil pH. Nestedness in AM fungal community along pH gradients may have important implications for plant community resilience and early primary succession after disturbance in acidic soils. PMID:27755574

Development of a composite soil degradation assessment index for cocoa agroecosystems in southwestern Nigeria

NASA Astrophysics Data System (ADS)

Adenrele Adeniyi, Sunday; de Clercq, Willem Petrus; van Niekerk, Adriaan

2017-08-01

Cocoa agroecosystems are a major land-use type in the tropical rainforest belt of West Africa, reportedly associated with several ecological changes, including soil degradation. This study aims to develop a composite soil degradation assessment index (CSDI) for determining the degradation level of cocoa soils under smallholder agroecosystems of southwestern Nigeria. Plots where natural forests have been converted to cocoa agroecosystems of ages 1-10, 11-40, and 41-80 years, respectively representing young cocoa plantations (YCPs), mature cocoa plantations (MCPs), and senescent cocoa plantations (SCPs), were identified to represent the biological cycle of the cocoa tree. Soil samples were collected at a depth of 0 to 20 cm in each plot and analysed in terms of their physical, chemical, and biological properties. Factor analysis of soil data revealed four major interacting soil degradation processes: decline in soil nutrients, loss of soil organic matter, increase in soil acidity, and the breakdown of soil textural characteristics over time. These processes were represented by eight soil properties (extractable zinc, silt, soil organic matter (SOM), cation exchange capacity (CEC), available phosphorus, total porosity, pH, and clay content). These soil properties were subjected to forward stepwise discriminant analysis (STEPDA), and the result showed that four soil properties (extractable zinc, cation exchange capacity, SOM, and clay content) are the most useful in separating the studied soils into YCP, MCP, and SCP. In this way, we have sufficiently eliminated redundancy in the final selection of soil degradation indicators. Based on these four soil parameters, a CSDI was developed and used to classify selected cocoa soils into three different classes of degradation. The results revealed that 65 % of the selected cocoa farms are moderately degraded, while 18 % have a high degradation status. The numerical value of the CSDI as an objective index of soil degradation under cocoa agroecosystems was statistically validated. The results of this study reveal that soil management should promote activities that help to increase organic matter and reduce Zn deficiency over the cocoa growth cycle. Finally, the newly developed CSDI can provide an early warning of soil degradation processes and help farmers and extension officers to implement rehabilitation practices on degraded cocoa soils.

Nestedness in Arbuscular Mycorrhizal Fungal Communities along Soil pH Gradients in Early Primary Succession: Acid-Tolerant Fungi Are pH Generalists.

PubMed

Kawahara, Ai; An, Gi-Hong; Miyakawa, Sachie; Sonoda, Jun; Ezawa, Tatsuhiro

2016-01-01

Soil acidity is a major constraint on plant productivity. Arbuscular mycorrhizal (AM) fungi support plant colonization in acidic soil, but soil acidity also constrains fungal growth and diversity. Fungi in extreme environments generally evolve towards specialists, suggesting that AM fungi in acidic soil are acidic-soil specialists. In our previous surveys, however, some AM fungi detected in strongly acidic soils could also be detected in a soil with moderate pH, which raised a hypothesis that the fungi in acidic soils are pH generalists. To test the hypothesis, we conducted a pH-manipulation experiment and also analyzed AM fungal distribution along a pH gradient in the field using a synthesized dataset of the previous and recent surveys. Rhizosphere soils of the generalist plant Miscanthus sinensis were collected both from a neutral soil and an acidic soil, and M. sinensis seedlings were grown at three different pH. For the analysis of field communities, rhizosphere soils of M. sinensis were collected from six field sites across Japan, which covered a soil pH range of 3.0-7.4, and subjected to soil trap culture. AM fungal community compositions were determined based on LSU rDNA sequences. In the pH-manipulation experiment the acidification of medium had a significant impact on the compositions of the community from the neutral soil, but the neutralization of the medium had no effect on those of the community from the acidic soil. Furthermore, the communities in lower -pH soils were subsets of (nested in) those in higher-pH soils. In the field communities a significant nestedness pattern was observed along the pH gradient. These observations suggest that the fungi in strongly acidic soils are pH generalists that occur not only in acidic soil but also in wide ranges of soil pH. Nestedness in AM fungal community along pH gradients may have important implications for plant community resilience and early primary succession after disturbance in acidic soils.

Soil microbial characteristics and seed bank dynamics of stock-piled top soils in ther western Rio Grande Plains

USDA-ARS?s Scientific Manuscript database

Increased energy extraction has impacted rangelands throughout the western U.S. Ecological restoration can be enhanced with proper management of affected top soils. Little information exists on effects of stockpiling on soil microbial community composition and functionality and seed bank dynamics. T...

Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests.

PubMed

Bachelot, Benedicte; Uriarte, María; Zimmerman, Jess K; Thompson, Jill; Leff, Jonathan W; Asiaii, Ava; Koshner, Jenny; McGuire, Krista

2016-09-01

Our understanding of the long-lasting effects of human land use on soil fungal communities in tropical forests is limited. Yet, over 70% of all remaining tropical forests are growing in former agricultural or logged areas. We investigated the relationship among land use history, biotic and abiotic factors, and soil fungal community composition and diversity in a second-growth tropical forest in Puerto Rico. We coupled high-throughput DNA sequencing with tree community and environmental data to determine whether land use history had an effect on soil fungal community descriptors. We also investigated the biotic and abiotic factors that underlie such differences and asked whether the relative importance of biotic (tree diversity, basal tree area, and litterfall biomass) and abiotic (soil type, pH, iron, and total carbon, water flow, and canopy openness) factors in structuring soil fungal communities differed according to land use history. We demonstrated long-lasting effects of land use history on soil fungal communities. At our research site, most of the explained variation in soil fungal composition (R 2  = 18.6%), richness (R 2  = 11.4%), and evenness (R 2  = 10%) was associated with edaphic factors. Areas previously subject to both logging and farming had a soil fungal community with lower beta diversity and greater evenness of fungal operational taxonomic units (OTUs) than areas subject to light logging. Yet, fungal richness was similar between the two areas of historical land use. Together, these results suggest that fungal communities in disturbed areas are more homogeneous and diverse than in areas subject to light logging. Edaphic factors were the most strongly correlated with soil fungal composition, especially in areas subject to light logging, where soils are more heterogenous. High functional tree diversity in areas subject to both logging and farming led to stronger correlations between biotic factors and fungal composition than in areas subject to light logging. In contrast, fungal richness and evenness were more strongly correlated with biotic factors in areas of light logging, suggesting that these metrics might reflect long-term associations in old-growth forests. The large amount of unexplained variance in fungal composition suggests that these communities are structured by both stochastic and niche assemblage processes. © 2016 by the Ecological Society of America.

Characteristic variations in reflectance of surface soils

NASA Technical Reports Server (NTRS)

Stoner, E. R.; Baumgardner, M. F. (Principal Investigator)

1982-01-01

Surface soil samples from a wide range of naturally occurring soils were obtained for the purpose of studying the characteristic variations in soil reflectance as these variations relate to other soil properties and soil classification. A total 485 soil samples from the U.S. and Brazil representing 30 suborders of the 10 orders of 'Soil Taxonomy' was examined. The spectral bidirectional reflectance factor was measured on uniformly moist soils over the 0.52 to 2.32 micron wavelength range with a spectroradiometer adapted for indoor use. Five distinct soil spectral reflectance curve forms were identified according to curve shape, the presence or absence of absorption bands, and the predominance of soil organic matter and iron oxide composition. These curve forms were further characterized according to generically homogeneous soil properties in a manner similar to the subdivisions at the suborder level of 'Soil Taxonomy'. Results indicate that spectroradiometric measurements of soil spectral bidirectional reflectance factor can be used to characterize soil reflectance in terms that are meaningful to soil classification, genesis, and survey.

Influence of Vinasse Application in the Structure and Composition of the Bacterial Community of the Soil under Sugarcane Cultivation

PubMed Central

de Camargo, André Ferreira; Goulart, Karla Cristina Stropa; Lemos, Eliana Gertrudes de Macedo

2016-01-01

Although the use of vinasse as a waste helps replenish soil nutrients and improves the quality of the sugarcane crop, it is known that vinasse residues alter the diversity of bacteria naturally present in the soil. The actual impacts of vinasse application on the selection of bacterial taxa are not understood because no studies have addressed this phenomenon directly. Analysis of 16S rRNA gene clone sequences from four soil types showed that the soil planted with sugarcane and fertilized with vinasse has a high diversity of bacteria compared to other biomes, where Acidobacteria were the second most abundant phylum. Although the composition and structure of bacterial communities differ significantly in the four environments (Libshuff's test), forest soils and soil planted with sugarcane without vinasse fertilizer were similar to each other because they share at least 28 OTUs related to Rhizobiales, which are important agents involved in nitrogen fixation. OTUs belonging to Actinomycetales were detected more often in the soil that had vinasse applied, indicating that these groups are more favored by this type of land management. PMID:27528875

Afforestation alters community structure of soil fungi.

PubMed

Carson, Jennifer K; Gleeson, Deirdre B; Clipson, Nicholas; Murphy, Daniel V

2010-07-01

Relatively little is known about the effect of afforestation on soil fungal communities. This study demonstrated that afforestation altered fungal community structure and that changes were correlated to pools of soil C. Pasture at three locations on the same soil type was afforested with Eucalyptus globulus or Pinus pinaster. The structure of fungal communities under the three land uses was measured after 13y using automated ribosomal intergenic spacer analysis (ARISA). Afforestation significantly altered the structure of fungal communities. The effect of location on the structure of fungal communities was limited to pasture soils; although these contained the same plant species, the relative composition of each species varied between locations. Differences in the structure of fungal communities between pasture, E. globulus and P. pinaster were significantly correlated with changes in the amount of total organic C and microbial biomass-C in soil. Afforestation of patches of agricultural land may contribute to conserving soil fungi in agricultural landscapes by supporting fungal communities with different composition to agricultural soils. Copyright © 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Salecan Enhances the Activities of β-1,3-Glucanase and Decreases the Biomass of Soil-Borne Fungi

PubMed Central

Chen, Yunmei; Xu, Haiyang; Zhou, Mengyi; Wang, Yang; Wang, Shiming; Zhang, Jianfa

2015-01-01

Salecan, a linear extracellular polysaccharide consisting of β-1,3-D-glucan, has potential applications in the food, pharmaceutical and cosmetic industries. The objective of this study was to evaluate the effects of salecan on soil microbial communities in a vegetable patch. Compositional shifts in the genetic structure of indigenous soil bacterial and fungal communities were monitored using culture-dependent dilution plating, culture-independent PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR. After 60 days, soil microorganism counts showed no significant variation in bacterial density and a marked decrease in the numbers of fungi. The DGGE profiles revealed that salecan changed the composition of the microbial community in soil by increasing the amount of Bacillus strains and decreasing the amount of Fusarium strains. Quantitative PCR confirmed that the populations of the soil-borne fungi Fusarium oxysporum and Trichoderma spp. were decreased approximately 6- and 2-fold, respectively, in soil containing salecan. This decrease in the amount of fungi can be explained by salecan inducing an increase in the activities of β-1,3-glucanase in the soil. These results suggest the promising application of salecan for biological control of pathogens of soil-borne fungi. PMID:26247592

Biomimetic Hydrogel Composites for Soil Stabilization and Contaminant Mitigation.

PubMed

Zhao, Zhi; Hamdan, Nasser; Shen, Li; Nan, Hanqing; Almajed, Abdullah; Kavazanjian, Edward; He, Ximin

2016-11-15

We have developed a novel method to synthesize a hyper-branched biomimetic hydrogel network across a soil matrix to improve the mechanical strength of the loose soil and simultaneously mitigate potential contamination due to excessive ammonium. This method successfully yielded a hierarchical structure that possesses the water retention, ion absorption, and soil aggregation capabilities of plant root systems in a chemically controllable manner. Inspired by the robust organic-inorganic composites found in many living organisms, we have combined this hydrogel network with a calcite biomineralization process to stabilize soil. Our experiments demonstrate that poly(acrylic acid) (PAA) can work synergistically with enzyme-induced carbonate precipitation (EICP) to render a versatile, high-performance soil stabilization method. PAA-enhanced EICP provides multiple benefits including lengthening of water supply time, localization of cementation reactions, reduction of harmful byproduct ammonium, and achievement of ultrahigh soil strength. Soil crusts we have obtained can sustain up to 4.8 × 10 3 kPa pressure, a level comparable to cementitious materials. An ammonium removal rate of 96% has also been achieved. These results demonstrate the potential for hydrogel-assisted EICP to provide effective soil improvement and ammonium mitigation for wind erosion control and other applications.

High heterogeneity in soil composition and quality in different mangrove forests of Venezuela.

PubMed

Otero, X L; Méndez, A; Nóbrega, G N; Ferreira, T O; Meléndez, W; Macías, F

2017-09-18

Mangrove forests play an important role in biogeochemical cycles of metals, nutrients, and C in coastal ecosystems. However, these functions could be strongly affected by the mangrove soil degradation. In this study, we performed an intensive sampling characterizing mangrove soils under different types of environment (lagoon/gulf) and vegetation (Rhizophora/Avicennia/dead mangrove) in the Venezuelan coast. To better understand the spatial heterogeneity of the composition and characteristics of the soils, a wide range of the soil attributes were analyzed. In general, the soils were anoxic (Eh < 200 mV), with a neutral pH and low concentration in toxic metals; nevertheless, they varied widely in the soil and its quality-defining parameters (e.g., clay contents, total organic carbon, Fe, Al, toxic trace metals). It is noteworthy that the mangroves presented a low Fe Pyrite content due to a limitation in the Fe oxyhydroxide contents, especially in soils with higher organic C content (TOC > 15%). Finally, the dead mangrove showed significantly lower amounts of TOC and fibers (in comparison to the well-preserved mangrove forest), which indicates that the C pools in mangrove soils are highly sensitive also to natural impact, such as ENSO.

Microbial composition in microcosms amended with natural and mineral fertilizers under different water regimes

NASA Astrophysics Data System (ADS)

Brad, Traian; Chiriac, Cecilia; Szekeres, Edina; Coman, Cristian; Rudi, Knut; Sandor, Mignon

2017-04-01

Twenty microcosm enclosures containing two types of soil (i.e. a rich Chernozemic and a poorer soil) were fertilized with mineral (NPK-complex) and organic (Gülle, manure and a green fertilizer) materials and placed under dry and wet water regimes. After 10, 20 and 30 days of the experiment, soil samples were analyzed for the structure and composition of microbial communities using next generation sequencing techniques (Illumina) and statistical analysis. The differences between bacteria communities in different soil types, and in different fertilization and hydric treatments were analyzed using quantitative phylogenetic distances and the ANOSIM test. The two types of soil especially selected for the structure of microbial communities, while moisture and the type of fertilizer appeared to have a smaller influence on microbial diversity in microcosms. The alpha-diversity indices (species richness, evenness and phylogenetic diversity) had higher values for the poorer soil compared to the rich Chernozemic soil. For both soil types, the highest bacteria diversity values were obtained after fertilization with manure. The microbial communities in the analyzed soils were complex and dominated by sequences belonging to Actinobacteria, Proteobacteria, Acidobacteria and Firmicutes.

Composition and Maturity of Apollo 16 Regolith Core 60013/14

NASA Technical Reports Server (NTRS)

Korotev, Randy T.; Morris, Richard V.

1993-01-01

Samples from every half-centimeter dissection interval of double drive tube 60013/14 (sections 60013 and 60014) were analyzed by magnetic techniques for Fe concentration and surface maturity parameter I(sub s)/ Fe(O), and by neutron activation for concentrations of 25 lithophile and siderophile elements. Core 60013/14 is one of three regolith cores taken in a triangular array 40-50 m apart on the Cayley plains during Apollo 16 mission to the Moon. The core can be divided into three zones based both on I(sub s)/FeO and composition. Unit A (0-44 cm depth) is compositionally similar to other soils from the surface of the central region of the site and is mature throughout, although maturity decreases with depth. Unit B (44-59 cm) is submature and compositionally more feldspathic than Unit A. Regions of lowest maturity in Unit B are characterized by lower Sm/Sc ratios than any soil obtained from the Cayley plains as a result of some unidentified lithologic component with low surface maturity. The component is probably some type of mafic anorthosite that does not occur in such high abundance in any of the other returned soils. Unit C (59-62 cm) is more mature than Unit B and compositionally equivalent to an 87: 13 mixture of soil such as that from Unit A and plagioclase such as found in ferroan anorthosite. Similar soils, but containing greater abundances of anorthosite (plagioclase), are found at depth in the other two cores of the array. These units of immature to submature soil enriched to varying degrees (compared to the mature surface soil) in ferroan anorthosite consisting of approx. 99% plagioclase are the only compositionally distinct subsurface similarities among the three cores. Each of the cores contains other units that are compositionally dissimilar to any soil unit in the other two cores. These compositionally distinct units probably derive from local subsurface blocks deposited by the event(s) that formed the Cayley plains. The ferroan anorthosite with approx. 99% plagioclase, however, must represent some subsurface lithology that is significant on the scale of tens of meters. The compositional uniformity of the surface soil (0-10 cm depth) over distances of kilometers reflects the large-scale uniformity of the plains deposits; the fine- structure reflects small-scale nonuniformity and the inefficiency of the impact-mixing process at depths as shallow as even one meter.

A Sampling of Martian Soils

NASA Image and Video Library

2012-12-03

This collage shows the variety of soils found at landing sites on Mars. The elemental composition of the typical, reddish soils were investigated by NASA Viking, Pathfinder and Mars Exploration Rover missions, and now with the Curiosity rover.

Soil, the orphan hydrological compartment: evidence from O and H stable isotopes?

NASA Astrophysics Data System (ADS)

Hissler, Christophe; Legout, Arnaud; Barnich, François; Pfister, Laurent

2015-04-01

O and H stable isotopes have been successfully used for decades for studying the exchange of waters between the hydrosphere, the pedosphere and the biosphere. They greatly contribute to improve our understanding of soil-water-plant interactions. In particular, the recent hydrological concept of "two water worlds" (separation of meteoric water that infiltrates the soil as (i) mobile water, which can reach the groundwater and can enter the stream, and as (ii) tightly bound water, which is trapped in the soil microporosity and used by plants) calls for a substantial revision of our perceptual models of runoff generation. Nevertheless, there is a need for testing the applicability of this concept over a large range of ecosystemic contexts (i.e.soil and vegetation types). To date, many investigations have focused on the relationship between the various processes triggering isotope fractionation within soils. So far, the dominating perception is that the isotope profile of water observed in soils is solely due to evaporative fractionation and its shape is dependent on climate and soil parameters. However, as of today the influence of biogeochemical processes on the spatio-temporal variability of δ18O and δD of the soil solutions has been rarely quantified. O and H exchanges between soil water and other soil compartments (living organisms, minerals, exchange capacity, organic matter) remain poorly known and require deeper investigations. Eventually, we need to better understand the distribution of O and H isotopes throughout the soil matrix. In order to address these issues, we have designed and carried out two complementary isotope experiments that use one liter soil columns of a 2mm-sieved and air-dried soil. Our objectives were (1) to observe the temporal evolution of the water O and H isotopic composition starting from the field capacity to the complete drying of the soil and (2) to determine the impact of soil biogeochemical properties on the isotopic composition of different water types in soil (weakly-, moderately- and tightly-bound). Our results show that mobile and tightly bound water may have different hydrogen isotopic signatures and that their respective isotopic signatures may vary between horizons and soil types. However, it is not yet possible to quantify the contribution of different bio-physico-chemical processes to the oxygen and hydrogen isotopic composition of the soil water because the techniques at hand for water separation are not yet reliable enough. Prior to this type of quantifications, we need to focus in a next step at the improvement of water extraction methods.

Noble gas evidence for the depositional and irradiational history of 60010-60009 core soils

NASA Technical Reports Server (NTRS)

Bogard, D. D.; Hirsch, W. C.

1977-01-01

Isotopic abundances of the noble gases have been determined in grain size separates of eleven soils from different depths in the 60010-60009 double drive tube and in magnetic and plagioclase separates from a few of these soils. Data for the 60010 core are presented here. The entire core was deposited a maximum of approximately 125 m.y. ago as deduced from the Ar-38 cosmic ray exposure age of soil 60009,457. Soils in the topmost 12 cm of the core show loss of cosmogenic He-3 and Ne-21 and gain of trapped solar gases in proportion to the degree of surface reworking by micrometeorites as deduced from FMR data. A variety of compositional and irradiational evidence suggests that soils in the core were formed by mixing of three or more components during or immediately prior to core deposition less than about 125 m.y. ago. Based on cosmogenic noble gases and a variety of other data soils 60009,457 and 60010,3107 are similar (and possibly identical) to two of the end member soils which formed the mixture. More mature soils in the core, however, could not have matured in situ from these two soils because of significant differences in noble gas abundances and chemical composition.

Hydrocarbon status of soils in the asphalt deposit area (Samara Bend)

NASA Astrophysics Data System (ADS)

Pikovskiy, Yu. I.; Gennadiev, A. N.; Kovach, R. G.; Zhidkin, A. P.; Khlynina, N. I.; Kiseleva, A. Yu.

2017-04-01

The composition and distribution features of the main components of soil hydrocarbon complex― organic (noncarbonate) carbon, hexane bitumoids, and individual polycyclic aromatic hydrocarbons (PAHs)―in the area of depleted Bakhilovo asphalt deposit (Samara oblast) have been studied. According to their proportions, three genetic types of soil hydrocarbon status are distinguished: (a) emanation-injection type prevailing within the limits of the former production field and characterized by anomalous contents of heavy resinous bitumoids (5000-7000 mg/kg on the average) throughout the soil profile and a high content of PAHs (4-9 mg/kg on the average, 29 mg/kg as the maximum, with the dominance of naphthalene homologues); (b) emanation-biogeochemical type confined to mechanogenically undisturbed soils within and beyond the deposit area, where the emanation component is manifested in soils with heavy texture and higher concentrations and very light composition of bitumoids in the lower parts of the soil profile; and (c) atmosedimentation-biogeochemical type characteristic of conventionally background soils with light texture; benzo[ a]pyrene traces are detected among PAHs in the upper soil horizon, which indicates the input of this hydrocarbon with aerosols from the atmosphere; the concentrations of bitumoids and PAHs in parent rocks are lower than in the soils.

Long-term effects of timber harvesting on forest soil communities and their catabolic capacity

NASA Astrophysics Data System (ADS)

Mohn, W. W.

2016-12-01

We examined the effect of forest harvesting on metagenomes of soil communities in ecozones across North America. The overall effect of harvesting on community composition was very small relative to major differences between soil horizons and among geographically distinct ecozones. However, in some ecozones, harvesting substantially altered bacterial and fungal community composition and diminished the genetic potential for biomass decomposition while increasing the potential for nitrogen cycling. Stable isotope probing identified populations involved in hemicellulose and cellulose decomposition. Known cellulolytic organisms were found in the organic soil layer, while novel cellulolytic organisms were identified in the mineral soil layer. Lignolytic populations identified were mainly bacterial, and metagenomics analysis identified lignin degradation enzymes in the genomes of some of these populations. In some ecozones, cellulolytic and hemicellulolytic populations were substantially impacted by harvesting. Soil carbon, nitrogen and pH were related to the relative susceptibility of forest soil communities in the different ecozones to harvesting impacts.

Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia)

PubMed Central

Schneider, Dominik; Engelhaupt, Martin; Allen, Kara; Kurniawan, Syahrul; Krashevska, Valentyna; Heinemann, Melanie; Nacke, Heiko; Wijayanti, Marini; Meryandini, Anja; Corre, Marife D.; Scheu, Stefan; Daniel, Rolf

2015-01-01

Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations. PMID:26696965

Dry/Wet Cycles Change the Activity and Population Dynamics of Methanotrophs in Rice Field Soil

PubMed Central

Ma, Ke; Conrad, Ralf

2013-01-01

The methanotrophs in rice field soil are crucial in regulating the emission of methane. Drainage substantially reduces methane emission from rice fields. However, it is poorly understood how drainage affects microbial methane oxidation. Therefore, we analyzed the dynamics of methane oxidation rates, composition (using terminal restriction fragment length polymorphism [T-RFLP]), and abundance (using quantitative PCR [qPCR]) of methanotroph pmoA genes (encoding a subunit of particulate methane monooxygenase) and their transcripts over the season and in response to alternate dry/wet cycles in planted paddy field microcosms. In situ methane oxidation accounted for less than 15% of total methane production but was enhanced by intermittent drainage. The dry/wet alternations resulted in distinct effects on the methanotrophic communities in different soil compartments (bulk soil, rhizosphere soil, surface soil). The methanotrophic communities of the different soil compartments also showed distinct seasonal dynamics. In bulk soil, potential methanotrophic activity and transcription of pmoA were relatively low but were significantly stimulated by drainage. In contrast, however, in the rhizosphere and surface soils, potential methanotrophic activity and pmoA transcription were relatively high but decreased after drainage events and resumed after reflooding. While type II methanotrophs dominated the communities in the bulk soil and rhizosphere soil compartments (and to a lesser extent also in the surface soil), it was the pmoA of type I methanotrophs that was mainly transcribed under flooded conditions. Drainage affected the composition of the methanotrophic community only minimally but strongly affected metabolically active methanotrophs. Our study revealed dramatic dynamics in the abundance, composition, and activity of the various type I and type II methanotrophs on both a seasonal and a spatial scale and showed strong effects of dry/wet alternation cycles, which enhanced the attenuation of methane flux into the atmosphere. PMID:23770899

Anthropogenic N deposition increases soil organic matter accumulation without altering its biochemical composition.

PubMed

Zak, Donald R; Freedman, Zachary B; Upchurch, Rima A; Steffens, Markus; Kögel-Knabner, Ingrid

2017-02-01

Accumulating evidence indicates that future rates of atmospheric N deposition have the potential to increase soil C storage by reducing the decay of plant litter and soil organic matter (SOM). Although the microbial mechanism underlying this response is not well understood, a decline in decay could alter the amount, as well as biochemical composition of SOM. Here, we used size-density fractionation and solid-state 13 C-NMR spectroscopy to explore the extent to which declines in microbial decay in a long-term (ca. 20 yrs.) N deposition experiment have altered the biochemical composition of forest floor, bulk mineral soil, as well as free and occluded particulate organic matter. Significant amounts of organic matter have accumulated in occluded particulate organic matter (~20%; oPOM); however, experimental N deposition had not altered the abundance of carboxyl, aryl, alkyl, or O/N-alkyl C in forest floor, bulk mineral soil, or any soil fraction. These observations suggest that biochemically equivalent organic matter has accumulated in oPOM at a greater rate under experimental N deposition, relative to the ambient treatment. Although we do not understand the process by which experimental N deposition has fostered the occlusion of organic matter by mineral soil particles, our results highlight the importance of interactions among the products of microbial decay and the chemical and physical properties of silt and clay particles that occlude organic matter from microbial attack. Because oPOM can reside in soils for decades to centuries, organic matter accumulating under future rates of anthropogenic N deposition could remain in soil for long periods of time. If temperate forest soils in the Northern Hemisphere respond like those in our experiment, then unabated deposition of anthropogenic N from the atmosphere has the potential to foster greater soil C storage, especially in fine-texture forest soils. © 2016 John Wiley & Sons Ltd.

Tillage and crop residue management methods had minor effects on the stock and stabilization of topsoil carbon in a 30-year field experiment.

PubMed

Singh, Pooja; Heikkinen, Jaakko; Ketoja, Elise; Nuutinen, Visa; Palojärvi, Ansa; Sheehy, Jatta; Esala, Martti; Mitra, Sudip; Alakukku, Laura; Regina, Kristiina

2015-06-15

We studied the effects of tillage and straw management on soil aggregation and soil carbon sequestration in a 30-year split-plot experiment on clay soil in southern Finland. The experimental plots were under conventional or reduced tillage with straw retained, removed or burnt. Wet sieving was done to study organic carbon and soil composition divided in four fractions: 1) large macroaggregates, 2) small macroaggregates, 3) microaggregates and 4) silt and clay. To further estimate the stability of carbon in the soil, coarse particulate organic matter, microaggregates and silt and clay were isolated from the macroaggregates. Total carbon stock in the topsoil (equivalent to 200 kg m(-2)) was slightly lower under reduced tillage (5.0 kg m(-2)) than under conventional tillage (5.2 kg m(-2)). Reduced tillage changed the soil composition by increasing the percentage of macroaggregates and decreasing the percentage of microaggregates. There was no evidence of differences in the composition of the macroaggregates or carbon content in the macroaggregate-occluded fractions. However, due to the higher total amount of macroaggregates in the soil, more carbon was bound to the macroaggregate-occluded microaggregates in reduced tillage. Compared with plowed soil, the density of deep burrowing earthworms (Lumbricus terrestris) was considerably higher under reduced tillage and positively associated with the percentage of large macroaggregates. The total amount of microbial biomass carbon did not differ between the treatments. Straw management did not have discernible effects either on soil aggregation or soil carbon stock. We conclude that although reduced tillage can improve clay soil structure, generally the chances to increase topsoil carbon sequestration by reduced tillage or straw management practices appear limited in cereal monoculture systems of the boreal region. This may be related to the already high C content of soils, the precipitation level favoring decomposition and aggregate turnover in the winter with topsoil frost. Copyright © 2015. Published by Elsevier B.V.

Exploring functional relationships between post-fire soil water repellency, soil structure and physico-chemical properties

NASA Astrophysics Data System (ADS)

Quarfeld, Jamie; Brook, Anna; Keestra, Saskia; Wittenberg, Lea

2016-04-01

Soil water repellency (WR) and aggregate stability (AS) are two soil properties that are typically modified after burning and impose significant influence on subsequent hydrological and geomorphological dynamics. The response of AS and soil WR to fire depends upon how fire has influenced other key soil properties (e.g. soil OM, mineralogy). Meanwhile, routine thinning of trees and woody vegetation may alter soil properties (e.g. structure and porosity, wettability) by use of heavy machinery and species selection. The study area is situated along a north-facing slope of Mount Carmel national park (Israel). The selected sites are presented as a continuum of management intensity and fire histories. To date, the natural baseline of soil WR has yet to be thoroughly assessed and must be investigated alongside associated soil aggregating parameters in order to understand its overall impact. This study examines (i) the natural baseline of soil WR and physical properties compared to those of disturbed sites in the immediate (controlled burn) and long-term (10-years), and (ii) the interactions of soil properties with different control factors (management, surface cover, seasonal-temporal, burn temperature, soil organic carbon (OC) and mineralogy) in Mediterranean calcareous soils. Analysis of surface soil samples before and after destruction of WR by heating (200-600°C) was implemented using a combination of traditional methods and infrared (IR) spectroscopy. Management and surface cover type conditioned the wettability, soil structure and porosity of soils in the field, although this largely did not affect the heat-induced changes observed in the lab. A positive correlation was observed along an increasing temperature gradient, with relative maxima of MWD and BD reached by most soils at the threshold of 400-500°C. Preliminary analyses of soil OC (MIR) and mineralogical composition (VIS-NIR) support existing research regarding: (i) the importance of soil OC quality and composition in determining wettability rather than quantity, as evidenced both by the high variation observed in the field and the strong presence of aliphatic functional groups in the absence of WR; and (ii) commonly proposed mechanisms affecting soil aggregate properties - albeit with differing temperature thresholds and longer exposure times employed in this study. Namely, these mechanisms tend to involve: (i) soil OM and WR reduction at low to moderate temperatures, and (ii) thermal fusion of particles within moderate to high temperatures. Overall, results suggest a positive influence of management on soil properties as well as high soil resilience to moderate severity fire disturbance in the studied areas. However, the specific changes in soil OM and mineral composition that are responsible for destruction of WR and subsequent changes in AS remain poorly understood. Based on these results, a key next step within this study will entail a closer examination of OC ratios and their potential links with certain mineral species known to influence soil aggregation and soil WR. Noting the importance of soil OM-mineralogical interactions on run-off and erosion processes, results may contribute to better prediction of post-fire responses in the future and improve the ability to fine-tune site specific management approaches accordingly.

Constraints on Martian Soil Composition as Inferred from Viking XRFS and Pathfinder APXS and IMP Data

NASA Technical Reports Server (NTRS)

Bridges, N. T.; Crisp, J. A.

2000-01-01

With the successful operation of the Alpha Proton X-Ray Spectrometer (APXS) during 1997's Mars Pathfinder (MPF) mission, geochemistry data are now available from three sites on Mars. APXS raw spectra for six soils and five rocks have been converted to compositional abundances. The Viking Lander X-Ray Fluorescence Spectrometer (XRFS) successfully measured elemental abundances of nine soils at Viking 1 and eight soils at Viking 2. Although the three landing sites are located in different parts of Mars, the soils exhibit broad similarities, with an iron-rich chemistry similar to that of palagonite. However, the Pathfinder sods show some significant differences from Viking soils, notably an enrichment in silica and depletion in sulfur. The XRFS samples consisted of near-surface and deep (up to 22 cm) soils acquired by a collector head at the cod of a retractable boom. It was possible to collect and analyze pebbles as large a 2 cm, but only sod, some in the form of consolidated clods, was sampled. In contrast, the APXS measured materials in situ. This resulted in MPF "rock" analyses that probably had a significant dust component and, as explored here, "soil" analyses that may have contained a rocky component We examine several possibilities to explain these differences and other attributes of the APXS and XRFS data sets: 1) The APXS soil measurements actually sampled a mixture of Viking-like soil and small bits of high-silica, low-sulfur rock, 2) The soils were derived from high-silica rocks mixed with a minor component of globally-homogenized dust; these soils are chemically distinct and have a separate geologic history from the Viking soils. 3) The weathering environment was different at the Pathfinder landing site compared to the Viking sites, and 4) Uncertainties in the XRFS and APXS measurements result in reported elemental abundances different than those that are actually present We show that none of the possibilities can be discounted, but that an MPF soil distinct in composition from Viking sods is best supported by the available data.

Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils.

PubMed

Romdhane, Sana; Devers-Lamrani, Marion; Barthelmebs, Lise; Calvayrac, Christophe; Bertrand, Cédric; Cooper, Jean-François; Dayan, Franck E; Martin-Laurent, Fabrice

2016-01-01

The ecotoxicological impact of leptospermone, a β-triketone bioherbicide, on the bacterial community of two arable soils was investigated. Soil microcosms were exposed to 0 × (control), 1 × or 10 × recommended dose of leptospermone. The β-triketone was moderately adsorbed to both soils (i.e.,: K fa ~ 1.2 and K oc ~ 140 mL g(-1)). Its dissipation was lower in sterilized than in unsterilized soils suggesting that it was mainly influenced by biotic factors. Within 45 days, leptospermone disappeared almost entirely from one of the two soils (i.e., DT50 < 10 days), while 25% remained in the other. The composition of the microbial community assessed by qPCR targeting 11 microbial groups was found to be significantly modified in soil microcosms exposed to leptospermone. Pyrosequencing of 16S rRNA gene amplicons showed a shift in the bacterial community structure and a significant impact of leptospermone on the diversity of the soil bacterial community. Changes in the composition, and in the α- and β-diversity of microbial community were transient in the soil able to fully dissipate the leptospermone, but were persistent in the soil where β-triketone remained. To conclude the bacterial community of the two soils was sensitive to leptospermone and its resilience was observed only when leptospermone was fully dissipated.

Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils

PubMed Central

Romdhane, Sana; Devers-Lamrani, Marion; Barthelmebs, Lise; Calvayrac, Christophe; Bertrand, Cédric; Cooper, Jean-François; Dayan, Franck E.; Martin-Laurent, Fabrice

2016-01-01

The ecotoxicological impact of leptospermone, a β-triketone bioherbicide, on the bacterial community of two arable soils was investigated. Soil microcosms were exposed to 0 × (control), 1 × or 10 × recommended dose of leptospermone. The β-triketone was moderately adsorbed to both soils (i.e.,: Kfa ~ 1.2 and Koc ~ 140 mL g−1). Its dissipation was lower in sterilized than in unsterilized soils suggesting that it was mainly influenced by biotic factors. Within 45 days, leptospermone disappeared almost entirely from one of the two soils (i.e., DT50 < 10 days), while 25% remained in the other. The composition of the microbial community assessed by qPCR targeting 11 microbial groups was found to be significantly modified in soil microcosms exposed to leptospermone. Pyrosequencing of 16S rRNA gene amplicons showed a shift in the bacterial community structure and a significant impact of leptospermone on the diversity of the soil bacterial community. Changes in the composition, and in the α- and β-diversity of microbial community were transient in the soil able to fully dissipate the leptospermone, but were persistent in the soil where β-triketone remained. To conclude the bacterial community of the two soils was sensitive to leptospermone and its resilience was observed only when leptospermone was fully dissipated. PMID:27252691

Effect of soil composition, temperature, indigenous microflora, and environmental conditions on the survival of Escherichia coli O157:H7.

PubMed

Vidovic, Sinisa; Block, Hushton C; Korber, Darren R

2007-07-01

The survival of Escherichia coli O157:H7 in replicate soil microcosms was quantified in 2 types of silty clay loam soil (high carbon and low carbon) under either sterile or nonsterile conditions. Microcosms were held at -21, 4, and 22 degrees C under constant soil moisture content. Differences existed (P < 0.05) in survival of E. coli O157:H7 in low- and high-carbon soil at all temperatures, indicating an important role of soil composition on the survival of this pathogen. The highest death rate of E. coli O157:H7 in sterile soil occurred in the low-carbon soil at 4 degrees C, whereas in nonsterile soil the highest death rate was observed in the low-carbon soil at 22 degrees C. These results suggest that the most lethal effects on E. coli O157:H7 in the sterile system occurred via the synergy of nutrient limitation and cold stress, whereas in the nonsterile system lethality was owing to inhibition by indigenous soil microorganisms and starvation. Results obtained from an in situ field survival experiment demonstrated the apparent sensitivity of E. coli O157:H7 cells to dehydration, information that may be used to reduce environmental spread of this pathogen as well as formulate appropriate waste management strategies.

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico.

PubMed

Pajares, Silvia; Escalante, Ana E; Noguez, Ana M; García-Oliva, Felipe; Martínez-Piedragil, Celeste; Cram, Silke S; Eguiarte, Luis Enrique; Souza, Valeria

2016-01-01

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m(2) plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca(2), K(+)) and anions (HCO[Formula: see text], Cl(-), SO[Formula: see text]) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.

Soil microbiota respond to green manure in organic vineyards.

PubMed

Longa, C M O; Nicola, L; Antonielli, L; Mescalchin, E; Zanzotti, R; Turco, E; Pertot, I

2017-12-01

The aim of this work was to investigate the effects of biodynamic management with and without the addition of green manure, in comparison with organic management, on the microbiota in vineyards soil. High throughput sequencing was used to compare the taxonomic structure of the soil bacterial and fungal communities from vineyards managed with different methods (organic, biodynamic or biodynamic with green manure). Our results showed that microbial communities associated with biodynamic and organic farming systems were very similar, while green manure was the greatest source of soil microbial biodiversity and significantly changed microbial richness and community composition compared with other soils. Green manure also significantly enriched bacterial taxa involved in the soil nitrogen cycle (e.g. Microvirga sp., Pontibacter sp. and Nitrospira sp.). Our results showed that the diversity and composition of the microbial communities associated with biodynamic and organic farming systems were similar, indicating that the use of biodynamic preparations 500 and 501 did not cause any significant detectable changes to the soil microbial community in the short term, while the effects of green manure were significant in soil microbiota. The microbiological richness and structure of soil are used as a sensitive indicator of soil quality. The extension of organic/biodynamic farming, associated with green manure application, could contribute to increase the abundance of functional groups of biological and agronomical relevance and maintaining microbial biodiversity in vineyard soils. © 2017 The Society for Applied Microbiology.

Major and trace element chemistry of Luna 24 samples from Mare Crisium

NASA Technical Reports Server (NTRS)

Blanchard, D. P.; Brannon, J. C.; Aaboe, E.; Budahn, J. R.

1978-01-01

Atomic absorption spectrometry and instrumental neutron activation analysis were employed to analyze six Luna 24 soils for major and trace elements. The analysis revealed well-mixed soils, though size fractions of each of the soils showed quite dissimilar compositions. Thus the regolith apparently has not been extensively reworked. Noritic breccia admixed preferentially to the finest size fractions and differential comminution of one or more other soil components accounted for the observed elemental distributions as a function of grain size. The ferrobasalt composition and one or more components with higher MgO contents have been identified in the samples.

Soil Sampling Techniques For Alabama Grain Fields

NASA Technical Reports Server (NTRS)

Thompson, A. N.; Shaw, J. N.; Mask, P. L.; Touchton, J. T.; Rickman, D.

2003-01-01

Characterizing the spatial variability of nutrients facilitates precision soil sampling. Questions exist regarding the best technique for directed soil sampling based on a priori knowledge of soil and crop patterns. The objective of this study was to evaluate zone delineation techniques for Alabama grain fields to determine which method best minimized the soil test variability. Site one (25.8 ha) and site three (20.0 ha) were located in the Tennessee Valley region, and site two (24.2 ha) was located in the Coastal Plain region of Alabama. Tennessee Valley soils ranged from well drained Rhodic and Typic Paleudults to somewhat poorly drained Aquic Paleudults and Fluventic Dystrudepts. Coastal Plain s o i l s ranged from coarse-loamy Rhodic Kandiudults to loamy Arenic Kandiudults. Soils were sampled by grid soil sampling methods (grid sizes of 0.40 ha and 1 ha) consisting of: 1) twenty composited cores collected randomly throughout each grid (grid-cell sampling) and, 2) six composited cores collected randomly from a -3x3 m area at the center of each grid (grid-point sampling). Zones were established from 1) an Order 1 Soil Survey, 2) corn (Zea mays L.) yield maps, and 3) airborne remote sensing images. All soil properties were moderately to strongly spatially dependent as per semivariogram analyses. Differences in grid-point and grid-cell soil test values suggested grid-point sampling does not accurately represent grid values. Zones created by soil survey, yield data, and remote sensing images displayed lower coefficient of variations (8CV) for soil test values than overall field values, suggesting these techniques group soil test variability. However, few differences were observed between the three zone delineation techniques. Results suggest directed sampling using zone delineation techniques outlined in this paper would result in more efficient soil sampling for these Alabama grain fields.

Topographic controls on black carbon accumulation in Alaskan black spruce forest soils: implications for organic matter dynamics

Treesearch

E.S. Kane; W.C. Hockaday; M.R. Turetsky; C.A. Masiello; D.W. Valentine; B.P. Finney; J.A. Badlock

2010-01-01

There is still much uncertainty as to how wildfire affects the accumulation of burn residues (such as black carbon [BC]) in the soil, and the corresponding changes in soil organic carbon (SOC) composition in boreal forests. We investigated SOC and BC composition in black spruce forests on different landscape positions in Alaska, USA. Mean BC stocks in surface mineral...

Lignin decomposition and microbial community in paddy soils: effects of alternating redox conditions

NASA Astrophysics Data System (ADS)

Cerli, Chiara; Liu, Qin; Hanke, Alexander; Kaiser, Klaus; Kalbitz, Karsten

2013-04-01

Paddy soils are characterised by interchanging cycles of anaerobic and aerobic conditions. Such fluctuations cause continuous changes in soil solution chemistry as well as in the composition and physiological responses of the microbial community. Temporary deficiency in oxygen creates conditions favourable to facultative or obligates anaerobic bacteria, while aerobic communities can thrive in the period of water absence. These alterations can strongly affect soil processes, in particular organic matter (OM) accumulation and mineralization. In submerged soils, lignin generally constitutes a major portion of the total OM because of hampered degradation under anoxic conditions. The alternating redox cycles resulting from paddy soil management might promote both degradation and preservation of lignin, affecting the overall composition and reactivity of total and dissolved OM. We sampled soils subjected to cycles of anoxic (rice growing period) and oxic (harvest and growth of other crops) conditions since 700 and 2000 years. We incubated suspended Ap material, sampled from the two paddy plus two corresponding non-paddy control soils under oxic and anoxic condition, for 3 months, interrupted by a short period of three weeks (from day 21 to day 43) with reversed redox conditions. At each sampling time (day 2, 21, 42, 63, 84), we determined lignin-derived phenols (by CuO oxidation) as well as phospholipids fatty acids contents and composition. We aimed to highlight changes in lignin decomposition as related to the potential rapid changes in microbial community composition. Since the studied paddy soils had a long history of wet rice cultivation, the microbial community should be well adapted to interchanging oxic and anoxic cycles, therefore fully expressing its activity at both conditions. In non-paddy soil changes in redox conditions caused modification of quantity and composition of the microbial community. On the contrary, in well-established paddy soils the microbial community appeared to be affected by alternating redox conditions more in quantity that in quality. Bacteria represented the largest portion of the living microorganisms, responding promptly to changes in soil redox status. However we did not detect any sign of lignin biodegradation. Relative short (3 weeks) changes in redox conditions had no effect on lignin decomposition or oxidation state. Also, lignin was not altered during oxic incubation. Since fungi represented only small portion of the microbial biomass in the studied soils, they were obviously not capable to cause much degradation, even under favourable conditions. On the contrary, changes in redox conditions strongly affected lignin extractability, regardless of the initial content and direction of change in both paddy and non-paddy soils. This was likely a result of (partial) dissolution and/or pH-induced changes of the surface properties of Fe and Mn hydrous oxides causing the release of mineral-associated lignin-derived phenols. Thus, we speculate that oxidised lignin fragments produced during the (oxic) dry period do not remain in the soils but percolate with water drainage during the flooding period.

Soil management shapes ecosystem service provision and trade-offs in agricultural landscapes.

PubMed

Tamburini, Giovanni; De Simone, Serena; Sigura, Maurizia; Boscutti, Francesco; Marini, Lorenzo

2016-08-31

Agroecosystems are principally managed to maximize food provisioning even if they receive a large array of supporting and regulating ecosystem services (ESs). Hence, comprehensive studies investigating the effects of local management and landscape composition on the provision of and trade-offs between multiple ESs are urgently needed. We explored the effects of conservation tillage, nitrogen fertilization and landscape composition on six ESs (crop production, disease control, soil fertility, water quality regulation, weed and pest control) in winter cereals. Conservation tillage enhanced soil fertility and pest control, decreased water quality regulation and weed control, without affecting crop production and disease control. Fertilization only influenced crop production by increasing grain yield. Landscape intensification reduced the provision of disease and pest control. We also found tillage and landscape composition to interactively affect water quality regulation and weed control. Under N fertilization, conventional tillage resulted in more trade-offs between ESs than conservation tillage. Our results demonstrate that soil management and landscape composition affect the provision of several ESs and that soil management potentially shapes the trade-offs between them. © 2016 The Author(s).

The influence of soil organic matter chemistry and site/soil properties in predicting the decomposability of tundra soils

NASA Astrophysics Data System (ADS)

Matamala, R.; Jastrow, J. D.; Fan, Z.; Liang, C.; Calderon, F.; Michaelson, G.; Mishra, U.; Ping, C. L.

2017-12-01

With the increase in high latitude warming, there is a need to better understand the potential vulnerability of soil organic matter (SOM) stored in Arctic regions. In this study, we used mid infrared spectroscopy (MidIR) to determine the influence of soil chemistry and site properties in the short-term mineralization potential of SOM stored in tundra soils. Soils from the active and permafrost layers were collected from four tundra sites on the Coastal Plain, and Arctic Foothills of the North Slope of Alaska and were incubated for 60 days at a range of temperatures. Site and soil properties including acidic versus non-acidic tundra, lowland versus upland areas, total soil organic carbon (TOC) and total nitrogen (TN) concentrations, 60-day carbon mineralization potential (CMP), MidIR spectra and the chemical composition of the SOM stored in these soils were determined. Partial least squares (PLS) models for CMP versus MidIR spectra were produced upon splitting the dataset into site and soil properties categories. We found that SOM composition determined by MidIR spectroscopy was most effective in predicting CMP for tundra soils and it was most relevant for the active-layer mineral and upper permafrost soil horizons and/or soils with C concentrations of 10% or lower. Analysis of the factor loadings and standardized beta coefficients from the CMP PLS models indicated that spectral bands associated with clay contents, phenolic OH, aliphatic, silicates, carboxylic acids, and polysaccharides were influential for lower TOC soils, but these bands were less important for higher TOC soils. High TOC soils were influenced by a combination of other factors. Our results suggest that different factors affect the short-term CMP of SOM in tundra soils depending on the amount of TOC present. We show MidIR as a powerful tool for quickly and reasonably estimating the short-term CMP of tundra soils. Widespread application of MidIR measurements to already collected and archived tundra region soils could provide a quick and reliable assessment of the CMP of these soils, reduce the need for incubation studies, and contribute to upscaling and model benchmarking of SOM mineralization of tundra soils.

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition

PubMed Central

Bang-Andreasen, Toke; Nielsen, Jeppe T.; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C. B.; Jacobsen, Carsten S.

2017-01-01

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha-1. We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha-1 to alkaline at 167 t ha-1. Bacterial numbers significantly increased up to a wood ash dose of 22 t ha-1 followed by significant decrease at 167 t ha-1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha-1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha-1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha-1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly explained by the wood ash induced changes in pH, electrical conductivity and the addition of wood ash inherent nutrients. PMID:28804476

Wood Ash Induced pH Changes Strongly Affect Soil Bacterial Numbers and Community Composition.

PubMed

Bang-Andreasen, Toke; Nielsen, Jeppe T; Voriskova, Jana; Heise, Janine; Rønn, Regin; Kjøller, Rasmus; Hansen, Hans C B; Jacobsen, Carsten S

2017-01-01

Recirculation of wood ash from energy production to forest soil improves the sustainability of this energy production form as recycled wood ash contains nutrients that otherwise would be lost at harvest. In addition, wood-ash is beneficial to many soils due to its inherent acid-neutralizing capabilities. However, wood ash has several ecosystem-perturbing effects like increased soil pH and pore water electrical conductivity both known to strongly impact soil bacterial numbers and community composition. Studies investigating soil bacterial community responses to wood ash application remain sparse and the available results are ambiguous and remain at a general taxonomic level. Here we investigate the response of bacterial communities in a spruce forest soil to wood ash addition corresponding to 0, 5, 22, and 167 t wood ash ha -1 . We used culture-based enumerations of general bacteria, Pseudomonas and sporeforming bacteria combined with 16S rRNA gene amplicon sequencing to valuate soil bacterial responses to wood ash application. Results showed that wood ash addition strongly increased soil pH and electrical conductivity. Soil pH increased from acidic through neutral at 22 t ha -1 to alkaline at 167 t ha -1 . Bacterial numbers significantly increased up to a wood ash dose of 22 t ha -1 followed by significant decrease at 167 t ha -1 wood ash. The soil bacterial community composition changed after wood ash application with copiotrophic bacteria responding positively up to a wood ash dose of 22 t ha -1 while the adverse effect was seen for oligotrophic bacteria. Marked changes in bacterial community composition occurred at a wood ash dose of 167 t ha -1 with a single alkaliphilic genus dominating. Additionally, spore-formers became abundant at an ash dose of 167 t ha -1 whereas this was not the case at lower ash doses. Lastly, bacterial richness and diversity strongly decreased with increasing amount of wood ash applied. All of the observed bacterial responses can be directly explained by the wood ash induced changes in pH, electrical conductivity and the addition of wood ash inherent nutrients.

Interactive effects of elevated CO2 and nitrogen deposition on fatty acid molecular and isotope composition of above- and belowground tree biomass and forest soil fractions.

PubMed

Griepentrog, Marco; Eglinton, Timothy I; Hagedorn, Frank; Schmidt, Michael W I; Wiesenberg, Guido L B

2015-01-01

Atmospheric carbon dioxide (CO2) and reactive nitrogen (N) concentrations have been increasing due to human activities and impact the global carbon (C) cycle by affecting plant photosynthesis and decomposition processes in soil. Large amounts of C are stored in plants and soils, but the mechanisms behind the stabilization of plant- and microbial-derived organic matter (OM) in soils are still under debate and it is not clear how N deposition affects soil OM dynamics. Here, we studied the effects of 4 years of elevated (13C-depleted) CO2 and N deposition in forest ecosystems established in open-top chambers on composition and turnover of fatty acids (FAs) in plants and soils. FAs served as biomarkers for plant- and microbial-derived OM in soil density fractions. We analyzed above- and belowground plant biomass of beech and spruce trees as well as soil density fractions for the total organic C and FA molecular and isotope (δ13C) composition. FAs did not accumulate relative to total organic C in fine mineral fractions, showing that FAs are not effectively stabilized by association with soil minerals. The δ13C values of FAs in plant biomass increased under high N deposition. However, the N effect was only apparent under elevated CO2 suggesting a N limitation of the system. In soil fractions, only isotope compositions of short-chain FAs (C16+18) were affected. Fractions of 'new' (experimental-derived) FAs were calculated using isotope depletion in elevated CO2 plots and decreased from free light to fine mineral fractions. 'New' FAs were higher in short-chain compared to long-chain FAs (C20-30), indicating a faster turnover of short-chain compared to long-chain FAs. Increased N deposition did not significantly affect the quantity of 'new' FAs in soil fractions, but showed a tendency of increased amounts of 'old' (pre-experimental) C suggesting that decomposition of 'old' C is retarded by high N inputs. © 2014 John Wiley & Sons Ltd.

Nitrogen Addition Altered the Effect of Belowground C Allocation on Soil Respiration in a Subtropical Forest

PubMed Central

He, Tongxin; Wang, Qingkui; Wang, Silong; Zhang, Fangyue

2016-01-01

The availabilities of carbon (C) and nitrogen (N) in soil play an important role in soil carbon dioxide (CO2) emission. However, the variation in the soil respiration (Rs) and response of microbial community to the combined changes in belowground C and N inputs in forest ecosystems are not yet fully understood. Stem girdling and N addition were performed in this study to evaluate the effects of C supply and N availability on Rs and soil microbial community in a subtropical forest. The trees were girdled on 1 July 2012. Rs was monitored from July 2012 to November 2013, and soil microbial community composition was also examined by phospholipid fatty acids (PLFAs) 1 year after girdling. Results showed that Rs decreased by 40.5% with girdling alone, but N addition only did not change Rs. Interestingly, Rs decreased by 62.7% under the girdling with N addition treatment. The reducing effect of girdling and N addition on Rs differed between dormant and growing seasons. Girdling alone reduced Rs by 33.9% in the dormant season and 54.8% in the growing season compared with the control. By contrast, girdling with N addition decreased Rs by 59.5% in the dormant season and 65.4% in the growing season. Girdling and N addition significantly decreased the total and bacterial PLFAs. Moreover, the effect of N addition was greater than girdling. Both girdling and N addition treatments separated the microbial groups on the basis of the first principal component through principal component analysis compared with control. This indicated that girdling and N addition changed the soil microbial community composition. However, the effect of girdling with N addition treatment separated the microbial groups on the basis of the second principal component compared to N addition treatment, which suggested N addition altered the effect of girdling on soil microbial community composition. These results suggest that the increase in soil N availability by N deposition alters the effect of belowground C allocation on the decomposition of soil organic matter by altering the composition of the soil microbial community. PMID:27213934

Plant rhizosphere species-specific stoichiometry and regulation of extracellular enzyme and microbial community structure

NASA Astrophysics Data System (ADS)

Bell, C. W.; Calderon, F.; Pendall, E.; Wallenstein, M. D.

2012-12-01

Plant communities affect the activity and composition of soil microbial communities through alteration of the soil environment during root growth; substrate availability through root exudation; nutrient availability through plant uptake; and moisture regimes through transpiration. As a result, positive feedbacks in soil properties can result from alterations in microbial community composition and function in the rhizosphere zone. At the ecosystem-scale, many properties of soil microbial communities can vary between forest stands dominated by different species, including community composition and stoichiometry. However, the influence of smaller individual plants on grassland soils and microbial communities is less well documented. There is evidence to suggest that some plants can modify their soil environment in a manner that favors their persistence. For example, when Bromus tectorum plants invade, soil microbial communities tend to have higher N mineralization rates (in the rhizosphere zone) relative to native plants. If tight linkages between individual plant species and microbial communities inhabiting the rhizosphere exist, we hypothesized that any differences among plant species specific rhizosphere zones could be observed by shifts in: 1) soil -rhizosphere microbial community structure, 2) enzymatic C:N:P acquisition activities, 3) alterations in the soil C chemistry composition in the rhizosphere, and 4) plant - soil - microbial C:N:P elemental stoichiometry. We selected and grew 4 different C3 grasses species including three species native to the Shortgrass Steppe region (Pascopyrum smithii, Koeleria macrantha, and Vulpia octoflora) and one exotic invasive plant species (B. tectorum) in root-boxes that are designed to allow for easy access to the rhizosphere. The field soil was homogenized using a 4mm sieve and mixed 1:1 with sterile sand and seeded as monocultures (24 replicate root - boxes for each species). Plant and soil samples (along with no - plant control soil samples) were collected on day 28, 78, and 148 (N = 4 /sample period/species). Microbial community structure was quantified using the barcoded pyrosequencing protocols. We measured the potential activity of seven hydrolytic soil enzymes to represent the degradation of C, N, and P-rich substrates. Soil microbial C:N biomass responses to specific plant rhizospheres (MBC and MBN) were measured using the chloroform fumigation extraction method followed by DOC & N analysis. Fourier Transform Infrared Spectroscopy was used to assess differences in plant and soil C chemistry. We found that species specific rhizospheres are characteristic of very different soil chemical, edaphic, and microbial properties. These plant species act as gateways that introduce variability into soil C, N, and P ecosystem functional dynamics directly facilitated by rhizosphere - microbe associations. Our results suggest that nutrient stoichiometry within plant species' rhizospheres is a useful tool for identifying intra-ecosystem functional patterns. By identifying what and how specific species rhizospheres differ among the overall plant community, we can better predict how below-ground microbial community function and subsequent ecosystem processes can be influenced by alterations in plant community shifts based on the rhizosphere effects.

Effects of the seasonal flooding on riparian soil seed bank in the Three Gorges Reservoir Region: a case study in Shanmu River.

PubMed

Zhang, Miao; Chen, Fangqing; Chen, Shaohua; Wang, Yajin; Wang, Jianzhu

2016-01-01

The water-level fluctuation in the Three Gorges Reservoir Region has changed dramatically as a result of the hydroelectric project for flood control and power generation. The riparian seasonal hydrological environment also has changed from summer flooding with winter drought to summer drought with winter flooding. The changes of riparian seed bank and vegetation were investigated to determine the effects of the seasonal flooding on the composition and spatial distribution of riparian soil seed bank and the similarity of seed bank to standing vegetation. We conducted intensive riparian soil sampling (525 samples) along altitude gradient in the Shanmu River, a tributary of the Yangzi River in the reservoir region of China. Seed bank density, species richness and composition of soil seed bank were examined using the seedling-emergence method. The seasonal hydrological conditions resulted in a decrease in species diversity and an increase in the distribution heterogeneity of the soil seed bank. The soil seed bank was composed of 48 species from 22 families and 40 genera. Most species were annual and perennial herbaceous Polygonaceae, Asteraceae, and Poaceae. Rumex dentatus was the predominant species accounting for 27.0 % of the total seeds. Diversity and composition of the seed bank changed along an altitude gradient and soil depth. Maximum species richness was found in the top soil layer at 165 m and 175 m above sea level. The mean overall seed density of the soil seed bank was 13,475.3 ind m(-2). Density and the number of seeds increased initially and then decreased with increased altitude. Maximum seed density (22,500.2 ind m(-2)) was found at 165 m above sea level in the intermediately flooded riverbank, with the seed number accounting for 27.8 % of the total soil seed bank. Average seed density declined significantly with soil depth. The similarity of seed bank to standing vegetation was relatively high. The environmental heterogeneity created by the wide range and seasonal flooding led to the changes in biodiversity and seed density along altitude gradient. The seasonal flooding also led to the increase in the similarity of seed bank to standing vegetation as their composition both degraded. The seasonal flooding due to the dam reshape the composition and spatial distribution of riparian soil seed bank and limit the vegetation to a grassland dominated by a few annuals and perennials in the Three Gorges Reservoir Region.

Soil pH determines microbial diversity and composition in the park grass experiment.

PubMed

Zhalnina, Kateryna; Dias, Raquel; de Quadros, Patricia Dörr; Davis-Richardson, Austin; Camargo, Flavio A O; Clark, Ian M; McGrath, Steve P; Hirsch, Penny R; Triplett, Eric W

2015-02-01

The Park Grass experiment (PGE) in the UK has been ongoing since 1856. Its purpose is to study the response of biological communities to the long-term treatments and associated changes in soil parameters, particularly soil pH. In this study, soil samples were collected across pH gradient (pH 3.6-7) and a range of fertilizers (nitrogen as ammonium sulfate, nitrogen as sodium nitrate, phosphorous) to evaluate the effects nutrients have on soil parameters and microbial community structure. Illumina 16S ribosomal RNA (rRNA) amplicon sequencing was used to determine the relative abundances and diversity of bacterial and archaeal taxa. Relationships between treatments, measured soil parameters, and microbial communities were evaluated. Clostridium, Bacteroides, Bradyrhizobium, Mycobacterium, Ruminococcus, Paenibacillus, and Rhodoplanes were the most abundant genera found at the PGE. The main soil parameter that determined microbial composition, diversity, and biomass in the PGE soil was pH. The most probable mechanism of the pH impact on microbial community may include mediation of nutrient availability in the soil. Addition of nitrogen to the PGE plots as ammonium sulfate decreases soil pH through increased nitrification, which causes buildup of soil carbon, and hence increases C/N ratio. Plant species richness and plant productivity did not reveal significant relationships with microbial diversity; however, plant species richness was positively correlated with soil microbial biomass. Plants responded to the nitrogen treatments with an increase in productivity and a decrease in the species richness.

Bacterial community composition in Brazilian Anthrosols and adjacent soils characterized using culturing and molecular identification.

PubMed

O'Neill, B; Grossman, J; Tsai, M T; Gomes, J E; Lehmann, J; Peterson, J; Neves, E; Thies, J E

2009-07-01

Microbial community composition was examined in two soil types, Anthrosols and adjacent soils, sampled from three locations in the Brazilian Amazon. The Anthrosols, also known as Amazonian dark earths, are highly fertile soils that are a legacy of pre-Columbian settlement. Both Anthrosols and adjacent soils are derived from the same parent material and subject to the same environmental conditions, including rainfall and temperature; however, the Anthrosols contain high levels of charcoal-like black carbon from which they derive their dark color. The Anthrosols typically have higher cation exchange capacity, higher pH, and higher phosphorus and calcium contents. We used culture media prepared from soil extracts to isolate bacteria unique to the two soil types and then sequenced their 16S rRNA genes to determine their phylogenetic placement. Higher numbers of culturable bacteria, by over two orders of magnitude at the deepest sampling depths, were counted in the Anthrosols. Sequences of bacteria isolated on soil extract media yielded five possible new bacterial families. Also, a higher number of families in the bacteria were represented by isolates from the deeper soil depths in the Anthrosols. Higher bacterial populations and a greater diversity of isolates were found in all of the Anthrosols, to a depth of up to 1 m, compared to adjacent soils located within 50-500 m of their associated Anthrosols. Compared to standard culture media, soil extract media revealed diverse soil microbial populations adapted to the unique biochemistry and physiological ecology of these Anthrosols.

Soil fungal abundance and diversity: another victim of the invasive plant Centaurea maculosa.

PubMed

Broz, Amanda K; Manter, Daniel K; Vivanco, Jorge M

2007-12-01

Interactions between plants and soil microbes are important determinants of both above- and belowground community composition, and ultimately ecosystem function. As exotic plants continue to invade and modify native plant communities, there has been increasing interest in determining the influence of exotic invasives on native soil microbial communities. Here, using highly sensitive molecular techniques, we examine fungal abundance and diversity in the soil surrounding a particularly aggressive invasive plant species in North America, Centaurea maculosa Lam. In mixed stands, we show that this invasive weed can alter the native fungal community composition within its own rhizosphere and that of neighboring native plants. At higher densities, the effect of C. maculosa on native soil fungal communities was even greater. Our results demonstrate that this invasive weed can have significant effects not only on visible aboveground biodiversity but also on the native soil microbial community that extends beyond its rhizosphere.

JMSS-1: a new Martian soil simulant

NASA Astrophysics Data System (ADS)

Zeng, Xiaojia; Li, Xiongyao; Wang, Shijie; Li, Shijie; Spring, Nicole; Tang, Hong; Li, Yang; Feng, Junming

2015-05-01

It is important to develop Martian soil simulants that can be used in Mars exploration programs and Mars research. A new Martian soil simulant, called Jining Martian Soil Simulant (JMSS-1), was developed at the Lunar and Planetary Science Research Center at the Institute of Geochemistry, Chinese Academy of Sciences. The raw materials of JMSS-1 are Jining basalt and Fe oxides (magnetite and hematite). JMSS-1 was produced by mechanically crushing Jining basalt with the addition of small amounts of magnetite and hematite. The properties of this simulant, including chemical composition, mineralogy, particle size, mechanical properties, reflectance spectra, dielectric properties, volatile content, and hygroscopicity, have been analyzed. On the basis of these test results, it was demonstrated that JMSS-1 is an ideal Martian soil simulant in terms of chemical composition, mineralogy, and physical properties. JMSS-1 would be an appropriate choice as a Martian soil simulant in scientific and engineering experiments in China's Mars exploration in the future.

[Distribution characteristics of soil organic carbon and its composition in Suaeda salsa wetland in the Yellow River delta].

PubMed

Dong, Hong-Fang; Yu, Jun-Bao; Guan, Bo

2013-01-01

Applying the method of physical fractionation, distribution characteristics of soil organic carbon and its composition in Suaeda salsa wetland in the Yellow River delta were studied. The results showed that the heavy fraction organic carbon was the dominant component of soil organic carbon in the studied region. There was a significantly positive relationship between the content of heavy fraction organic carbon, particulate organic carbon and total soil organic carbon. The ranges of soil light fraction organic carbon ratio and content were 0.008% - 0.15% and 0.10-0.40 g x kg(-1), respectively, and the range of particulate organic carbon ratio was 8.83% - 30.58%, indicating that the non-protection component of soil organic carbon was low and the carbon pool was relatively stable in Suaeda salsa wetland of the Yellow River delta.

Restoration of Soils and Vegetation on Reclamation Sites of the Kingisepp Phosphorite Field

NASA Astrophysics Data System (ADS)

Dmitrakova, Ya. A.; Abakumov, E. V.

2018-05-01

Processes of initial soil formation were studied on long-term monitoring plots on dump rocks of quarry no. 3 of the Phosphorite production company in Kingisepp district of Leningrad oblast. Observations were performed in 1998, 2004, and 2014. It was shown that vegetation succession on the plots proceeds relatively quickly, and that the species composition of phytocenoses formed is typical of the areas with soddy-calcareous soils. Soil development proved to be correlated with the development of vegetation. Maximum changes in soil characteristics were observed with an increase in the density of forest vegetation and a decrease in the role of herbs. The molecular composition of humic acids in the studied soils remained stable; in particular, the ratio of aliphatic to alkyl aromatic fragments was virtually constant. This phenomenon could be due to the great amount of aliphatic components in the falloff of coniferous species subjected to humification.

Phosphorus Dynamics in High Latitude Soils

NASA Astrophysics Data System (ADS)

Vincent, A. G.; Vestergren, J.; Gröbner, G.; Wardle, D.; Schleucher, J.; Giesler, R.

2016-12-01

Phosphorus (P) is an important macronutrient in boreal forests and arctic and subarctic tundra, and elucidating the factors that control its bioavailability is essential to understand the function of these ecosystems, now and under global change. We tested several hypotheses about differences in soil P composition along natural gradients of temperature, ecosystem development, soil metal concentration, and fire frequency in Northern Sweden. To characterise P composition we used traditional soil P fractionation procedures as well as 1-dimensional 31P Nuclear Magnetic Resonance (NMR) and novel 2-dimensional 1H-31P NMR techniques. Here we synthesize the main patterns emerging from this work. Temperature seems to be an important driver of P bioavailability regardless of vegetation type in subarctic tundra, given a positive correlation between temperature and the concentration of bioavailable soil P along an elevational gradient. In boreal forest, stage of ecosystem development along a 7800 year old chronosequence created by glacial isostatic adjustment was associated with marked, yet not unidirectional, shifts in the composition of soil P, which suggests ongoing changes in unknown ecological processes. Naturally higher concentrations of iron and aluminium in soils due to groundwater recharge and discharge were related with higher concentrations of P compounds widely considered to be recalcitrant, such as inositol phosphates. Finally, retrogressive forest ecosystems with low productivity growing on old soils did not have a relatively higher proportion of recalcitrant organic P compounds, contrary to our expectations based on current biogeochemistry theory. Finally, one of our most enigmatic findings is the high relative abundance of labile P compounds such as RNA in soil. This would suggest that a great proportion of soil P is located within live microbial cells, and therefore that microbial dynamics are a crucial control on P bioavailability in these ecosystems.

Field measures show methanotroph sensitivity to soil moisture follows precipitation regime of the grassland sites across the US Great Plains

NASA Astrophysics Data System (ADS)

Koyama, A.; Webb, C. T.; Johnson, N. G.; Brewer, P. E.; von Fischer, J. C.

2015-12-01

Methane uptake rates are known to have temporal variation in response to changing soil moisture levels. However, the relative importance of soil diffusivity vs. methanotroph physiology has not been disentangled to date. Testing methanotroph physiology in the laboratory can lead to misleading results due to changes in the fine-scale habitat where methanotrophs reside. To assay the soil moisture sensitivity of methanotrophs under field conditions, we studied 22 field plots scattered across eight Great Plains grassland sites that differed in precipitation regime and soil moisture, making ca. bi-weekly measures during the growing seasons over three years. Quantification of methanotroph activity was achieved from chamber-based measures of methane uptake coincident with SF6-derived soil diffusivity, and interpretation in a reaction-diffusion model. At each plot, we also measured soil water content (SWC), soil temperature and inorganic nitrogen (N) contents. We also assessed methanotroph community composition via 454 sequencing of the pmoA gene. Statistical analyses showed that methanotroph activity had a parabolic response with SWC (concave down), and significant differences in the shape of this response among sites. Moreover, we found that the SWC at peak methanotroph activity was strongly correlated with mean annual precipitation (MAP) of the site. The sequence data revealed distinct composition patterns, with structure that was associated with variation in MAP and soil texture. These results suggest that local precipitation regime shapes methanotroph community composition, which in turn lead to unique sensitivity of methane uptake rates with soil moisture. Our findings suggest that methanotroph activity may be more accurately modeled when the biological and environmental responses are explicitly described.

Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert.

PubMed

Řeháková, Klára; Chroňáková, Alica; Krištůfek, Václav; Kuchtová, Barbora; Čapková, Kateřina; Scharfen, Josef; Čapek, Petr; Doležal, Jiří

2015-01-01

Although bacterial assemblages are important components of soils in arid ecosystems, the knowledge about composition, life-strategies, and environmental drivers is still fragmentary, especially in remote high-elevation mountains. We compared the quality and quantity of heterotrophic bacterial assemblages between the rhizosphere of the dominant cushion-forming plant Thylacospermum ceaspitosum and its surrounding bulk soil in two mountain ranges (East Karakoram: 4850-5250 m and Little Tibet: 5350-5850 m), in communities from cold steppes to the subnival zone in Ladakh, arid Trans-Himalaya, northwest India. Bacterial communities were characterized by molecular fingerprinting in combination with culture-dependent methods. The effects of environmental factors (elevation, mountain range, and soil physico-chemical parameters) on the bacterial community composition and structure were tested by multivariate redundancy analysis and conditional inference trees. Actinobacteria dominate the cultivable part of community and represent a major bacterial lineage of cold desert soils. The most abundant genera were Streptomyces, Arthrobacter, and Paenibacillus, representing both r- and K-strategists. The soil texture is the most important factor for the community structure and the total bacteria counts. Less abundant and diverse assemblages are found in East Karakoram with coarser soils derived from leucogranite bedrock, while more diverse assemblages in Little Tibet are associated with finer soils derived from easily weathering gneisses. Cushion rhizosphere is in general less diverse than bulk soil, and contains more r-strategists. K-strategists are more associated with the extremes of the gradient, with drought at lowest elevations (4850-5000 m) and frost at the highest elevations (5750-5850 m). The present study illuminates the composition of soil bacterial assemblages in relation to the cushion plant T. ceaspitosum in a xeric environment and brings important information about heterotrophic bacteria in Himalayan soil.

Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters.

PubMed

de Menezes, Alexandre B; Prendergast-Miller, Miranda T; Richardson, Alan E; Toscas, Peter; Farrell, Mark; Macdonald, Lynne M; Baker, Geoff; Wark, Tim; Thrall, Peter H

2015-08-01

Network and multivariate statistical analyses were performed to determine interactions between bacterial and fungal community terminal restriction length polymorphisms as well as soil properties in paired woodland and pasture sites. Canonical correspondence analysis (CCA) revealed that shifts in woodland community composition correlated with soil dissolved organic carbon, while changes in pasture community composition correlated with moisture, nitrogen and phosphorus. Weighted correlation network analysis detected two distinct microbial modules per land use. Bacterial and fungal ribotypes did not group separately, rather all modules comprised of both bacterial and fungal ribotypes. Woodland modules had a similar fungal : bacterial ribotype ratio, while in the pasture, one module was fungal dominated. There was no correspondence between pasture and woodland modules in their ribotype composition. The modules had different relationships to soil variables, and these contrasts were not detected without the use of network analysis. This study demonstrated that fungi and bacteria, components of the soil microbial communities usually treated as separate functional groups as in a CCA approach, were co-correlated and formed distinct associations in these adjacent habitats. Understanding these distinct modular associations may shed more light on their niche space in the soil environment, and allow a more realistic description of soil microbial ecology and function. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Changes of soil prokaryotic communities after clear-cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes.

PubMed

Zhang, Xiao; Liu, Shirong; Li, Xiangzhen; Wang, Jingxin; Ding, Qiong; Wang, Hui; Tian, Chao; Yao, Minjie; An, Jiaxing; Huang, Yongtao

2016-03-01

To understand the temporal responses of soil prokaryotic communities to clear-cutting disturbance, we examined the changes in soil bacterial and archaeal community composition, structure and diversity along a chronosequence of forest successional restoration using high-throughput 16S rRNA gene sequencing. Our results demonstrated that clear-cutting significantly altered soil bacterial community structure, while no significant shifts of soil archaeal communities were observed. The hypothesis that soil bacterial communities would become similar to those of surrounding intact primary forest with natural regeneration was supported by the shifts in the bacterial community composition and structure. Bacterial community diversity patterns induced by clear-cutting were consistent with the intermediate disturbance hypothesis. Dynamics of bacterial communities was mostly driven by soil properties, which collectively explained more than 70% of the variation in bacterial community composition. Community assembly data revealed that clear-cutting promoted the importance of the deterministic processes in shaping bacterial communities, coinciding with the resultant low resource environments. But assembly processes in the secondary forest returned a similar level compared to the intact primary forest. These findings suggest that bacterial community dynamics may be predictable during the natural recovery process. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Compositional differences in simulated root exudates elicit a limited functional and compositional response in soil microbial communities.

PubMed

Strickland, Michael S; McCulley, Rebecca L; Nelson, Jim A; Bradford, Mark A

2015-01-01

Inputs of low molecular weight carbon (LMW-C) to soil - primarily via root exudates- are expected to be a major driver of microbial activity and source of stable soil organic carbon. It is expected that variation in the type and composition of LMW-C entering soil will influence microbial community composition and function. If this is the case then short-term changes in LMW-C inputs may alter processes regulated by these communities. To determine if change in the composition of LMW-C inputs influences microbial community function and composition, we conducted a 90 day microcosm experiment whereby soils sourced from three different land covers (meadows, deciduous forests, and white pine stands) were amended, at low concentrations, with one of eight simulated root exudate treatments. Treatments included no addition of LMW-C, and the full factorial combination of glucose, glycine, and oxalic acid. After 90 days, we conducted a functional response assay and determined microbial composition via phospholipid fatty acid analysis. Whereas we noted a statistically significant effect of exudate treatments, this only accounted for ∼3% of the variation observed in function. In comparison, land cover and site explained ∼46 and ∼41% of the variation, respectively. This suggests that exudate composition has little influence on function compared to site/land cover specific factors. Supporting the finding that exudate effects were minor, we found that an absence of LMW-C elicited the greatest difference in function compared to those treatments receiving any LMW-C. Additionally, exudate treatments did not alter microbial community composition and observable differences were instead due to land cover. These results confirm the strong effects of land cover/site legacies on soil microbial communities. In contrast, short-term changes in exudate composition, at meaningful concentrations, may have little impact on microbial function and composition.

Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

PubMed Central

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P. A.; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes

Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale.

PubMed

Chemidlin Prévost-Bouré, Nicolas; Dequiedt, Samuel; Thioulouse, Jean; Lelièvre, Mélanie; Saby, Nicolas P A; Jolivet, Claudy; Arrouays, Dominique; Plassart, Pierre; Lemanceau, Philippe; Ranjard, Lionel

2014-01-01

Spatial scaling of microorganisms has been demonstrated over the last decade. However, the processes and environmental filters shaping soil microbial community structure on a broad spatial scale still need to be refined and ranked. Here, we compared bacterial and fungal community composition turnovers through a biogeographical approach on the same soil sampling design at a broad spatial scale (area range: 13300 to 31000 km2): i) to examine their spatial structuring; ii) to investigate the relative importance of environmental selection and spatial autocorrelation in determining their community composition turnover; and iii) to identify and rank the relevant environmental filters and scales involved in their spatial variations. Molecular fingerprinting of soil bacterial and fungal communities was performed on 413 soils from four French regions of contrasting environmental heterogeneity (Landes

Alterations of lead speciation by sulfate from addition of flue gas desulfurization gypsum (FGDG) in two contaminated soils

EPA Science Inventory

This is the first study to evaluate the potential application of FGDG as an in situ Pb stabilizer in contaminated soils with two different compositions and to explain the underlying mechanisms. A smelter Pb contaminated soil (SM-soil), rich in ferrihydrite bound Pb (FH-Pb), ceru...

Seasonal switchgrass ecotype contributions to soil organic carbon, deep soil microbial community composition and rhizodeposit uptake during an extreme drought

USDA-ARS?s Scientific Manuscript database

More than 50% of the world’s soil C stocks reside below 30 cm, but relatively little is known about the importance of rhizodeposit C and associated microbial communities in deep soil processes. Phenotypic variability in plant root biomass could impact C cycling through belowground plant allocation,...

Indexing Soil Conservation: Farmer Perceptions of Agroforestry Benefits

Treesearch

Subhrendu K. Pattanayak; D. Evan Mercer

2002-01-01

Soil erosion poses economic and environmental concerns in many tropical uplands. Agroforestry has been proposed as a sustainable land use that can mitigate soil erosion and promote the economic welfare of small farmers. To evaluate such claims, we must (a) develop a composite measure of effectiveness, such as a soil conservation index, and (b) define it in terms...

Biological soil crust succession impact on soil moisture and temperature in the sub-surface along a rainfall gradient

NASA Astrophysics Data System (ADS)

Zaady, E.; Yizhaq, H.; Ashkenazy, Y.

2012-04-01

Biological soil crusts produce mucilage sheets of polysaccharides that cover the soil surface. This hydrophobic coating can seal the soil micro-pores and thus cause reduction of water permeability and may influence soil temperature. This study evaluates the impact of crust composition on sub-surface water and temperature over time. We hypothesized that the successional stages of biological soil crusts, affect soil moisture and temperature differently along a rainfall gradient throughout the year. Four experimental sites were established along a rainfall gradient in the western Negev Desert. At each site three treatments; crust removal, pure sand (moving dune) and natural crusted were monitored. Crust successional stage was measured by biophysiological and physical measurements, soil water permeability by field mini-Infiltrometer, soil moisture by neutron scattering probe and temperature by sensors, at different depths. Our main interim conclusions from the ongoing study along the rainfall gradient are: 1. the biogenic crust controls water infiltration into the soil in sand dunes, 2. infiltration was dependent on the composition of the biogenic crust. It was low for higher successional stage crusts composed of lichens and mosses and high with cyanobacterial crust. Thus, infiltration rate controlled by the crust is inverse to the rainfall gradient. Continuous disturbances to the crust increase infiltration rates, 3. despite the different rainfall amounts at the sites, soil moisture content below 50 cm is almost the same. We therefore predict that climate change in areas that are becoming dryer (desertification) will have a positive effect on soil water content and vice versa.

Colonization and community structure of root-associated microorganisms of Sabina vulgaris with soil depth in a semiarid desert ecosystem with shallow groundwater.

PubMed

Taniguchi, Takeshi; Usuki, Hiroyuki; Kikuchi, Junichi; Hirobe, Muneto; Miki, Naoko; Fukuda, Kenji; Zhang, Guosheng; Wang, Linhe; Yoshikawa, Ken; Yamanaka, Norikazu

2012-08-01

Arbuscular mycorrhizal fungi (AMF) have been observed in deep soil layers in arid lands. However, change in AMF community structure with soil depth and vertical distributions of the other root-associated microorganisms are unclear. Here, we examined colonization by AMF and dark septate fungi (DSF), as well as the community structure of AMF and endophytic fungi (EF) and endophytic bacteria (EB) in association with soil depth in a semiarid desert with shallow groundwater. Roots of Sabina vulgaris and soils were collected from surface to groundwater level at 20-cm intervals. Soil chemistry (water content, total N, and available P) and colonization of AMF and DSF were measured. Community structures of AMF, EF, and EB were examined by terminal restriction fragment length polymorphism analysis. AMF colonization decreased with soil depth, although it was mostly higher than 50%. Number of AMF phylotypes decreased with soil depth, but more than five phylotypes were observed at depths up to 100 cm. Number of AMF phylotypes had a significant and positive relationship with soil moisture level within 0-15% of soil water content. DSF colonization was high but limited to soil surface. Number of phylotypes of EF and EB were diverse even in deep soil layers, and the community composition was associated with the colonization and community composition of AMF. This study indicates that AMF species richness in roots decreases but is maintained in deep soil layers in semiarid regions, and change in AMF colonization and community structure associates with community structure of the other root-associated microorganisms.

Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing

PubMed Central

Penton, C. Ryan; Gupta, V. V. S. R.; Tiedje, James M.; Neate, Stephen M.; Ophel-Keller, Kathy; Gillings, Michael; Harvey, Paul; Pham, Amanda; Roget, David K.

2014-01-01

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils ‘suppressive’ or ‘non-suppressive’ for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. PMID:24699870

Evaluation of soils for use as liner materials: a soil chemistry approach.

PubMed

DeSutter, Tom M; Pierzynski, Gary M

2005-01-01

Movement of NH(4)(+) below animal waste lagoons is generally a function of the whole-lagoon seepage rate, soil mineralogy, cations in the lagoon liquor, and selectivity for NH(4)(+) on the soil-exchange sites. Binary exchange reactions (Ca(2+)-K(+), Ca(2+)-NH(4)(+), and K(+)-NH(4)(+)) were conducted on two soils from the Great Plains and with combinations of these soils with bentonite or zeolite added. Binary exchanges were used to predict ternary exchanges Ca(2+)-K(+)-NH(4)(+) following the Rothmund-Kornfeld approach and Gaines-Thomas convention. Potassium and NH(4)(+) were preferred over Ca(2+), and K(+) was preferred over NH(4)(+) in all soils and soils with amendments. Generally, the addition of bentonite did not change cation selectivity over the native soils, whereas the addition of zeolite did. The Rothmund-Kornfeld approach worked well for predicting equivalent fractions of cations on the exchanger phase when only ternary-solution phase compositions were known. Actual swine- and cattle-lagoon solution compositions and the Rothmund-Kornfeld approach were used to project that native soils are predicted to retain 53 and 23%, respectively, of the downward-moving NH(4)(+) on their exchange sites. Additions of bentonite or zeolite to soils under swine lagoons may only slightly improve the equivalent fraction of NH(4)(+) on the exchange sites. Although additions of bentonite or zeolite may not help increase the NH(4)(+) selectivity of a liner material, increases in the overall cation exchange capacity (CEC) of a soil will ultimately decrease the amount of soil needed to adsorb downward-moving NH(4)(+).

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-11-01

Incorporation of organic material into soils is an important element of organic farming practices that can affect the composition of the soil bacterial communities that carry out nutrient cycling and other functions crucial to crop health and growth. We conducted a field experiment to determine the effects of cover crops and fertilizers on bacterial community structure in agricultural soils under long-term organic management. Illumina sequencing of 16S rDNA revealed diverse communities comprising 45 bacterial phyla in corn rhizosphere and bulk field soil. Community structure was most affected by location and by the rhizosphere effect, followed by sampling time and amendment treatment. These effects were associated with soil physicochemical properties, including pH, moisture, organic matter, and nutrient levels. Treatment differences were apparent in bulk and rhizosphere soils at the time of peak corn growth in the season following cover crop and fertilizer application. Cover crop and fertilizer treatments tended to lower alpha diversity in early season samples. However, winter rye, oilseed radish, and buckwheat cover crop treatments increased alpha diversity in some later season samples compared to a no-amendment control. Fertilizer treatments and some cover crops decreased relative abundance of members of the ammonia-oxidizing family Nitrosomonadaceae. Pelleted poultry manure and Sustane® (a commercial fertilizer) decreased the relative abundance of Rhizobiales. Our data point to a need for future research exploring how (1) cover crops influence bacterial community structure and functions, (2) these effects differ with biomass composition and quantity, and (3) existing soil conditions and microbial community composition influence how soil microbial populations respond to agricultural management practices.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature

PubMed Central

Khachane, Amit; Dungait, Jennifer A. J.; Fraser, Fiona; Hopkins, David W.; Wookey, Philip A.; Singh, Brajesh K.; Freitag, Thomas E.; Hartley, Iain P.; Prosser, James I.

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited. PMID:27798702

The influence of tree species composition on the storage and mobility of semivolatile organic compounds in forest soils.

PubMed

Komprdová, Klára; Komprda, Jiří; Menšík, Ladislav; Vaňková, Lenka; Kulhavý, Jiří; Nizzetto, Luca

2016-05-15

Soil contamination with PCBs and PAHs in adjacent forest plots, characterized by a distinct composition in tree species (spruce only, mixed and beech only), was analyzed to investigate the influence of ecosystem type on contaminant mobility in soil under very similar climate and exposure conditions. Physical-chemical properties and contaminant concentrations in litter (L), organic (F, H) and mineral (A, B) soil horizons were analyzed. Contaminant distribution in the soil core varied both in relation to forest type and contaminant group/properties. Contaminant mobility in soil was assessed by examining the ratios of total organic carbon (TOC)-standardized concentrations across soil horizons (Enrichment factors, EFTOC) and the relationship between EFTOC and the octanol-water equilibrium partitioning coefficient (KOW). Contaminant distribution appeared to be highly unsteady, with pedogenic/biogeochemical drivers controlling contaminant mobility in organic layers and leaching controlling accumulation in mineral layers. Lighter PCBs displayed higher mobility in all forest types primarily controlled by leaching and, to a minor extent, diffusion. Pedogenic processes controlling the formation of soil horizons were found to be crucial drivers of PAHs and heavier PCBs distribution. All contaminants appeared to be more mobile in the soil of the broadleaved plot, followed by mixed canopy and spruce forest. Increasing proportion of deciduous broadleaf species in the forest can thus lead to faster degradation or the faster leaching of PAHs and PCBs. The composition of humic substances was found to be a better descriptor of contaminant concentration than TOC. Copyright © 2016 Elsevier B.V. All rights reserved.

The chemistry and mineralogy of Mars soil and dust

NASA Technical Reports Server (NTRS)

Banin, A.

1991-01-01

A single geological unit consisting of fine, apparently weathered soil material is covering large portions of the surface of Mars. This soil material has been thoroughly homogenized by global dust storms and it is plausible to assume that Mars dust is strongly correlated with it. The chemical-elemental composition of the soil was directly measured by the Viking Landers. Positive detection of Si, Al, Fe, Mg, Ca, Ti, S, Cl, and Br was achieved. Analyses of the SNC meteorites, a group of meteorites that has been suggested to be ejected Martian rocks, supply additional elemental-concentration data, broadening considerably the chemical data-base on the surface materials. A composition model for Mars soil, giving selected average elemental concentrations of major and trace elements, was recently suggested. It was constructed by combining the Viking Lander data, the SNC meteorite analyses, and other analyses. The mineralogy of the surface materials on Mars has not been directly measured yet. By use of various indirect approaches, including chemical correspondence to the surface analyses, spectral analogies, simulations of Viking Lander experiments, analyses of the SNC meteorites and various modeling efforts, the mineralogical composition was constrained to some extent. No direct analyses of soil reactivity have been done yet. Indirect evidence, mostly from the Viking biology experimental results, suggests that the soil probably has a slightly acidic reaction and is generally oxidized. Unambiguous identification of the Mars soil minerals by direct mineralogical analyses, and non-disturbed or in-situ measurements of the soil's reactivity, are of primary importance in future Mars research.

The Role of Microbial Community Composition in Controlling Soil Respiration Responses to Temperature.

PubMed

Auffret, Marc D; Karhu, Kristiina; Khachane, Amit; Dungait, Jennifer A J; Fraser, Fiona; Hopkins, David W; Wookey, Philip A; Singh, Brajesh K; Freitag, Thomas E; Hartley, Iain P; Prosser, James I

2016-01-01

Rising global temperatures may increase the rates of soil organic matter decomposition by heterotrophic microorganisms, potentially accelerating climate change further by releasing additional carbon dioxide (CO2) to the atmosphere. However, the possibility that microbial community responses to prolonged warming may modify the temperature sensitivity of soil respiration creates large uncertainty in the strength of this positive feedback. Both compensatory responses (decreasing temperature sensitivity of soil respiration in the long-term) and enhancing responses (increasing temperature sensitivity) have been reported, but the mechanisms underlying these responses are poorly understood. In this study, microbial biomass, community structure and the activities of dehydrogenase and β-glucosidase enzymes were determined for 18 soils that had previously demonstrated either no response or varying magnitude of enhancing or compensatory responses of temperature sensitivity of heterotrophic microbial respiration to prolonged cooling. The soil cooling approach, in contrast to warming experiments, discriminates between microbial community responses and the consequences of substrate depletion, by minimising changes in substrate availability. The initial microbial community composition, determined by molecular analysis of soils showing contrasting respiration responses to cooling, provided evidence that the magnitude of enhancing responses was partly related to microbial community composition. There was also evidence that higher relative abundance of saprophytic Basidiomycota may explain the compensatory response observed in one soil, but neither microbial biomass nor enzymatic capacity were significantly affected by cooling. Our findings emphasise the key importance of soil microbial community responses for feedbacks to global change, but also highlight important areas where our understanding remains limited.

An Underground Revolution: Biodiversity and Soil Ecological Engineering for Agricultural Sustainability.

PubMed

Bender, S Franz; Wagg, Cameron; van der Heijden, Marcel G A

2016-06-01

Soil organisms are an integral component of ecosystems, but their activities receive little recognition in agricultural management strategies. Here we synthesize the potential of soil organisms to enhance ecosystem service delivery and demonstrate that soil biodiversity promotes multiple ecosystem functions simultaneously (i.e., ecosystem multifunctionality). We apply the concept of ecological intensification to soils and we develop strategies for targeted exploitation of soil biological traits. We compile promising approaches to enhance agricultural sustainability through the promotion of soil biodiversity and targeted management of soil community composition. We present soil ecological engineering as a concept to generate human land-use systems, which can serve immediate human needs while minimizing environmental impacts. Copyright © 2016 Elsevier Ltd. All rights reserved.

SUPERFUND TREATABILITY CLEARINGHOUSE: COMPOSITING EXPLOSIVES/ORGANICS CONTAMINATED SOILS

EPA Science Inventory

Laboratory scale and pilot scale studies were conducted to evaluate composting to treat sediments and soils containing explosive and organic compounds. Sediment and soil from lagoons at Army ammunition plants, located in Louisiana, Wisconsin and Pennsylvania contained high...

Changes in soil water availability in vineyards can be traced by the carbon and nitrogen isotope composition of dried wines.

PubMed

Spangenberg, Jorge E; Zufferey, Vivian

2018-04-13

The grapevine is one of the most important edible fruit plants cultivated worldwide, and it is highly sensitive to changes in the soil water content. We studied the total carbon and nitrogen contents and stable isotope compositions (C/N WSR , δ 13 C WSR and δ 15 N WSR values) of the solid residues obtained by freeze-drying wines produced from two white grapevine cultivars (Vitis vinifera L. cv Chasselas and Petite Arvine) field grown under different soil water regimes while maintaining other climatic and ecopedological conditions identical. These experiments simulated the more frequent and extended climate change-induced periods of soil water shortage. The wines were from the 2009-2014 vintages, produced using the same vinification procedure. The plant water status, reflecting soil water availability, was assessed by the predawn leaf water potential (Ψ pd ), monitored in the field during the growing seasons. For both wine varieties, the δ 13 C WSR values are highly correlated with Ψ pd values and record the soil water availability set by soil water holding capacity, rainfall and irrigation water supply. These relationships were the same as those observed for the carbon isotope composition of fruit sugars (i.e., must sugars) and plant water status. In Chasselas wines, the nitrogen content and δ 15 N WSR values decreased with soil water deficit, indicating control of the flux of soil-water soluble nutrients into plants by soil water availability. Such a correlation was not found for Petite Arvine, probably due to different N-metabolism processes in this genetically atypical cultivar. The results presented in this study confirm and generalize what was previously found for red wine (Pinot noir); the carbon isotope composition of wine solid residues is a reliable indicator of the soil and the plant water status and thus can be used to trace back local climatic conditions in the vineyard's region. In most wines (except Petite Arvine) the C/N WSR and δ 15 N WSR values are indicators of the origin of the nitrogen supplied to the plant's fruit (grape) that can be used to assess the N dynamics in the soil-water-plant system. Copyright © 2018 Elsevier B.V. All rights reserved.

Impact of diverse soil microbial communities on crop residues decomposition

NASA Astrophysics Data System (ADS)

Mrad, Fida; Bennegadi-Laurent, Nadia; Ailhas, Jérôme; Leblanc, Nathalie; Trinsoutrot-Gattin, Isabelle; Laval, Karine; Gattin, Richard

2017-04-01

Soils provide many basic ecosystem services for our society and most of these services are carried out by the soil communities, thus influencing soils quality. Soil organic matter (SOM) can be considered as one of the most important soil quality indices for it plays a determinant role in many physical, chemical and biological processes, such as soil structure and erosion resistance, cation exchange capacity, nutrient cycling and biological activity (Andrews et al., 2004). Since a long time, exogenous organic inputs are largely used for improving agricultural soils, affecting highly soil fertility and productivity. The use of organic amendments such as crop residues influences the soil microbial populations' diversity and abundance. In the meantime, soil microbial communities play a major role in the organic matter degradation, and the effect of different microbial communities on the decomposition of crop residues is not well documented. In this context, studying the impact of crop residues on soil microbial ecology and the processes controlling the fate of plant residues in different management practices is essential for understanding the long-term environmental and agronomic effects on soil and organic matters. Our purpose in the present work was to investigate the decomposition by two contrasting microbial communities of three crop residues, and compare the effect of different residues amendments on the abundance and function of each soil microbial communities. Among the main crops which produce large amounts of residues, we focused on three different plants: wheat (Triticum aestivum L.), rape (Brassica napus) and sunflower (Helianthus annuus). The residues degradation in two soils of different management practices and the microbial activity were evaluated by: microbial abundance (microbial carbon, culturable bacteria, total DNA, qPCR), in combination with functional indicators (enzymatic assays and Biolog substrate utilization), kinetics of C and N mineralization, and chemical measures. Physicochemical composition of crop residues was assessed by Fourier transform infrared spectroscopy FTIR technique at 0 and 83 days. The experiment was conducted in microcosms over 83 days for the biological measurements and 175 days for the C mineralization. The first results showed variations in the C & N rates, and the microbial abundances and functions over time, with a peak at 5 days and a decrease at 83 days for most of the measurements. The soil microbial communities' composition (different management practices) highly impacted the crop residues decomposition. The biochemical composition of crop residues influenced less the microbial communities of each soil. Further studies on the valorization of these residues into agro materials will be carried out. References: Andrews SS., Karlen DL., and Cambardella CA. (2004) The soil management assessment framework: a quantitative soil quality evaluation method. Soil Science Society of America, 68: 1945-1962

Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species

PubMed Central

Bowsher, Alan W.; Ali, Rifhat; Harding, Scott A.; Tsai, Chung-Jui; Donovan, Lisa A.

2016-01-01

Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments. PMID:26824236

Soil organic carbon dynamics jointly controlled by climate, carbon inputs, soil properties and soil carbon fractions.

PubMed

Luo, Zhongkui; Feng, Wenting; Luo, Yiqi; Baldock, Jeff; Wang, Enli

2017-10-01

Soil organic carbon (SOC) dynamics are regulated by the complex interplay of climatic, edaphic and biotic conditions. However, the interrelation of SOC and these drivers and their potential connection networks are rarely assessed quantitatively. Using observations of SOC dynamics with detailed soil properties from 90 field trials at 28 sites under different agroecosystems across the Australian cropping regions, we investigated the direct and indirect effects of climate, soil properties, carbon (C) inputs and soil C pools (a total of 17 variables) on SOC change rate (r C , Mg C ha -1  yr -1 ). Among these variables, we found that the most influential variables on r C were the average C input amount and annual precipitation, and the total SOC stock at the beginning of the trials. Overall, C inputs (including C input amount and pasture frequency in the crop rotation system) accounted for 27% of the relative influence on r C , followed by climate 25% (including precipitation and temperature), soil C pools 24% (including pool size and composition) and soil properties (such as cation exchange capacity, clay content, bulk density) 24%. Path analysis identified a network of intercorrelations of climate, soil properties, C inputs and soil C pools in determining r C . The direct correlation of r C with climate was significantly weakened if removing the effects of soil properties and C pools, and vice versa. These results reveal the relative importance of climate, soil properties, C inputs and C pools and their complex interconnections in regulating SOC dynamics. Ignorance of the impact of changes in soil properties, C pool composition and C input (quantity and quality) on SOC dynamics is likely one of the main sources of uncertainty in SOC predictions from the process-based SOC models. © 2017 John Wiley & Sons Ltd.

Soil pH effects on the interactions between dissolved zinc, non-nano- and nano-ZnO with soil bacterial communities.

PubMed

Read, Daniel S; Matzke, Marianne; Gweon, Hyun S; Newbold, Lindsay K; Heggelund, Laura; Ortiz, Maria Diez; Lahive, Elma; Spurgeon, David; Svendsen, Claus

2016-03-01

Zinc oxide nanoparticles (ZnO NPs) are used in an array of products and processes, ranging from personal care products to antifouling paints, textiles, food additives, antibacterial agents and environmental remediation processes. Soils are an environment likely to be exposed to manmade nanoparticles due to the practice of applying sewage sludge as a fertiliser or as an organic soil improver. However, understanding on the interactions between soil properties, nanoparticles and the organisms that live within soil is lacking, especially with regards to soil bacterial communities. We studied the effects of nanoparticulate, non-nanoparticulate and ionic zinc (in the form of zinc chloride) on the composition of bacterial communities in soil with a modified pH range (from pH 4.5 to pH 7.2). We observed strong pH-dependent effects on the interaction between bacterial communities and all forms of zinc, with the largest changes in bacterial community composition occurring in soils with low and medium pH levels (pH 4.8 and 5.9). The high pH soil (pH 7.2) was less susceptible to the effects of zinc exposure. At the highest doses of zinc (2500 mg/kg dw soil), both nano and non-nano particulate zinc applications elicited a similar response in the soil bacterial community, and this differed significantly to the ionic zinc salt treatment. The results highlight the importance of considering soil pH in nanotoxicology studies, although further work is needed to determine the exact mechanisms controlling the toxicity and fate and interactions of nanoparticles with soil microbial communities.

[Soil humus differentiation and correlation with other soil biochemical properties in pure forests in semi-arid low-hilly area of Inner Mongolia, China].

PubMed

Zhang, Xiao-Xi; Liu, Zeng-Wen; Bing, Yuan-Hao; Zhu, Bo-Chao; Huang, Liang-Jia

2014-10-01

Whether the content and composition of soil humus in pure forest change due to its simple component of litter and specificity of single-species dominant community is a key problem for forest sustainable management. In this study, soils from 6 kind of pure forests in semi-arid low-hilly area of Inner Mongolia were collected and their humus and other biochemical properties were measured to investigate the differentiation of soil humus and the impact factors. The results showed that the soil of Picea asperata and Betula platyphylla pure forests had the highest contents of humus and better condensation degrees and stabilities, followed by that of Populus simonii, Larix principis-rupprechtii and Ulmus pumila pure forests, while the soil of Pinus tabuliformis pure forest had the lowest content of humus, condensation degree and stability. There were significant positive correlations between soil microorganism biomass, activity of phosphatase and the content and stability of soil humus. In contrast, the soil peroxidate, dehydrogenase activity and soil humus content showed significant negative correlations with each other. Furthermore, the enhancement of dehydrogenase activity might decrease the stability of humus. There were significant positive correlations between available N and the content and stability of soil humus, but total Cu, Zn and Fe had negative correlations with them, and total Cu and Fe might reduce the stability of humus as well. The particularity of pure forest environment and litter properties might be the key inducement to soil humus differentiation, thus reforming the pure forest through mixing with other tree species or planting understory vegetation would be the fundamental way to improve the soil humus composition and stability.

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

Evolutionary Divergences in Root Exudate Composition among Ecologically-Contrasting Helianthus Species.

PubMed

Bowsher, Alan W; Ali, Rifhat; Harding, Scott A; Tsai, Chung-Jui; Donovan, Lisa A

2016-01-01

Plant roots exude numerous metabolites into the soil that influence nutrient availability. Although root exudate composition is hypothesized to be under selection in low fertility soils, few studies have tested this hypothesis in a phylogenetic framework. In this study, we examined root exudates of three pairs of Helianthus species chosen as phylogenetically-independent contrasts with respect to native soil nutrient availability. Under controlled environmental conditions, seedlings were grown to the three-leaf-pair stage, then transferred to either high or low nutrient treatments. After five days of nutrient treatments, we used gas chromatography-mass spectrometry for analysis of root exudates, and detected 37 metabolites across species. When compared in the high nutrient treatment, species native to low nutrient soils exhibited overall higher exudation than their sister species native to high nutrient soils in all three species pairs, providing support for repeated evolutionary shifts in response to native soil fertility. Species native to low nutrient soils and those native to high nutrient soils responded similarly to low nutrient treatments with increased exudation of organic acids (fumaric, citric, malic acids) and glucose, potentially as a mechanism to enhance nutrition acquisition. However, species native to low nutrient soils also responded to low nutrient treatments with a larger decrease in exudation of amino acids than species native to high nutrient soils in all three species pairs. This indicates that species native to low nutrient soils have evolved a unique sensitivity to changes in nutrient availability for some, but not all, root exudates. Overall, these repeated evolutionary divergences between species native to low nutrient soils and those native to high nutrient soils provide evidence for the adaptive value of root exudation, and its plasticity, in contrasting soil environments.

The nitrogen isotopic composition in soils and plants: Its use in environmental studies (A Review)

NASA Astrophysics Data System (ADS)

Makarov, M. I.

2009-12-01

The results of studying the isotopic composition of the nitrogen in soils and plants and its use for characterizing the nitrogen cycle in ecosystems, the transformation of nitrogen compounds in soils, the sources of nitrogen nutrition for plants, and the assessment of the symbiotic nitrogen fixation’s contribution to the nitrogen budget of ecosystems were considered for a wide variety of natural and agricultural ecosystems.

The influence of wildfire severity on soil char composition and nitrogen dynamics

NASA Astrophysics Data System (ADS)

Rhoades, Charles; Fegel, Timothy; Chow, Alex; Tsai, Kuo-Pei; Norman, John, III; Kelly, Eugene

2017-04-01

Forest fires cause lasting ecological changes and alter the biogeochemical processes that control stream water quality. Decreased plant nutrient uptake is the mechanism often held responsible for lasting post-fire shifts in nutrient supply and demand, though other upland and in-stream factors also likely contribute to elevated stream nutrient losses. Soil heating, for example, creates pyrogenic carbon (C) and char layers that influence C and nitrogen (N) cycling. Char layer composition and persistence vary across burned landscapes and are influenced first by fire behavior through the temperature and duration of combustion and then by post-fire erosion. To evaluate the link between soil char and stream C and N export we studied areas burned by the 2002 Hayman Fire, the largest wildfire in Colorado, USA history. We compared soil C and N pools and processes across ecotones that included 1) unburned forests, 2) areas with moderate and 3) high wildfire severity. We analyzed 1-2 cm thick charred organic layers that remain visible 15 years after the fire, underlying mineral soils, and soluble leachate from both layers. Unburned soils released more dissolved organic C and N (DOC and DON) from organic and mineral soil layers than burned soils. The composition of DOC leachate characterized by UV-fluorescence, emission-excitation matrices (EEMs) and Fluorescence Regional Integration (FRI) found similarity between burned and unburned soils, underscoring a common organic matter source. Humic and fulvic acid-like fractions, contained in regions V and III of the FRI model, comprised the majority of the fluorescing DOM in both unburned and char layers. Similarity between two EEMs indices (Fluorescence and Freshness), further denote that unburned soils and char layers originate from the same source and are consistent with visual evidence char layers contain significant amounts of unaltered OM. However, the EEMs humification index (HIX) and compositional analysis with pyrolysis GCMS both indicate that C contained or leached from severely-burned char layers has higher aromaticity and thus chemical stability compared to C in unburned soils. Mineral soil (0-5 cm depth) beneath char layers in high severity portions of the Hayman Fire had significantly more soil N and C and lower pH. Potential net mineralization - an index of the supply of plant-available nitrogen - differed between the severely-burned areas and both unburned and moderately-burn areas. Negative net mineralization in unburned and moderately burned soils indicates immobilization or retention of inorganic N by soil microbes. In contrast, soils burned at high severity produced inorganic N sources available to plants, leaching and gas losses. Water soluble nitrate comprised a larger proportion of inorganic N leached from the char layer of high severity burns. Mineral soil in those areas had both higher water soluble nitrate and total inorganic N in leachate. Char layers that have persisted for fifteen years influence soil N turnover within the Hayman Fire affected area and may contribute to elevated N losses in streams burned at high severity. The chemical stability of soil char layers perpetuates their importance for C sequestration and N dynamics in burned landscapes.

The contribution of vapor deposition to amorphous rims on lunar soil grains. [Abstract only

NASA Technical Reports Server (NTRS)

Keller, L. P.; Mckay, D. S.

1994-01-01

Recent analysis analytical electron microscope study of lunar soils showed that the approximately 60-nm-wide amorphous rims surrounding many lunar soils grains exhibit distinct compositional differences from their hosts. On average, the amorphous rim compositions reflect the local bulk soil composition with the exceptions of Si and S, which are enriched relative to the bulk soil. These chemical trends led us to propose that the amorphous rims were in fact deposits of impact-generated vapors produced during regolith gardening, a hypothesis that runs contrary to the generally accepted view that the rims are produced through amorphization of the outer parts of mineral grains by interaction with the solar wind. Analytical data are reported for amorphous rims on individual minerals in lunar soils in order to show that the magnitude of the chemical differences between rim and host are so great that they require a major addition of foreign elements to the grain surfaces. The average composition of amorphous rims is listed as a function of host mineralogy as determined in microtone thin sections using energy-dispersive X-ray spectrometry in the transmission electron microscope. As the host mineral becomes chemically more complex, the chemical differences are not as clear. The average rim compositions are remarkably similar and are independent of the host grain mineralogy. Whether there are 'sputtering' or radiation effects superimposed on the vapor-deposited material can be debated. We do not explicitly exclude the effects of radiation damage as a contributing factor to the formation of amorphous rims; we are merely emphasizing the major role played by condensed vapors in the formation of amorphous rims on lunar soil grains.

[Effects of grazing on the composition of soil animals and their decomposition function to Stipa grandis litter in Inner Mongolia typical steppe, China.

PubMed

Yang, Zhi Min; Hasitamier; Liu, Xin Min

2016-09-01

Grazing has been considered to be an important factor determining the composition of soil animals and decomposition of leaf litter in grassland ecosystem. Sampling plots were selected in ungrazed grassland, grazed grassland and sandy land. Litter bags were used to compare the changes of physicochemical properties of Stipa grandis litter and the composition of soil fauna in the process of the litter decomposition in Baiyinxile, Inner Mongolia, since 2010 to 2012. A total number of 67056 soil animals were captured, belonging to five phyla and eight classes, including 23 families of mites and 19 families of insects. After 780 days' decomposition, the loss of the organic matter of S. grandis litter was from 92.5% to 40.0% in the ungrazed grassland, and to 41.3% in the grazed grassland, with no significant difference observed. However, there was a significant difference (P<0.05) between the ratio of litter residues of the ungrazed grassland (50.0%) and that of the grazed grassland (23.0%). The abundance of soil animals in the residual litters was significantly decreased in the grazed grassland compared to the ungrazed grassland. When the litter was moved into the sandy land, the decomposition rate of organic matter in the residual litter was not significant changed but the ratio of litter residue declined significantly, and the composition of mite community in the resi-dual litter changed significantly. Our results illustrated that grazing activity could affect the composition and abundance of soil fauna in temperate grassland, but slightly influenced the decomposition of organic matter. Therefore, soil animals had relatively weak direct effects on the decomposition of litter in this semi-arid region.

Comparison of Hard Surface and Soft Soil Impact Performance of a Crashworthy Composite Fuselage Concept

NASA Technical Reports Server (NTRS)

Sareen, Ashish K.; Sparks, Chad; Mullins, B. R., Jr.; Fasanella, Edwin; Jackson, Karen

2002-01-01

A comparison of the soft soil and hard surface impact performance of a crashworthy composite fuselage concept has been performed. Specifically, comparisons of the peak acceleration values, pulse duration, and onset rate at specific locations on the fuselage were evaluated. In a prior research program, the composite fuselage section was impacted at 25 feet per second onto concrete at the Impact Dynamics Research Facility (IDRF) at NASA Langley Research Center. A soft soil test was conducted at the same impact velocity as a part of the NRTC/RITA Crashworthy and Energy Absorbing Structures project. In addition to comparisons of soft soil and hard surface test results, an MSC. Dytran dynamic finite element model was developed to evaluate the test analysis correlation. In addition, modeling parameters and techniques affecting test analysis correlation are discussed. Once correlated, the analytical methodology will be used in follow-on work to evaluate the specific energy absorption of various subfloor concepts for improved crash protection during hard surface and soft soil impacts.

New Amphiphilic Composite for Preparing Efficient Coated Potassium-Fertilizers for Top-Dressing Fertilization of Annual Crops.

PubMed

Urrutia, Oscar; Erro, Javier; Zabini, Andre; Hoshiba, Kent; Blandin, Anne F; Baigorri, Roberto; Martín-Pastor, Manuel; Alis, Yves; Yvin, Jean C; García-Mina, José M

2018-05-16

This study describes the efficiency of a new coating material for preparing granulated potassium-fertilizers with a potassium release to the soil solution sensitive to rainfall intensity. The composite is prepared by reaction of an alkyd-resin with cement in the absence of water. The complementary use of diverse analytical techniques showed that the presence of the cement fraction induced alkyd resin reticulation and gradual cement-resin hardening. Scanning electron microscopy revealed the formation of micro and nanopores within cement-clusters, whose water permeability is affected by the resin reticulation and amphiphilic character. Potassium release was evaluated in water, soil-columns, and in soil-plant trials in pots and open-field. Agronomic results were consistent with potassium release rates obtained in water solution and soil columns. The composite-coated potassium fertilizer was more efficient than the noncoated one in providing plant available potassium, with this effect being dependent on water presence in soil.

Changes in macrominerals, trace elements and pigments content during lettuce (Lactuca sativa L.) growth: influence of soil composition.

PubMed

Pinto, Edgar; Almeida, Agostinho A; Aguiar, Ana A R M; Ferreira, Isabel M P L V O

2014-01-01

Changes in macrominerals, trace elements and photosynthetic pigments were monitored at 5 stages of lettuce growth. Plants were grown in three experimental agriculture greenhouse fields (A1, A2 and A3). Soil composition was also monitored to understand its influence on lettuce composition. In general, the content of macrominerals, trace elements, chlorophylls and carotenoids decreased during lettuce growth and consequently, high nutritional value was observed at younger stages. A2 lettuces showed an increase of Fe, Al, Cr, V and Pb due to the different soil physicochemical parameters. Multiple linear regression analysis with stepwise variable selection, indicated that soil characteristics, namely, pH(CaCl2) for Fe and Cr, silt and fine-sand for Al and V, OM for Al and Pb, coarse-sand and CEC for Cr, had a key role determining element bioavailability and plant mineral content. Thus, lettuce nutritional value was strongly dependent of growth stage and soil characteristics. Copyright © 2013 Elsevier Ltd. All rights reserved.

Composition and Mineralogy of Martian Soils

NASA Astrophysics Data System (ADS)

Bell, J. F.

2007-05-01

The soils of Mars--the fine-grained, porous, uppermost layer of the planet's regolith--appear to have been created by a combination of physical and chemical weathering processes that can provide insights about the evolution of the martian surface and climate. Remote sensing and in situ measurements and analyses of soils from five different landing sites have revealed both surprising similarities and important (sometimes unexpected) differences among soils across the planet. Among the similarities are the ubiquitous presence and homogeneity of "dust" at widely-separated landing sites. Dust is the finest-grained (less than 5 microns) fraction of the soil, and the fact that it is easily suspended and transported by dust devils and dust storms explains its ubiquity. The reddish color and small size of dust particles had been cited as evidence for its origin as perhaps physically or chemically comminuted and heavily-oxidized (ferric) secondary weathering products. New results from the MER Sprit and Opportunity missions, however, indicate that dust grains may instead be volumetrically mostly unoxidized (ferrous) material, with visual color properties imparted by only a thin rind or coating of ferric oxides/oxyhydroxides. Another fine-grained global-scale unit is dark, silt- to sand-sized soils that occur in dunes, drifts, and ripples. Dark sands exhibit rather homogeneous composition and mineralogy (dominated by olivine and pyroxene) across the landing sites, suggesting that they, too, are globally-transported materials. Examples of the kinds of variability detected in martian soils are the hematite-rich spherules, sulfur/jarosite-rich outcrop- derived soils, and basaltic clastic fragments encountered in Meridiani Planum, the hematite, goethite, and ferric- sulfate bearing soils encountered in Gusev crater, and crusted/armored soils and rinds encountered at both Viking and both MER sites. Much of the observed martian soil variability may result from the action of local-scale weathering processes and/or reflect the diversity of local precursor bedrock sources. This presentation will provide an overview of what we know about the composition and mineralogy of martian soils, will review current models for martian soil formation in light of the currently-available data, and will describe ways that these models might be tested with ongoing and future Mars surface exploration missions.

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils

PubMed Central

Torres, Maria Pilar; Montesinos-Navarro, Alicia; Roldán, Antonio

2016-01-01

ABSTRACT We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. IMPORTANCE Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions. PMID:27016567

Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils.

PubMed

Alguacil, Maria Del Mar; Torres, Maria Pilar; Montesinos-Navarro, Alicia; Roldán, Antonio

2016-06-01

We investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil of Brachypodium retusum in six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations. Communities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

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

USGS Publications Warehouse

Waldrop, M.P.; Harden, J.W.

2008-01-01

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.

Divergent Responses of Forest Soil Microbial Communities under Elevated CO 2 in Different Depths of Upper Soil Layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Hao; He, Zhili; Wang, Aijie

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2) at different soil depth profiles in forest ecosystems. In this paper, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional genemore » structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. The concentration of atmospheric carbon dioxide (CO 2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO 2 at both soil depths. Finally, more functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO 2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.« less

Divergent Responses of Forest Soil Microbial Communities under Elevated CO 2 in Different Depths of Upper Soil Layers

DOE PAGES

Yu, Hao; He, Zhili; Wang, Aijie; ...

2017-10-27

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2) at different soil depth profiles in forest ecosystems. In this paper, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional genemore » structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3-N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. The concentration of atmospheric carbon dioxide (CO 2) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO 2 at both soil depths. Finally, more functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO 2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm.« less

Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers.

PubMed

Yu, Hao; He, Zhili; Wang, Aijie; Xie, Jianping; Wu, Liyou; Van Nostrand, Joy D; Jin, Decai; Shao, Zhimin; Schadt, Christopher W; Zhou, Jizhong; Deng, Ye

2018-01-01

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2 ) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3 -N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. IMPORTANCE The concentration of atmospheric carbon dioxide (CO 2 ) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2 ) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial communities shifted under eCO 2 at both soil depths. More functional genes involved in carbon, nitrogen, and phosphorus cycling were stimulated under eCO 2 at the soil depth of 0 to 5 cm than at the depth of 5 to 15 cm. Copyright © 2017 American Society for Microbiology.

Variation in photosynthetic and nonphotosynthetic vegetation along edaphic and compositional gradients in northwestern Amazonia

NASA Astrophysics Data System (ADS)

Higgins, M. A.; Asner, G. P.; Perez, E.; Elespuru, N.; Alonso, A.

2014-03-01

Tropical forests vary substantially in aboveground properties such as canopy height, canopy structure, and plant species composition, corresponding to underlying variations in soils and geology. Forest properties are often difficult to detect and map in the field, however, due to the remoteness and inaccessibility of these forests. Spectral mixture analysis of Landsat imagery allows mapping of photosynthetic and nonphotosynthetic vegetation quantities (PV and NPV), corresponding to biophysical properties such as canopy openness, forest productivity, and disturbance. Spectral unmixing has been used for applications ranging from deforestation monitoring to identifying burn scars from past fires, but little is known about variations in PV and NPV in intact rainforest. Here we use spectral unmixing of Landsat imagery to map PV and NPV in northern Amazonia, and to test their relationship to soils and plant species composition. To do this we sampled 117 sites crossing a geological boundary in northwestern Amazonia for soil cation concentrations and plant species composition. We then used the Carnegie Landsat Analysis System to map PV and NPV for these sites from multiple dates of Landsat imagery. We found that soil cation concentrations and plant species composition consistently explain a majority of the variation in remotely sensed PV and NPV values. After combining PV and NPV into a single variable (PV-NPV), we determined that the influence of soil properties on canopy properties was inseparable from the influence of plant species composition. In all cases, patterns in PV and NPV corresponded to underlying geological patterns. Our findings suggest that geology and soils regulate canopy PV and NPV values in intact tropical forest, possibly through changes in plant species composition.

Variation in photosynthetic and nonphotosynthetic vegetation along edaphic and compositional gradients in northwestern Amazonia

NASA Astrophysics Data System (ADS)

Higgins, M. A.; Asner, G. P.; Perez, E.; Elespuru, N.; Alonso, A.

2014-07-01

Tropical forests vary substantially in aboveground properties such as canopy height, canopy structure, and plant species composition, corresponding to underlying variations in soils and geology. Forest properties are often difficult to detect and map in the field, however, due to the remoteness and inaccessibility of these forests. Spectral mixture analysis of Landsat imagery allows mapping of photosynthetic and nonphotosynthetic vegetation quantities (PV and NPV), corresponding to biophysical properties such as canopy openness, forest productivity, and disturbance. Spectral unmixing has been used for applications ranging from deforestation monitoring to identifying burn scars from past fires, but little is known about variations in PV and NPV in intact rainforests. Here we use spectral unmixing of Landsat imagery to map PV and NPV in northern Amazonia, and to test their relationship to soils and plant species composition. To do this we sampled 117 sites crossing a geological boundary in northwestern Amazonia for soil cation concentrations and plant species composition. We then used the Carnegie Landsat Analysis System to map PV and NPV for these sites from multiple dates of Landsat imagery. We found that soil cation concentrations and plant species composition consistently explain a majority of the variation in remotely sensed PV and NPV values. After combining PV and NPV into a single variable (PV-NPV), we determined that the influence of soil properties on canopy properties was inseparable from the influence of plant species composition. In all cases, patterns in PV and NPV corresponded to underlying geological patterns. Our findings suggest that geology and soils regulate canopy PV and NPV values in intact tropical forests, possibly through changes in plant species composition.

Composition and Color of Martian Soil from Oxidation of Meteoritic Material

NASA Technical Reports Server (NTRS)

Yen, A. S.

2001-01-01

Aqueous weathering is not necessary for formation of the martian soils. The chemical composition and oxidation state of the surface fines can be attributed to meteoritic influx. Additional information is contained in the original extended abstract.

Drivers of lignin composition in boreal forest organic soils across a climate gradient

NASA Astrophysics Data System (ADS)

Myers-Pigg, A.; Kaiser, K.; Benner, R. H.; Ziegler, S. E.

2017-12-01

Lignin diagenesis in soils, including the cumulative effects of degradation and leaching, increases with experimental warming, signifying a potentially important change relevant to soil organic matter accumulation and fate. However, decadal to centennial climatic effects including changes in precipitation, litterfall inputs, and understory sources, on lignin composition are poorly constrained. We examined the lignin content and composition, via cupric oxide oxidation (CuO), within the organic layers of podzolic soils under similar balsam fir forests across a latitudinal climate gradient in Atlantic Canada. By exploring variation in lignin by both soil depth and climate region, this study informs on the climate drivers of lignin stability within boreal forest soil. A two-way analysis of variance (ANOVA) revealed significant variations in common signatures of CuO by-products with depth and/or site, indicating source and/or diagenetic controllers. Importantly, none of these signatures, with the exception of p-hydroxyphenols, exhibited a site by depth interaction indicating a similar degree of diagenetic alternation with depth across climates. The site by depth interaction for p-hydroxyphenols is a result of greater moss input in the northernmost site. To better elucidate this climate-induced source variation on our interpretation of lignin diagenesis, a principle component (PCA) model was built using signatures varying by site (p<0.01). These signatures loaded uniquely with the percentage of wood, needles, and mosses within the L layer in each region. Site differences in this loading indicate that shifts in understory input is a major climate effect controlling lignin composition in these forest soils. A lignin diagenesis PCA model was built using (1) all non-moss related signatures identified in the first PCA model, and (2) scores for additional sites within each region, calculated from modeled lignin composition based on 13C-NMR spectra. The combined results indicate that the lignin diagenetic states among soils is similar, despite the large increase in soil C turnover with climate warming across this transect. Thus our results indicate that shifts in moss contribution, and not increased diagenesis, controls CuO by-products with climate change in these moist boreal forests.

Predicting the mineral composition of dust aerosols – Part 1: Representing key processes

DOE PAGES

Perlwitz, J. P.; Perez Garcia-Pando, C.; Miller, R. L.

2015-10-21

Soil dust aerosols created by wind erosion are typically assigned globally uniform physical and chemical properties within Earth system models, despite known regional variations in the mineral content of the parent soil. Mineral composition of the aerosol particles is important to their interaction with climate, including shortwave absorption and radiative forcing, nucleation of cloud droplets and ice crystals, heterogeneous formation of sulfates and nitrates, and atmospheric processing of iron into bioavailable forms that increase the productivity of marine phytoplankton. Here, aerosol mineral composition is derived by extending a method that provides the composition of a wet-sieved soil. The extension accountsmore » for measurements showing significant differences between the mineral fractions of the wet-sieved soil and the emitted aerosol concentration. For example, some phyllosilicate aerosols are more prevalent at silt sizes, even though they are nearly absent at these diameters in a soil whose aggregates are dispersed by wet sieving. We calculate the emitted mass of each mineral with respect to size by accounting for the disintegration of soil aggregates during wet sieving. These aggregates are emitted during mobilization and fragmentation of the original undispersed soil that is subject to wind erosion. The emitted aggregates are carried far downwind from their parent soil. The soil mineral fractions used to calculate the aggregates also include larger particles that are suspended only in the vicinity of the source. We calculate the emitted size distribution of these particles using a normalized distribution derived from aerosol measurements. In addition, a method is proposed for mixing minerals with small impurities composed of iron oxides. These mixtures are important for transporting iron far from the dust source, because pure iron oxides are more dense and vulnerable to gravitational removal than most minerals comprising dust aerosols. Finally, a limited comparison to measurements from North Africa shows that the model extensions result in better agreement, consistent with a more extensive comparison to global observations as well as measurements of elemental composition downwind of the Sahara, as described in companion articles.« less

Stable isotope composition (δ(13)C and δ(15)N values) of slime molds: placing bacterivorous soil protozoans in the food web context.

PubMed

Tiunov, Alexei V; Semenina, Eugenia E; Aleksandrova, Alina V; Tsurikov, Sergey M; Anichkin, Alexander E; Novozhilov, Yuri K

2015-08-30

Data on the bulk stable isotope composition of soil bacteria and bacterivorous soil animals are required to estimate the nutrient and energy fluxes via bacterial channels within detrital food webs. We measured the isotopic composition of slime molds (Myxogastria, Amoebozoa), a group of soil protozoans forming macroscopic spore-bearing fruiting bodies. An analysis of largely bacterivorous slime molds can provide information on the bulk stable isotope composition of soil bacteria. Fruiting bodies of slime molds were collected in a monsoon tropical forest of Cat Tien National Park, Vietnam, and analyzed by continuous-flow isotope ratio mass spectrometry. Prior to stable isotope analysis, carbonates were removed from a subset of samples by acidification. To estimate the trophic position of slime molds, their δ(13) C and δ(15) N values were compared with those of plant debris, soil, microbial destructors (litter-decomposing, humus-decomposing, and ectomycorrhizal fungi) and members of higher trophic levels (oribatid mites, termites, predatory macroinvertebrates). Eight species of slime molds represented by at least three independent samples were 3-6‰ enriched in (13) C and (15) N relative to plant litter. A small but significant difference in the δ(13) C and δ(15) N values suggests that different species of myxomycetes can differ in feeding behavior. The slime molds were enriched in (15) N compared with litter-decomposing fungi, and depleted in (15) N compared with mycorrhizal or humus-decomposing fungi. Slime mold sporocarps and plasmodia largely overlapped with oribatid mites in the isotopic bi-plot, but were depleted in (15) N compared with predatory invertebrates and humiphagous termites. A comparison with reference groups of soil organisms suggests strong trophic links of slime molds to saprotrophic microorganisms which decompose plant litter, but not to humus-decomposing microorganisms or to mycorrhizal fungi. Under the assumption that slime molds are primarily feeding on bacteria, the isotopic similarity of slime molds and mycophagous soil animals indicates that saprotrophic soil bacteria and fungi are similar in bulk isotopic composition. Copyright © 2015 John Wiley & Sons, Ltd.

Amorphous Analogs of Martian Global Soil: Pair Distribution Function Analyses and Implications for Scattering Models of Chemin X-ray Diffraction Data

NASA Technical Reports Server (NTRS)

Achilles, C. N.; Bish, D. L.; Rampe, E. B.; Morris, R. V.

2015-01-01

Soils on Mars have been analyzed by the Mars Exploration Rovers (MER) and most recently by the Mars Science Laboratory (MSL) rover. Chemical analyses from a majority of soil samples suggest that there is a relatively uniform global soil composition across much of the planet. A soil site, Rocknest, was sampled by the MSL science payload including the CheMin X-ray diffractometer and the Alpha Particle X-ray Spectrometer (APXS). Che- Min X-ray diffraction (XRD) data revealed crystalline phases and a broad, elevated background, indicating the presence of amorphous or poorly ordered materials (Fig 1). Based on the chemical composition of the bulk soil measured by APXS and the composition of crystalline phases derived from unit-cell parameters determined with CheMin data, the percentages of crystalline and amorphous phases were calculated at 51% and 49%, respectively. Attempts to model the amorphous contribution to CheMin XRD patterns were made using amorphous standards and full-pattern fitting methods and show that the broad, elevated background region can be fitted by basaltic glass, allophane, and palagonite. However, the modeling shows only that these phases have scattering patterns similar to that for the soil, not that they represent unique solutions. Here, we use pair distribution function (PDF) analysis to determine the short-range order of amorphous analogs in martian soils and better constrain the amorphous material detected by CheMin.

Geophysical features influence the climate change sensitivity of northern Wisconsin pine and oak forests.

PubMed

Tweiten, Michael A; Calcote, Randy R; Lynch, Elizabeth A; Hotchkiss, Sara C; Schuurman, Gregor W

2015-10-01

Landscape-scale vulnerability assessment from multiple sources, including paleoecological site histories, can inform climate change adaptation. We used an array of lake sediment pollen and charcoal records to determine how soils and landscape factors influenced the variability of forest composition change over the past 2000 years. The forests in this study are located in northwestern Wisconsin on a sandy glacial outwash plain. Soils and local climate vary across the study area. We used the Natural Resource Conservation Service's Soil Survey Geographic soil database and published fire histories to characterize differences in soils and fire history around each lake site. Individual site histories differed in two metrics of past vegetation dynamics: the extent to which white pine (Pinus strobus) increased during the Little Ice Age (LIA) climate period and the volatility in the rate of change between samples at 50-120 yr intervals. Greater increases of white pine during the LIA occurred on sites with less sandy soils (R² = 0.45, P < 0.0163) and on sites with relatively warmer and drier local climate (R² = 0.55, P < 0.0056). Volatility in the rate of change between samples was positively associated with LIA fire frequency (R² = 0.41, P < 0.0256). Over multi-decadal to centennial timescales, forest compositional change and rate-of-change volatility were associated with higher fire frequency. Over longer (multi-centennial) time frames, forest composition change, especially increased white pine, shifted most in sites with more soil moisture. Our results show that responsiveness of forest composition to climate change was influenced by soils, local climate, and fire. The anticipated climatic changes in the next century will not produce the same community dynamics on the same soil types as in the past, but understanding past dynamics and relationships can help us assess how novel factors and combinations of factors in the future may influence various site types. Our results support climate change adaptation efforts to monitor and conserve the landscape's full range of geophysical features.

Cell Wall Ultrastructure of Stem Wood, Roots, and Needles of a Conifer Varies in Response to Moisture Availability

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pattathil, Sivakumar; Ingwers, Miles W.; Victoriano, Olivia L.

The composition, integrity, and architecture of the macromolecular matrix of cell walls, collectively referred to as cell wall ultrastructure, exhibits variation across species and organs and among cell types within organs. Indirect approaches have suggested that modifications to cell wall ultrastructure occur in response to abiotic stress; however, modifications have not been directly observed. Glycome profiling was used to study cell wall ultrastructure by examining variation in composition and extractability of non-cellulosic glycans in cell walls of stem wood, roots, and needles of loblolly pine saplings exposed to high and low soil moisture. Soil moisture influenced physiological processes and themore » overall composition and extractability of cell wall components differed as a function of soil moisture treatments. The strongest response of cell wall ultrastructure to soil moisture was increased extractability of pectic backbone epitopes in the low soil moisture treatment. The higher abundance of these pectic backbone epitopes in the oxalate extract indicate that the loosening of cell wall pectic components could be associated with the release of pectic signals as a stress response. The increased extractability of pectic backbone epitopes in response to low soil moisture availability was more pronounced in stem wood than in roots or needles. Additional responses to low soil moisture availability were observed in lignin associated carbohydrates released in chlorite extracts of stem wood, including an increased abundance of pectic arabinogalactan epitopes. Overall, these results indicate that cell walls of loblolly pine organs undergo changes in their ultrastructural composition and extractability as a response to soil moisture availability and that cell walls of the stem wood are more responsive to low soil moisture availability compared to cell walls of roots and needles. In conclusion, to our knowledge, this is the first direct evidence, delineated by glycomic analyses, that abiotic stress affects cell wall ultrastructure. This study is also unique in that glycome profiling of pine needles has never before been reported.« less

Cell Wall Ultrastructure of Stem Wood, Roots, and Needles of a Conifer Varies in Response to Moisture Availability.

PubMed

Pattathil, Sivakumar; Ingwers, Miles W; Victoriano, Olivia L; Kandemkavil, Sindhu; McGuire, Mary Anne; Teskey, Robert O; Aubrey, Doug P

2016-01-01

The composition, integrity, and architecture of the macromolecular matrix of cell walls, collectively referred to as cell wall ultrastructure, exhibits variation across species and organs and among cell types within organs. Indirect approaches have suggested that modifications to cell wall ultrastructure occur in response to abiotic stress; however, modifications have not been directly observed. Glycome profiling was used to study cell wall ultrastructure by examining variation in composition and extractability of non-cellulosic glycans in cell walls of stem wood, roots, and needles of loblolly pine saplings exposed to high and low soil moisture. Soil moisture influenced physiological processes and the overall composition and extractability of cell wall components differed as a function of soil moisture treatments. The strongest response of cell wall ultrastructure to soil moisture was increased extractability of pectic backbone epitopes in the low soil moisture treatment. The higher abundance of these pectic backbone epitopes in the oxalate extract indicate that the loosening of cell wall pectic components could be associated with the release of pectic signals as a stress response. The increased extractability of pectic backbone epitopes in response to low soil moisture availability was more pronounced in stem wood than in roots or needles. Additional responses to low soil moisture availability were observed in lignin-associated carbohydrates released in chlorite extracts of stem wood, including an increased abundance of pectic arabinogalactan epitopes. Overall, these results indicate that cell walls of loblolly pine organs undergo changes in their ultrastructural composition and extractability as a response to soil moisture availability and that cell walls of the stem wood are more responsive to low soil moisture availability compared to cell walls of roots and needles. To our knowledge, this is the first direct evidence, delineated by glycomic analyses, that abiotic stress affects cell wall ultrastructure. This study is also unique in that glycome profiling of pine needles has never before been reported.

Pyrolysis-field ionization mass spectrometry of rhizodeposits - a new approach to identify potential effects of genetically modified plants on soil organisms.

PubMed

Melnitchouck, Alexei; Leinweber, Peter; Broer, Inge; Eckhardt, Kai-Uwe

2006-01-01

The objectives of the present study were (1) to investigate the qualitative composition of rhizodeposits leached from soils cropped with non-transgenic and genetically modified (GM) potatoes, and disclose if there were GM-specific modifications in potato rhizodeposition, and (2) to compare these results with conventional bulk parameters of microbial activity in soil. We have raised potatoes from a non-transgenic line (Solanum tuberosum L. cv. Désirée) and three GM lines, which expressed a gene for the resistance to kanamycin (DLH 9000) and a gene for T4 lysozyme (DL10 and DL12). A sandy soil placed in 340 cm3-"CombiSart" containers was used, from which the rhizodeposit was leached after a six-week growth period. The freeze-dried leachates were analyzed by pyrolysis-field ionization mass spectrometry (Py-FIMS). The Py-FI mass spectra gave detailed molecular-chemical information about the composition of leachates, indicating that the potato growth generally altered the composition of the soil solution. Moreover, a principal component analysis of the mass spectra showed differences between the leachates from the non-transgenic parent line and the GM potatoes as well as among the latter group. However, these differences in molecular composition could not be assigned to the release of T4-lysozyme into soil. Dehydrogenase activity and substrate-induced soil respiration as more common bulk parameters of soil microbial activity failed to disclose any significant effects of the various potatoes grown. The limitations of the described rhizodeposit leaching and analysis for risk assessment of GM potato cropping under field conditions are discussed critically. However, it could be concluded that the Py-FI mass spectrometric "fingerprint" can be developed as a fast, comprehensive, highly sensitive and reproducible analytical approach to discern any effects GM-crops may exert on soil ecological parameters.

Cell Wall Ultrastructure of Stem Wood, Roots, and Needles of a Conifer Varies in Response to Moisture Availability

DOE PAGES

Pattathil, Sivakumar; Ingwers, Miles W.; Victoriano, Olivia L.; ...

2016-06-24

The composition, integrity, and architecture of the macromolecular matrix of cell walls, collectively referred to as cell wall ultrastructure, exhibits variation across species and organs and among cell types within organs. Indirect approaches have suggested that modifications to cell wall ultrastructure occur in response to abiotic stress; however, modifications have not been directly observed. Glycome profiling was used to study cell wall ultrastructure by examining variation in composition and extractability of non-cellulosic glycans in cell walls of stem wood, roots, and needles of loblolly pine saplings exposed to high and low soil moisture. Soil moisture influenced physiological processes and themore » overall composition and extractability of cell wall components differed as a function of soil moisture treatments. The strongest response of cell wall ultrastructure to soil moisture was increased extractability of pectic backbone epitopes in the low soil moisture treatment. The higher abundance of these pectic backbone epitopes in the oxalate extract indicate that the loosening of cell wall pectic components could be associated with the release of pectic signals as a stress response. The increased extractability of pectic backbone epitopes in response to low soil moisture availability was more pronounced in stem wood than in roots or needles. Additional responses to low soil moisture availability were observed in lignin associated carbohydrates released in chlorite extracts of stem wood, including an increased abundance of pectic arabinogalactan epitopes. Overall, these results indicate that cell walls of loblolly pine organs undergo changes in their ultrastructural composition and extractability as a response to soil moisture availability and that cell walls of the stem wood are more responsive to low soil moisture availability compared to cell walls of roots and needles. In conclusion, to our knowledge, this is the first direct evidence, delineated by glycomic analyses, that abiotic stress affects cell wall ultrastructure. This study is also unique in that glycome profiling of pine needles has never before been reported.« less

Spatial modeling of biological soil crusts to support rangeland assessment and monitoring

USGS Publications Warehouse

Bowker, M.A.; Belnap, J.; Miller, M.E.

2006-01-01

Biological soil crusts are a diverse soil surface community, prevalent in semiarid regions, which function as ecosystem engineers and perform numerous important ecosystem services. Loss of crusts has been implicated as a factor leading to accelerated soil erosion and other forms of land degradation. To support assessment and monitoring efforts aimed at ensuring the sustainability of rangeland ecosystems, managers require spatially explicit information concerning potential cover and composition of biological soil crusts. We sampled low disturbance sites in Grand Staircase-Escalante National Monument (Utah, USA) to determine the feasibility of modeling the potential cover and composition of biological soil crusts in a large area. We used classification and regression trees to model cover of four crust types (light cyanobacterial, dark cyanobacterial, moss, lichen) and 1 cyanobacterial biomass proxy (chlorophyll a), based upon a parsimonious set of GIS (Geographic Information Systems) data layers (soil types, precipitation, and elevation). Soil type was consistently the best predictor, although elevation and precipitation were both invoked in the various models. Predicted and observed values for the dark cyanobacterial, moss, and lichen models corresponded moderately well (R 2 = 0.49, 0.64, 0.55, respectively). Cover of late successional crust elements (moss + lichen + dark cyanobacterial) was also successfully modeled (R2 = 0.64). We were less successful with models of light cyanobacterial cover (R2 = 0.22) and chlorophyll a (R2 = 0.09). We believe that our difficulty modeling chlorophyll a concentration is related to a severe drought and subsequent cyanobacterial mortality during the course of the study. These models provide the necessary reference conditions to facilitate the comparison between the actual cover and composition of biological soil crusts at a given site and their potential cover and composition condition so that sites in poor condition can be identified and management actions can be taken.

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome.

PubMed

Neilson, Julia W; Califf, Katy; Cardona, Cesar; Copeland, Audrey; van Treuren, Will; Josephson, Karen L; Knight, Rob; Gilbert, Jack A; Quade, Jay; Caporaso, J Gregory; Maier, Raina M

2017-01-01

Global deserts occupy one-third of the Earth's surface and contribute significantly to organic carbon storage, a process at risk in dryland ecosystems that are highly vulnerable to climate-driven ecosystem degradation. The forces controlling desert ecosystem degradation rates are poorly understood, particularly with respect to the relevance of the arid-soil microbiome. Here we document correlations between increasing aridity and soil bacterial and archaeal microbiome composition along arid to hyperarid transects traversing the Atacama Desert, Chile. A meta-analysis reveals that Atacama soil microbiomes exhibit a gradient in composition, are distinct from a broad cross-section of nondesert soils, and yet are similar to three deserts from different continents. Community richness and diversity were significantly positively correlated with soil relative humidity (SoilRH). Phylogenetic composition was strongly correlated with SoilRH, temperature, and electrical conductivity. The strongest and most significant correlations between SoilRH and phylum relative abundance were observed for Acidobacteria , Proteobacteria , Planctomycetes , Verrucomicrobia , and Euryarchaeota (Spearman's rank correlation [ r s ] = >0.81; false-discovery rate [ q ] = ≤0.005), characterized by 10- to 300-fold decreases in the relative abundance of each taxon. In addition, network analysis revealed a deterioration in the density of significant associations between taxa along the arid to hyperarid gradient, a pattern that may compromise the resilience of hyperarid communities because they lack properties associated with communities that are more integrated. In summary, results suggest that arid-soil microbiome stability is sensitive to aridity as demonstrated by decreased community connectivity associated with the transition from the arid class to the hyperarid class and the significant correlations observed between soilRH and both diversity and the relative abundances of key microbial phyla typically dominant in global soils. IMPORTANCE We identify key environmental and geochemical factors that shape the arid soil microbiome along aridity and vegetation gradients spanning over 300 km of the Atacama Desert, Chile. Decreasing average soil relative humidity and increasing temperature explain significant reductions in the diversity and connectivity of these desert soil microbial communities and lead to significant reductions in the abundance of key taxa typically associated with fertile soils. This finding is important because it suggests that predicted climate change-driven increases in aridity may compromise the capacity of the arid-soil microbiome to sustain necessary nutrient cycling and carbon sequestration functions as well as vegetative cover in desert ecosystems, which comprise one-third of the terrestrial biomes on Earth.

Non-destructive estimates of soil carbonic anhydrase activity and associated soil water oxygen isotope composition

NASA Astrophysics Data System (ADS)

Jones, Sam P.; Ogée, Jérôme; Sauze, Joana; Wohl, Steven; Saavedra, Noelia; Fernández-Prado, Noelia; Maire, Juliette; Launois, Thomas; Bosc, Alexandre; Wingate, Lisa

2017-12-01

The contribution of photosynthesis and soil respiration to net land-atmosphere carbon dioxide (CO2) exchange can be estimated based on the differential influence of leaves and soils on budgets of the oxygen isotope composition (δ18O) of atmospheric CO2. To do so, the activity of carbonic anhydrases (CAs), a group of enzymes that catalyse the hydration of CO2 in soils and plants, needs to be understood. Measurements of soil CA activity typically involve the inversion of models describing the δ18O of CO2 fluxes to solve for the apparent, potentially catalysed, rate of CO2 hydration. This requires information about the δ18O of CO2 in isotopic equilibrium with soil water, typically obtained from destructive, depth-resolved sampling and extraction of soil water. In doing so, an assumption is made about the soil water pool that CO2 interacts with, which may bias estimates of CA activity if incorrect. Furthermore, this can represent a significant challenge in data collection given the potential for spatial and temporal variability in the δ18O of soil water and limited a priori information with respect to the appropriate sampling resolution and depth. We investigated whether we could circumvent this requirement by inferring the rate of CO2 hydration and the δ18O of soil water from the relationship between the δ18O of CO2 fluxes and the δ18O of CO2 at the soil surface measured at different ambient CO2 conditions. This approach was tested through laboratory incubations of air-dried soils that were re-wetted with three waters of different δ18O. Gas exchange measurements were made on these soils to estimate the rate of hydration and the δ18O of soil water, followed by soil water extraction to allow for comparison. Estimated rates of CO2 hydration were 6.8-14.6 times greater than the theoretical uncatalysed rate of hydration, indicating that CA were active in these soils. Importantly, these estimates were not significantly different among water treatments, suggesting that this represents a robust approach to assay the activity of CA in soil. As expected, estimates of the δ18O of the soil water that equilibrates with CO2 varied in response to alteration to the δ18O of soil water. However, these estimates were consistently more negative than the composition of the soil water extracted by cryogenic vacuum distillation at the end of the gas measurements with differences of up to -3.94 ‰ VSMOW-SLAP. These offsets suggest that, at least at lower water contents, CO2-H2O isotope equilibration primarily occurs with water pools that are bound to particle surfaces and are depleted in 18O compared to bulk soil water.

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression

PubMed Central

O’Callaghan, Maureen; Condron, Leo M.; Kowalchuk, George A.; Van Nostrand, Joy D.; Zhou, Jizhong; Wakelin, Steven A.

2018-01-01

Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity. PMID:29734390

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

PubMed Central

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-01-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration. PMID:28349918

Effects of Formica ants on soil fauna-results from a short-term exclusion and a long-term natural experiment.

PubMed

Lenoir, Lisette; Bengtsson, Jan; Persson, Tryggve

2003-02-01

Wood ants (Formica spp.) were hypothesised to affect the composition and greatly reduce the abundance of large-sized soil fauna by predation. This was tested in two ways. Firstly, a 4-year-long experimental study was carried out in a mixed forest. Five ant-free 1.3-m(2) plots were created by fenced exclosures within an ant territory. Five nearby plots had fences with entrances for the ants. In addition, five non-fenced control plots were selected. Soil fauna (e.g. Coleoptera, Diptera larvae, Collembola and Araneae) was sampled during the summers of 1997-2000. The soil fauna was affected by the exclosures but there was no detectable effect of ants on the soil fauna. Secondly, soil fauna was studied within a large-scale natural experiment in which the long-term (30 years) effects of red wood ants could be assessed inside and outside ant territories. This long-term natural experiment revealed no significant effects of ants on the abundance or composition of soil fauna. The results from the two studies indicate that the effects of wood ants on soil fauna are fairly small. The hypothesis that wood ants are key-stone predators on soil fauna could, thus, not be supported.

Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function.

PubMed

Ruiz-González, Clara; Archambault, Esther; Laforest-Lapointe, Isabelle; Del Giorgio, Paul A; Kembel, Steven W; Messier, Christian; Nock, Charles A; Beisner, Beatrix E

2018-06-14

Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages.

Community and functional shifts in ammonia oxidizers across terrestrial and marine (soil/sediment) boundaries in two coastal Bay ecosystems.

PubMed

Zhang, Li-Mei; Duff, Aoife M; Smith, Cindy J

2018-04-24

Terrestrial-marine boundaries are significant sites of biogeochemical activity with delineated gradients from land to sea. While niche differentiation of ammonia-oxidizing archaea (AOA) and bacteria (AOB) driven by pH and nitrogen is well known, the patterns and environmental drivers of AOA and AOB community structure and activity across soil-sediment boundaries have not yet been determined. In this study, nitrification potential rate, community composition and transcriptional activity of AOA and AOB in soil, soil/sediment interface and sediments of two coastal Bays were characterized using a combination of field investigations and microcosm incubations. At DNA level, amoA gene abundances of AOA were significantly greater than AOB in soil, while in sediments AOB were significantly more abundant than AOA, but at the soil/sediment interface there were equal numbers of AOA and AOB amoA genes. Microcosm incubations provided further evidence, through qPCR and DGGE-sequencing analysis of amoA transcripts, that AOA were active in soil, AOB in sediment and both AOA and AOB were active at the soil/sediment interface. The AOA and AOB community composition shifted across the coastal soil-interface-sediment gradient with salinity and pH identified as major environmental drivers. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression.

PubMed

Dignam, Bryony E A; O'Callaghan, Maureen; Condron, Leo M; Kowalchuk, George A; Van Nostrand, Joy D; Zhou, Jizhong; Wakelin, Steven A

2018-01-01

Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity.

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China

NASA Astrophysics Data System (ADS)

Tian, Qin; Taniguchi, Takeshi; Shi, Wei-Yu; Li, Guoqing; Yamanaka, Norikazu; Du, Sheng

2017-03-01

Similar land-use types usually have similar soil properties, and, most likely, similar microbial communities. Here, we assessed whether land-use types or soil chemical properties are the primary drivers of soil microbial community composition, and how changes in one part of the ecosystem affect another. We applied Ion Torrent sequencing to the bacterial and fungal communities of five different land-use (vegetation) types in the Loess Plateau of China. We found that the overall trend of soil quality was natural forest > plantation > bare land. Dominant bacterial phyla consisted of Proteobacteria (42.35%), Actinobacteria (15.61%), Acidobacteria (13.32%), Bacteroidetes (8.43%), and Gemmatimonadetes (6.0%). The dominant fungi phyla were Ascomycota (40.39%), Basidiomycota (38.01%), and Zygomycota (16.86%). The results of Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA) based on land-use types displayed groups according to the land-use types. Furthermore, the bacterial communities were mainly organized by soil organic carbon (SOC). The fungal communities were mainly related to available phosphorus (P). The results suggested that the changes of land use type generated changes in soil chemical properties, controlling the composition of microbial community in the semiarid Loess Plateau region. The microbial community could be an indicator for soil quality with respect to ecological restoration.

New Approaches in Soil Organic Matter Fluorescence; A Solid Phase Fluorescence Approach

NASA Astrophysics Data System (ADS)

Bowman, M. M.; Sanclements, M.; McKnight, D. M.

2017-12-01

Fluorescence spectroscopy is a well-established technique to investigate the composition of organic matter in aquatic systems and is increasingly applied to soil organic matter (SOM). Current methods require that SOM be extracted into a liquid prior to analysis by fluorescence spectroscopy. Soil extractions introduce an additional layer of complexity as the composition of the organic matter dissolved into solution varies based upon the selected extractant. Water is one of the most commonly used extractant, but only extracts the water-soluble fraction of the SOM with the insoluble soil organic matter fluorescence remaining in the soil matrix. We propose the use of solid phase fluorescence on whole soils as a potential tool to look at the composition of organic matter without the extraction bias and gain a more complete understand of the potential for fluorescence as a tool in terrestrial studies. To date, the limited applications of solid phase fluorescence have ranged from food and agriculture to pharmaceutical with no clearly defined methods and limitations available. We are aware of no other studies that use solid phase fluorescence and thus no clear methods to look at SOM across a diverse set of soil types and ecosystems. With this new approach to fluorescence spectroscopy there are new challenges, such as blank correction, inner filter effect corrections, and sample preparation. This work outlines a novel method for analyzing soil organic matter using solid phase fluorescence across a wide range of soils collected from the National Ecological Observatory Network (NEON) eco-domains. This method has shown that organic matter content in soils must be diluted to 2% to reduce backscattering and oversaturation of the detector in forested soils. In mineral horizons (A) there is observed quenching of the humic-like organic matter, which is likely a result of organo-mineral complexation. Finally, we present preliminary comparisons between solid and liquid phase fluorescence, which provide new insights into fluorescence studies in terrestrial systems.

Soils at the hyperarid margin: The isotopic composition of soil carbonate from the Atacama Desert, Northern Chile

USGS Publications Warehouse

Quade, Jay; Rech, Jason A.; Latorre, Claudio; Betancourt, Julio L.; Gleeson, Erin; Kalin, Mary T.K.

2007-01-01

We evaluate the impact of exceptionally sparse plant cover (0–20%) and rainfall (2–114 mm/yr) on the stable carbon and oxygen composition of soil carbonate along elevation transects in what is among the driest places on the planet, the Atacama Desert in northern Chile. δ13C and δ18O values of carbonates from the Atacama are the highest of any desert in the world. δ13C (VPDB) values from soil carbonate range from -8.2% at the wettest sites to +7.9% at the driest. We measured plant composition and modeled respiration rates required to form these carbonate isotopic values using a modified version of the soil diffusion model of [Cerling (1984) Earth Planet. Sci. Lett.71, 229–240], in which we assumed an exponential form of the soil CO2 production function, and relatively shallow (20–30 cm) average production depths. Overall, we find that respiration rates are the main predictor of the δ13C value of soil carbonate in the Atacama, whereas the fraction C3 to C4 biomass at individual sites has a subordinate influence. The high average δ13C value (+4.1%) of carbonate from the driest study sites indicates it formed&mdahs;perhaps abiotically—in the presence of pure atmospheric CO2. δ18O (VPDB) values from soil carbonate range from -5.9% at the wettest sites to +7.3% at the driest and show much less regular variation with elevation change than δ13C values. δ18O values for soil carbonate predicted from local temperature and δ18O values of rainfall values suggest that extreme (>80% in some cases) soil dewatering by evaporation occurs at most sites prior to carbonate formation. The effects of evaporation compromise the use of δ18O values from ancient soil carbonate to reconstruct paleoelevation in such arid settings.

Interactive effects of preindustrial, current and future atmospheric CO2 concentrations and temperature on soil fungi associated with two Eucalyptus species.

PubMed

Anderson, Ian C; Drigo, Barbara; Keniry, Kerry; Ghannoum, Oula; Chambers, Susan M; Tissue, David T; Cairney, John W G

2013-02-01

Soil microbial processes have a central role in global fluxes of the key biogenic greenhouse gases and are likely to respond rapidly to climate change. Whether climate change effects on microbial processes lead to a positive or negative feedback for terrestrial ecosystem resilience is unclear. In this study, we investigated the interactive effects of [CO(2)] and temperature on soil fungi associated with faster-growing Eucalyptus saligna and slower-growing Eucalyptus sideroxylon, and fungi that colonised hyphal in-growth bags. Plants were grown in native soil under controlled soil moisture conditions, while subjecting the above-ground compartment to defined atmospheric conditions differing in CO(2) concentrations (290, 400, 650 μL L(-1)) and temperature (26 and 30 °C). Terminal restriction fragment length polymorphism and sequencing methods were used to examine effects on the structure of the soil fungal communities. There was no significant effect of host plant or [CO(2)]/temperature treatment on fungal species richness (α diversity); however, there was a significant effect on soil fungal community composition (β diversity) which was strongly influenced by eucalypt species. Interestingly, β diversity of soil fungi associated with both eucalypt species was significantly influenced by the elevated [CO(2) ]/high temperature treatment, suggesting that the combination of future predicted levels of atmospheric [CO(2)] and projected increases in global temperature will significantly alter soil fungal community composition in eucalypt forest ecosystems, independent of eucalypt species composition. These changes may arise through direct effects of changes in [CO(2)] and temperature on soil fungi or through indirect effects, which is likely the case in this study given the plant-dependent nature of our observations. This study highlights the role of plant species in moderating below-ground responses to future predicted changes to [CO(2)] and temperature and the importance of considering integrated plant-soil system responses. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Water repellency and organic matter composition after a wildfire: new insights using thermal analysis

NASA Astrophysics Data System (ADS)

Neris, Jonay; Doerr, Stefan

2014-05-01

Water repellency, a key parameter in the hydrological and ecological behaviour of ecosystems, is one of the main soil properties affected by wildfire through its impact on organic matter (Shakesby and Doerr, 2006). This study examines the link between post-fire organic matter quantity and composition, soil water repellency and related hydrological properties in order to (i) examine the influence of different organic matter pools on soil hydrological properties and (ii) to explore the use of these links as a proxy for soil hydrological impacts of fire. Soil samples from five fire-affected burned and unburned control sites in Andisols terrain in Tenerife, previously studied for water repellency and hydrology-related properties (Neris et al., 2013), were selected and thermogravimetric analysis (TG) carried out to evaluate fire impacts on their organic matter composition. A decrease in the organic matter quantity as well as in the relative amount of the labile organic matter pool and an increase in the recalcitrant and/or refractory pool depending was observed in the burned soils. TG data, using 10 ºC temperature range steps, allowed reasonable prediction of soil properties evaluated, with R2 ranging from 0.4 to 0.8. The labile pool showed a broad and positive influence on most soil properties evaluated, whereas the refractory pool and the dehydration range affected the surface water holding capacity and water repellency. These results, in conjunction with the simplicity of the TG analysis suggest that, following a calibration step to link TG data to the site-specific post-fire soil properties, this method may be a useful tool for rapid and cost-effective soil hydrological response evaluation after the fire. References Neris, J., Tejedor, M., Fuentes, J., Jiménez, C., 2013. Infiltration, runoff and soil loss in Andisols affected by forest fire (Canary Islands, Spain). Hydrological Processes 27(19), 2814-2824. Shakesby, R.A., Doerr, S.H., 2006. Wildfire as a hydrological and geomorphological agent. Earth-Science Reviews 74(3-4), 269-307.

Stages of the development of alluvial soils in the Bikin River valley (the Amur River basin) in the Middle and Late Holocene

NASA Astrophysics Data System (ADS)

Nazarkina, A. V.; Belyanin, P. S.

2014-05-01

The evolution of alluvial soils in the Bikin River basin in the Middle and the Late Holocene is discussed. On the basis of biostratigraphic data, four pollen zones have been identified in the soils: Pinus koraiensis- Picea, Pinus koraiensis- Quercus- Sphagnum, Betula- Alnus- Alnaster, and Quercus. A set of soil characteristics (texture, acid-base properties, and the organic matter content and group composition) have also been determined. These data allow us to distinguish between four stages of alluvial soil formation in the Bikin River basin. They characterize humus-forming conditions in the Middle and the Late Holocene. Reconstruction of ancient vegetation conditions makes it possible to conclude that climatic fluctuations were synchronous with changes in the soil characteristics. During the Holocene climatic optimum, humus was formed in a slightly acid medium, and humic acids predominated. In cold periods with increased precipitation, fulvic acids predominated in the composition of humus, and the portion of insoluble residue was high because of the more acid medium. The stages of alluvial pedogenesis in the Bikin River valley follow the sedimentation model of soil evolution. Alluvial gray humus soils evolved from typical gray humus soils under meadow communities during warm periods to gleyic and gleyed soils under birch shrubs and alder groves in colder and wetter periods.

pH dominates variation in tropical soil archaeal diversity and community structure.

PubMed

Tripathi, Binu M; Kim, Mincheol; Lai-Hoe, Ang; Shukor, Nor A A; Rahim, Raha A; Go, Rusea; Adams, Jonathan M

2013-11-01

Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

To Grow, Nurture, and Maintain: Soil

NASA Astrophysics Data System (ADS)

Joshi, I.; Lam, K.; Hennelly, L. O.; Archie, J. P.

2012-12-01

The importance and difficulties encountered in a sustainable urban farm can be witnessed at the Stanford Earth Systems Educational Garden, in the growth, maintenance, and nurturing of the soil. Techniques and chemicals developed in the mid to late 1900's have infiltrated the traditional farming techniques that allowed humans to continuously farm for hundreds of years. The sudden spur of interest in sustainability has lead many, including Stanford Earth Systems, to reincorporate traditional methods in conjunction with modern technology. To override the damage made by chemicals and industrial farming, we had to recognize that healthy crops originated from healthy soil; thus we began investigating how to nourish soil. We began to research the ideal composition and structure of soil and methods to create and maintain fertile soil. Secondly, we prioritized the importance of nurturing plants and fed the plants with a plethora of natural fertilizers. We also created a compost pile so that the soil could rehabilitate and refill with nutrients with help provided by bacteria. Lastly, we had to maintain the soil to keep the soil viable for future crops. To do this, we had to acknowledge the chemical composition of the soil and plant cover crops to ensure that the nutrients are replenished. Our experiences enabled us to understand the time and effort required to manage suitable crops, animals, and structures for an urban farm.

Use of LANDSAT data to define soil boundaries in Carroll County, Missouri

NASA Technical Reports Server (NTRS)

Davidson, S. E.

1981-01-01

Bands 4, 5 and 7 false color composite photographs were prepared using data from LANDSAT scenes acquired during April 1977 and April 1981 on computer compatible tapes, and these color composites were compared with band 7 black and white photographs prepared for the entire county. Delineations of soil boundaries at the soil association level were achieved using LANDSAT spectral reflectance data and slope maps for a portion of Carroll County, Missouri. Forty two spectral reflectance classes from April 1977 LANDSAT data were overlaid on digitized slope maps of nine USGS 7.5 minute series topographic quadrangle slope maps to achieve boundary delineations of the soil associations.

Soils from Mare Crisium - Agglutinitic glass chemistry and soil development

NASA Technical Reports Server (NTRS)

Hu, H.-N.; Taylor, L. A.

1978-01-01

Agglutinates were studied in 29 polished thin sections of grain mounts from various size fractions of six Luna 24 soil horizons. Three populations of agglutinitic glass compositions were found: a high-MgO, high-FeO group identified as a coarse-grained basaltic component; a low-MgO, low-FeO group from a highland source; and a low-MgO, high-FeO group probably from the subophitic basalt component. The presence of a significant amount of admixed highland component probably accounts for an enrichment in plagioclase and a depletion in ferromagnesian elements displayed by the agglutinitic glass compositions relative to the bulk soil.

Estimating forest-grassland dynamics using soil phytolith assemblages and δ13C of soil organic matter

Treesearch

Becky K. Kerns; Margeret M. Moore; Stephen C. Hart

2001-01-01

Our objectives were to examine the relationship between contemporary vegetation and surface soil phytolith assemblages, and use phytoliths and δ13C of soil organic matter (SOM) to explore forest-grassland vegetation dynamics. We established plots within three canopy types (open, old-growth, and dense young pine) with different grass species compositions in a...

Controls and dynamics of biochar decay and soil microbial abundance, carbon use efficiency during long-term biochar-amended soil incubations

USDA-ARS?s Scientific Manuscript database

Biochar addition to soil has been proposed as a management strategy to sequester a recalcitrant form of carbon (C). However, there is growing evidence that biochar can be degraded by soil microbes and modify their abundance, community composition and activity. Yet we lack an understanding of how mic...

Evidence that soil aluminum enforces site fidelity of southern New England forest trees

Treesearch

S. W. Bigelow; C. D. Canham

2010-01-01

Tree species composition of hardwood forests of the northeastern United States corresponds with soil chemistry, and differential performance along soil calcium (Ca) gradients has been proposed as a mechanism for enforcing this fidelity of species to site. We conducted studies in a southern New England forest to test if surface-soil Ca is more important than other...

Spatial and vertical distribution of soil physico-chemical properties and the content of heavy metals in the pedosphere in Poland

Treesearch

Marek Degorski

1998-01-01

The lithological and petrographical characteristics of soil pedogenesis was determined, and the spatial and vertical distribution of some soil physico-chemical properties (including heavy metal content) were studied along two transects in Poland. The genetic horizon for 22 soil profiles were described for particle size and petrographic composition, quartz grain...

Biomass Composition and Mineral Removal of Sugarcane and Energy Cane on a Sand Soil in Florida

USDA-ARS?s Scientific Manuscript database

Approximately 20% of Sugarcane is grown on sand soils in south Florida, but yields and profits are lower compared to sugarcane grown on organic soils in the region. Energy cane may be an alternative crop on sand soils in the future to improve profits because of the growing interest of increased biom...

Phosphorus dynamics in soils irrigated with reclaimed waste water or fresh water - A study using oxygen isotopic composition of phosphate

USGS Publications Warehouse

Zohar, I.; Shaviv, A.; Young, M.; Kendall, C.; Silva, S.; Paytan, A.

2010-01-01

Transformations of phosphate (Pi) in different soil fractions were tracked using the stable isotopic composition of oxygen in phosphate (??18Op) and Pi concentrations. Clay soil from Israel was treated with either reclaimed waste water (secondary, low grade) or with fresh water amended with a chemical fertilizer of a known isotopic signature. Changes of ??18Op and Pi within different soil fractions, during a month of incubation, elucidate biogeochemical processes in the soil, revealing the biological and the chemical transformation impacting the various P pools. P in the soil solution is affected primarily by enzymatic activity that yields isotopic equilibrium with the water molecules in the soil solution. The dissolved P interacts rapidly with the loosely bound P (extracted by bicarbonate). The oxides and mineral P fractions (extracted by NaOH and HCl, respectively), which are considered as relatively stable pools of P, also exhibited isotopic alterations in the first two weeks after P application, likely related to the activity of microbial populations associated with soil surfaces. Specifically, isotopic depletion which could result from organic P mineralization was followed by isotopic enrichment which could result from preferential biological uptake of depleted P from the mineralized pool. Similar transformations were observed in both soils although transformations related to biological activity were more pronounced in the soil treated with reclaimed waste water compared to the fertilizer treated soil. ?? 2010 Elsevier B.V.

The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

NASA Astrophysics Data System (ADS)

Rasche, Frank

2017-04-01

A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

Soil carbon and nitrogen stocks in forests along an altitudinal gradient in the eastern Himalayas and a meta-analysis of global data.

PubMed

Tashi, Sonam; Singh, Balwant; Keitel, Claudia; Adams, Mark

2016-06-01

High-altitude soils potentially store a large pool of carbon (C) and nitrogen (N). The assessment of total C and N stocks in soils is vital to understanding the C and N dynamics in terrestrial ecosystems. In this study, we examined effects of altitude and forest composition on soil C and N along a transect from 317 to 3300 m a.s.l. in the eastern Himalayas. We used meta-analysis to establish the context for our results on the effects of altitude on soil C, including variation with depth. Total C and N contents of soils significantly increased with altitude, but decreased with soil depth. Carbon and N were similarly correlated with altitude and temperature, and temperature was seemingly the main driver of soil C along the altitudinal gradient. Altitude accounted for 73% of the variation in C and 47% of the variation in N stocks. Soil pH and cation exchange capacity were correlated with both soil C and N stocks. Increases in soil C and N stocks were related to forest composition, forest basal area as well as quantity of leaf litter that were in turn influenced by altitude and temperature. Concentrations of C in foliage increased by 2.1% for every 1000 m rise in altitude, while that in leaf litter increased by 2.3%. © 2016 John Wiley & Sons Ltd.

Study on fluoride emission from soils at high temperature related to brick-making process.

PubMed

Xie, Z M; Wu, W H; Xu, J M

2003-02-01

Characteristics of fluoride emission from 12 soils at temperatures of 400-1,100 degrees C related to the brick-making process were studied. The results obtained in this study indicate that fluoride emission as gaseous HF and SiF4 was related to the firing temperature, soil total fluoride content, soil composition and calcium compounds added to soils. Soils began to release fluoride at temperatures between 500 and 700 degrees C. Marked increases of the average fluoride mission rate from 57.2% to 85.4% of soil total fluoride were noticed as the heating temperature was increased from 700 to 1,100 degrees C. It was found that the major proportion (over 50%) of the soil total fluoride was emitted from soils at approximate 800 degrees C. The amount of fluoride released into the atmosphere when heated depended on the total fluoride contents in the soils. Correlation analysis showed that the soil composition, such as cation exchange capacity, exchangeable calcium and CaCO3, had some influence on fluoride emission below 900 degrees C, but had no influence at temperatures above 900 degrees C. Addition of four calcium compounds (CaO, CaCO3, Ca(OH)2, and CaSO4) at 1.5% by weight raised the temperature at which fluoride began to be released to 700 degrees C. The greatest decrease in fluoride emission among the four calcium compound treatments was found with CaCO3.

p-Coumaric Acid Influenced Cucumber Rhizosphere Soil Microbial Communities and the Growth of Fusarium oxysporum f.sp. cucumerinum Owen

PubMed Central

Zhou, Xingang; Wu, Fengzhi

2012-01-01

Background Autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. However, how autotoxins affect soil microbial communities is not yet fully understood. Methodology/Principal Findings The aims of this study were to study the effects of an artificially applied autotoxin of cucumber, p-coumaric acid, on cucumber seedling growth, rhizosphere soil microbial communities, and Fusarium oxysporum f.sp. cucumerinum Owen (a soil-borne pathogen of cucumber) growth. Abundance, structure and composition of rhizosphere bacterial and fungal communities were analyzed with real-time PCR, PCR-denaturing gradient gel electrophoresis (DGGE) and clone library methods. Soil dehydrogenase activity and microbial biomass C (MBC) were determined to indicate the activity and size of the soil microflora. Results showed that p-coumaric acid (0.1–1.0 µmol/g soil) decreased cucumber leaf area, and increased soil dehydrogenase activity, MBC and rhizosphere bacterial and fungal community abundances. p-Coumaric acid also changed the structure and composition of rhizosphere bacterial and fungal communities, with increases in the relative abundances of bacterial taxa Firmicutes, Betaproteobacteria, Gammaproteobacteria and fungal taxa Sordariomycete, Zygomycota, and decreases in the relative abundances of bacterial taxa Bacteroidetes, Deltaproteobacteria, Planctomycetes, Verrucomicrobia and fungal taxon Pezizomycete. In addition, p-coumaric acid increased Fusarium oxysporum population densities in soil. Conclusions/Significance These results indicate that p-coumaric acid may play a role in the autotoxicity of cucumber via influencing soil microbial communities. PMID:23118972

p-Coumaric acid influenced cucumber rhizosphere soil microbial communities and the growth of Fusarium oxysporum f.sp. cucumerinum Owen.

PubMed

Zhou, Xingang; Wu, Fengzhi

2012-01-01

Autotoxicity of cucumber root exudates or decaying residues may be the cause of the soil sickness of cucumber. However, how autotoxins affect soil microbial communities is not yet fully understood. The aims of this study were to study the effects of an artificially applied autotoxin of cucumber, p-coumaric acid, on cucumber seedling growth, rhizosphere soil microbial communities, and Fusarium oxysporum f.sp. cucumerinum Owen (a soil-borne pathogen of cucumber) growth. Abundance, structure and composition of rhizosphere bacterial and fungal communities were analyzed with real-time PCR, PCR-denaturing gradient gel electrophoresis (DGGE) and clone library methods. Soil dehydrogenase activity and microbial biomass C (MBC) were determined to indicate the activity and size of the soil microflora. Results showed that p-coumaric acid (0.1-1.0 µmol/g soil) decreased cucumber leaf area, and increased soil dehydrogenase activity, MBC and rhizosphere bacterial and fungal community abundances. p-Coumaric acid also changed the structure and composition of rhizosphere bacterial and fungal communities, with increases in the relative abundances of bacterial taxa Firmicutes, Betaproteobacteria, Gammaproteobacteria and fungal taxa Sordariomycete, Zygomycota, and decreases in the relative abundances of bacterial taxa Bacteroidetes, Deltaproteobacteria, Planctomycetes, Verrucomicrobia and fungal taxon Pezizomycete. In addition, p-coumaric acid increased Fusarium oxysporum population densities in soil. These results indicate that p-coumaric acid may play a role in the autotoxicity of cucumber via influencing soil microbial communities.

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China

PubMed Central

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Xue, Yadong; Deng, Ye; Li, Hui; Zhou, Jizhong; Li, Diqiang

2015-01-01

Understanding biological diversity elevational pattern and the driver factors are indispensable to develop the ecological theories. Elevational gradient may minimize the impact of environmental factors and is the ideal places to study soil microbial elevational patterns. In this study, we selected four typical vegetation types from 1000 to 2800 m above the sea level on the northern slope of Shennongjia Mountain in central China, and analysed the soil bacterial community composition, elevational patterns and the relationship between soil bacterial diversity and environmental factors by using the 16S rRNA Illumina sequencing and multivariate statistical analysis. The results revealed that the dominant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Verrucomicrobia, which accounted for over 75% of the bacterial sequences obtained from tested samples, and the soil bacterial operational taxonomic unit (OTU) richness was a significant monotonous decreasing (P < 0.01) trend with the elevational increasing. The similarity of soil bacterial population composition decreased significantly (P < 0.01) with elevational distance increased as measured by the Jaccard and Bray–Curtis index. Canonical correspondence analysis and Mantel test analysis indicated that plant diversity and soil pH were significantly correlated (P < 0.01) with the soil bacterial community. Therefore, the soil bacterial diversity on Shennongjia Mountain had a significant and different elevational pattern, and plant diversity and soil pH may be the key factors in shaping the soil bacterial spatial pattern. PMID:26032124

Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead?

DOE PAGES

Classen, Aimée T.; Sundqvist, Maja K.; Henning, Jeremiah A.; ...

2015-08-07

Global change is altering species distributions and thus interactions among organisms. Organisms live in concert with thousands of other species, some beneficial, some pathogenic, some which have little to no effect in complex communities. Since natural communities are composed of organisms with very different life history traits and dispersal ability it is unlikely they will all respond to climatic change in a similar way. Disjuncts in plant-pollinator and plant-herbivore interactions under global change have been relatively well described, but plant-soil microorganism and soil microbe-microbe relationships have received less attention. Since soil microorganisms regulate nutrient transformations, provide plants with nutrients, allowmore » co-existence among neighbors, and control plant populations, changes in soil microorganism-plant interactions could have significant ramifications for plant community composition and ecosystem function. Finally, in this paper we explore how climatic change affects soil microbes and soil microbe-plant interactions directly and indirectly, discuss what we see as emerging and exciting questions and areas for future research, and discuss what ramifications changes in these interactions may have on the composition and function of ecosystems.« less

Microelements in anthropogenically contaminated soils in the central part of Petrozavodsk

NASA Astrophysics Data System (ADS)

Rybakov, D. S.; Kevlich, V. I.

2017-06-01

Urban soils (Urbic Technosols) formed within or near the industrial sites removed of service show a considerable excess over the regional background in the content of Pb, Zn, Cu, Mn, Cr, Ni, as well as over the average content of W, Mo, Pb, Sb, Cr, Cu, Sn, Ni, Zn, and Mn in urban soils. Microelements are concentrated for the most part in the soil fine earth, and above all, in the fraction with particle size <0.1 mm. Surface films (on quartz and feldspar grains) of quartz-feldspar-muscovite (partially with tremolite and chlorite) composition and undifferentiated dispersed mixture of quartz, albite, microcline, muscovite and organomineral soil substance are the strongest concentrators of heavy metals and metalloids. Pb and Sn are partially present in soils as oxides, and a part of Zn and Pb, in the form of substantial admixtures to technogenic chemical compounds. As a whole, distribution of elements in the studied soils is controlled by the specifics and type of contamination, resistance of coarser grains to weathering under the given physicochemical conditions, and by predominantly mineral (quartz-feldspar) composition of the solids in soil layers and the features of elements proper.

Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Classen, Aimée T.; Sundqvist, Maja K.; Henning, Jeremiah A.

Global change is altering species distributions and thus interactions among organisms. Organisms live in concert with thousands of other species, some beneficial, some pathogenic, some which have little to no effect in complex communities. Since natural communities are composed of organisms with very different life history traits and dispersal ability it is unlikely they will all respond to climatic change in a similar way. Disjuncts in plant-pollinator and plant-herbivore interactions under global change have been relatively well described, but plant-soil microorganism and soil microbe-microbe relationships have received less attention. Since soil microorganisms regulate nutrient transformations, provide plants with nutrients, allowmore » co-existence among neighbors, and control plant populations, changes in soil microorganism-plant interactions could have significant ramifications for plant community composition and ecosystem function. Finally, in this paper we explore how climatic change affects soil microbes and soil microbe-plant interactions directly and indirectly, discuss what we see as emerging and exciting questions and areas for future research, and discuss what ramifications changes in these interactions may have on the composition and function of ecosystems.« less

[Effect of afforestation modes on soil microbial community and nitrogen functional genes in Hippophae rhamnoides plantation].

PubMed

Yang, Dan; Yu, Xuan; Liu, Xu; Liu, Jin-liana; Zhang, Shun-xiang; Yu, Ze-qun

2015-12-01

The study aimed to assess the effect of different afforestation modes on microbial composition and nitrogen functional genes in soil. Soil samples from a pure Hippophae rhamnoides stand (SS) and three mixed stands, namely, H. rhamnoides and Pinus tabuliformis (SY), H. rhamnoides and Platycladus orientalis (SB), H. rhamnoides and Robinia pseucdoacacia (SC) were selected. The results showed that the total PLFA (TPLFA), bacterial PLFA, gram positive bacterial PLFA (G⁺PLFA) were significantly higher in soil samples from other three stands than those of the pure one. However, no significant difference was found for fungal PLFA among them. The abundance of nifH, amoA, nirK and narG genes were higher in SY and SC than in SS. The TPLFA, G⁺PLFA, gram negative bacterial PLFA (G⁻PLFA), and all of the detected gene abundance were significantly and positively correlated with soil pH, total organic carbon, total nitrogen, ammonium nitrogen and available potassium. Afforestation modes affected indirectly soil microbial composition and functional genes through soil properties. Mixing P. tabuliformis or P. orientalis with H. rhamnoides might be suitable afforestation modes, which might improve soil quality.

Let's Break It Down; a Study of Organic Decompostion in Clay Soil

NASA Astrophysics Data System (ADS)

Weiss, E.

2017-12-01

Things that can affect decomposition are the decomposers in the soil, temperature, and water or moisture. My secondary research also showed that PH and chemical composition of the soil affect the rate of decomposition. Cold or freezing temperatures can help preserve organic material in soil because it freezes the soil and moisture, making it too dense for the organic decomposers to break down the organic matter. Soil also can be preserved by drying out and being stored at 4º Celsius (or 39º Fahrenheit) for 28 days. However, soil can degrade slowly in these conditions because it is not frozen and can be oxidized.

Soil microbiological composition and its evolution along with forest succession in West Siberia

NASA Astrophysics Data System (ADS)

Naplekova, Nadezhda N.; Malakhova, Nataliya A.; Maksyutov, Shamil

2015-04-01

Natural forest succession process in West Siberia is mostly initiated by fire disturbance and involves changing tree species composition from pioneer species to late succession trees. Along with forest aging, litter and forest biomass accumulate. Changes of the soil nitrogen cycle between succession stages, important for plant functioning, have been reported in a number of studies. To help understanding the mechanism of the changes in the soil nitrogen cycle we analyzed soil microbiological composition for soil profiles (0-160 cm) taken at sites corresponding to three forest succession stages: (1) young pine, age 18-20 years, (2) mid age, dark coniferous, age 50-70 years, (3) mature, fir-spruce, age 170-180 years. Soil samples were taken from each soil horizon and analyzed in the laboratory for quantity and species composition of algae and other microorganisms. Algae community at all stages of succession is dominated by species typical for forest (pp. Chlorhormidium, Chlamydomonas, Chloroccocum, Pleurochloris, Stichococcus). Algae species composition is summarized by formulas: young forest C14X10Ch9H2P4Cf1B2amph4, mid age X16C15Ch10H4P4Cf1B2amph4, mature X24C22Ch17H10P2amph5Cf1, with designations C -- Cyanophyta, X -- Xantophyta, Ch -- Chlorophyta, B -- Bacillariophyta. Diversity is highest in upper two horizons and declines with depth. Microorganism composition on upper 20 cm was analyzed in three types of forests separately for consumers of protein (ammonifiers) and mineral nitrogen, fungi, azotobacter, Clostridium pasteurianum, oligonitrophylic (eg diazotrophs), nitrifiers and denitrifiers. Nitrogen biologic fixation in the mature forest soils is done mostly by oligonitrophyls and microorganisms of the genus Clostridium as well as сyanobacteria of sp. Nostoc, but the production rate appears low. Concentrations (count in gram soil) of nitrogen consumers (eg ammonifiers), oligonitrophyls, Clostridium and denitrifiers increase several fold from young forest to mid age, and from mid age to mature forest. On the contrary, azotobacter disappears in mature forest while nitrifiers decline by several times from young to mid age forest. Large variation in microbiological activity was observed between sites reaching different succession stage, however further studies are needed to discriminate between effects of the site productivity and forest age.

Two-dimensional NMR spectroscopy strongly enhances soil organic matter composition analysis

NASA Astrophysics Data System (ADS)

Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Hedenström, Mattias; Schleucher, Jürgen

2016-04-01

Soil organic matter (SOM) is the largest terrestrial carbon pool and strongly affects soil properties. With climate change, understanding SOM processes and turnover and how they could be affected by increasing temperatures becomes critical. This is particularly key for organic soils as they represent a huge carbon pool in very sensitive ecosystems, like boreal ecosystems and peatlands. Nevertheless, characterization of SOM molecular composition, which is essential to elucidate soil carbon processes, is not easily achieved, and further advancements in that area are greatly needed. Solid-state one-dimensional (1D) 13C nuclear magnetic resonance (NMR) spectroscopy is often used to characterize its molecular composition, but only provides data on a few major functional groups, which regroup many different molecular fragments. For instance, in the carbohydrates region, signals of all monosaccharides present in many different polymers overlap. This overlap thwarts attempts to identify molecular moieties, resulting in insufficient information to characterize SOM composition. Here we show that two-dimensional (2D) liquid-state 1H-13C NMR spectra provided much richer data on the composition of boreal plant litter and organic surface soil. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra and displayed signals from hundreds of identifiable molecular groups. For example, in the aromatics region, signals from individual lignin units could be recognized. It was hence possible to follow the fate of specific structural moieties in soils. We observed differences between litter and soil samples, and were able to relate them to the decomposition of identifiable moieties. Sample preparation and data acquisition were both simple and fast. Further, using multivariate data analysis, we aimed at linking the detailed chemical fingerprints of SOM to turnover rates in a soil incubation experiment. With the multivariate models, we were able to identify specific molecular moieties correlated to variability in the temperature response of organic matter decomposition, as assessed by Q10. Thus, 2D NMR methods, and their combination with multivariate analysis, can greatly improve analysis of litter and SOM composition, thereby facilitating elucidation of their roles in biogeochemical and ecological processes that are so critical to foresee associated feedback mechanisms on SOM turnover as a result of global environmental change.

Climate interacts with soil to produce beta diversity in Californian plant communities.

PubMed

Fernandez-Going, B M; Harrison, S P; Anacker, B L; Safford, H D

2013-09-01

Spatially distinct communities can arise through interactions and feedbacks between abiotic and biotic factors. We suggest that, for plants, patches of infertile soils such as serpentine may support more distinct communities from those in the surrounding non-serpentine matrix in regions where the climate is more productive (i.e., warmer and/or wetter). Where both soil fertility and climatic productivity are high, communities may be dominated by plants with fast-growing functional traits, whereas where either soils or climate impose low productivity, species with stress-tolerant functional traits may predominate. As a result, both species and functional composition may show higher dissimilarity between patch and matrix in productive climates. This pattern may be reinforced by positive feedbacks, in which higher plant growth under favorable climate and soil conditions leads to higher soil fertility, further enhancing plant growth. For 96 pairs of sites across a 200-km latitudinal gradient in California, we found that the species and functional dissimilarities between communities on infertile serpentine and fertile non-serpentine soils were higher in more productive (wetter) regions. Woody species had more stress-tolerant functional traits on serpentine than non-serpentine soil, and as rainfall increased, woody species functional composition changed toward fast-growing traits on non-serpentine, but not on serpentine soils. Soil organic matter increased with rainfall, but only on non-serpentine soils, and the difference in organic matter between soils was positively correlated with plant community dissimilarity. These results illustrate a novel mechanism wherein climatic productivity is associated with higher species, functional, and landscape-level dissimilarity (beta diversity).

Differences in the Activities of Eight Enzymes from Ten Soil Fungi and Their Possible Influences on the Surface Structure, Functional Groups, and Element Composition of Soil Colloids

PubMed Central

Wang, Wenjie; Li, Yanhong; Wang, Huimei; Zu, Yuangang

2014-01-01

How soil fungi function in soil carbon and nutrient cycling is not well understood by using fungal enzymatic differences and their interactions with soil colloids. Eight extracellular enzymes, EEAs (chitinase, carboxymethyl cellulase, β-glucosidase, protease, acid phosphatase, polyphenol oxidase, laccase, and guaiacol oxidase) secreted by ten fungi were compared, and then the fungi that showed low and high enzymatic activity were co-cultured with soil colloids for the purpose of finding fungi-soil interactions. Some fungi (Gomphidius rutilus, Russula integra, Pholiota adiposa, and Geastrum mammosum) secreted 3–4 enzymes with weak activities, while others (Cyathus striatus, Suillus granulate, Phallus impudicus, Collybia dryophila, Agaricus sylvicola, and Lactarius deliciosus) could secret over 5 enzymes with high activities. The differences in these fungi contributed to the alterations of functional groups (stretching bands of O-H, N-H, C-H, C = O, COO- decreased by 11–60%, while P = O, C-O stretching, O-H bending and Si-O-Si stretching increased 9–22%), surface appearance (disappearance of adhesive organic materials), and elemental compositions (11–49% decreases in C1s) in soil colloids. Moreover, more evident changes were generally in high enzymatic fungi (C. striatus) compared with low enzymatic fungi (G. rutilus). Our findings indicate that inter-fungi differences in EEA types and activities might be responsible for physical and chemical changes in soil colloids (the most active component of soil matrix), highlighting the important roles of soil fungi in soil nutrient cycling and functional maintenance. PMID:25398013

Differences in the activities of eight enzymes from ten soil fungi and their possible influences on the surface structure, functional groups, and element composition of soil colloids.

PubMed

Wang, Wenjie; Li, Yanhong; Wang, Huimei; Zu, Yuangang

2014-01-01

How soil fungi function in soil carbon and nutrient cycling is not well understood by using fungal enzymatic differences and their interactions with soil colloids. Eight extracellular enzymes, EEAs (chitinase, carboxymethyl cellulase, β-glucosidase, protease, acid phosphatase, polyphenol oxidase, laccase, and guaiacol oxidase) secreted by ten fungi were compared, and then the fungi that showed low and high enzymatic activity were co-cultured with soil colloids for the purpose of finding fungi-soil interactions. Some fungi (Gomphidius rutilus, Russula integra, Pholiota adiposa, and Geastrum mammosum) secreted 3-4 enzymes with weak activities, while others (Cyathus striatus, Suillus granulate, Phallus impudicus, Collybia dryophila, Agaricus sylvicola, and Lactarius deliciosus) could secret over 5 enzymes with high activities. The differences in these fungi contributed to the alterations of functional groups (stretching bands of O-H, N-H, C-H, C = O, COO- decreased by 11-60%, while P = O, C-O stretching, O-H bending and Si-O-Si stretching increased 9-22%), surface appearance (disappearance of adhesive organic materials), and elemental compositions (11-49% decreases in C1s) in soil colloids. Moreover, more evident changes were generally in high enzymatic fungi (C. striatus) compared with low enzymatic fungi (G. rutilus). Our findings indicate that inter-fungi differences in EEA types and activities might be responsible for physical and chemical changes in soil colloids (the most active component of soil matrix), highlighting the important roles of soil fungi in soil nutrient cycling and functional maintenance.

Microbial community dynamics in soil aggregates shape biogeochemical gas fluxes from soil profiles - upscaling an aggregate biophysical model.

PubMed

Ebrahimi, Ali; Or, Dani

2016-09-01

Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate-like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self-organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual-based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2 O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models. © 2016 John Wiley & Sons Ltd.

Finite element analysis of gravel pile composite foundation under flexible foundation of Airport Engineering

NASA Astrophysics Data System (ADS)

Luo, Min

2018-02-01

On the basis of consulting data, the bearing mechanism of gravel pile composite foundation is analyzed in this paper. The use of ANSYS software under flexible foundation according to the plum blossoms gravel pile additional stress between pile and soil additional stress distribution, load on pile top stress and pile bearing rate of modulus ratio between pile and soil on the pile top stress and rate of pile bearing capacity, pile-soil effect the stress ratio was calculated and analyzed, providing reasonable design reference for the design of gravel pile composite foundation.

Soil resources and topography shape local tree community structure in tropical forests

PubMed Central

Baldeck, Claire A.; Harms, Kyle E.; Yavitt, Joseph B.; John, Robert; Turner, Benjamin L.; Valencia, Renato; Navarrete, Hugo; Davies, Stuart J.; Chuyong, George B.; Kenfack, David; Thomas, Duncan W.; Madawala, Sumedha; Gunatilleke, Nimal; Gunatilleke, Savitri; Bunyavejchewin, Sarayudh; Kiratiprayoon, Somboon; Yaacob, Adzmi; Supardi, Mohd N. Nur; Dalling, James W.

2013-01-01

Both habitat filtering and dispersal limitation influence the compositional structure of forest communities, but previous studies examining the relative contributions of these processes with variation partitioning have primarily used topography to represent the influence of the environment. Here, we bring together data on both topography and soil resource variation within eight large (24–50 ha) tropical forest plots, and use variation partitioning to decompose community compositional variation into fractions explained by spatial, soil resource and topographic variables. Both soil resources and topography account for significant and approximately equal variation in tree community composition (9–34% and 5–29%, respectively), and all environmental variables together explain 13–39% of compositional variation within a plot. A large fraction of variation (19–37%) was spatially structured, yet unexplained by the environment, suggesting an important role for dispersal processes and unmeasured environmental variables. For the majority of sites, adding soil resource variables to topography nearly doubled the inferred role of habitat filtering, accounting for variation in compositional structure that would previously have been attributable to dispersal. Our results, illustrated using a new graphical depiction of community structure within these plots, demonstrate the importance of small-scale environmental variation in shaping local community structure in diverse tropical forests around the globe. PMID:23256196