The effect of row structure on soil moisture retrieval accuracy from passive microwave data.

PubMed

Xingming, Zheng; Kai, Zhao; Yangyang, Li; Jianhua, Ren; Yanling, Ding

2014-01-01

Row structure causes the anisotropy of microwave brightness temperature (TB) of soil surface, and it also can affect soil moisture retrieval accuracy when its influence is ignored in the inversion model. To study the effect of typical row structure on the retrieved soil moisture and evaluate if there is a need to introduce this effect into the inversion model, two ground-based experiments were carried out in 2011. Based on the observed C-band TB, field soil and vegetation parameters, row structure rough surface assumption (Q p model and discrete model), including the effect of row structure, and flat rough surface assumption (Q p model), ignoring the effect of row structure, are used to model microwave TB of soil surface. Then, soil moisture can be retrieved, respectively, by minimizing the difference of the measured and modeled TB. The results show that soil moisture retrieval accuracy based on the row structure rough surface assumption is approximately 0.02 cm(3)/cm(3) better than the flat rough surface assumption for vegetated soil, as well as 0.015 cm(3)/cm(3) better for bare and wet soil. This result indicates that the effect of row structure cannot be ignored for accurately retrieving soil moisture of farmland surface when C-band is used.

Influence of soil structure on nutrient cycling using microfluidic techniques

NASA Astrophysics Data System (ADS)

Arellano Caicedo, Carlos; Aleklett, Kristin; Ohlsson, Pelle; Hammer, Edith

2017-04-01

The rising of atmospheric CO2 levels and its effects on global warming make it necessary to understand the elements that regulate such levels and furthermore try to slow down the CO2 accumulation in the atmosphere. The exchange of carbon between soil and atmosphere plays a significant role in the atmospheric carbon budget. Soil organisms deposit organic compounds on and in soil aggregates, either as exudates or dead remains. Much of this dead organic material is quickly recycled, but a portion, however, will stay in the soil for long term. Evidence suggests that micro-scale biogeochemical interactions could play a highly significant role in degradation or persistence of organic matter in soils, thus, soil physical structure might play a decisive role in preventing accessibility of nutrients to microorganisms. For studying effects of spatial microstructure on soil nutrient cycles, we have constructed artificial habitats for microbes that simulate soil structures. Microfluidic, so called Lab-on-a-chip technologies, are one of the tools used to achieve our purpose. Such micro-habitats consist of pillar structures of difference density and surface area, tunnels with increasing depth, and mazes of increasing complexity to simulate different stages of soil aggregation. Using microscopy and analytical chemistry, we can follow the growth of microorganisms inoculated into the "soil chip" as well as the chemical degradation of organic matter compounds provided as nutrient source. In this way, we want to be able to predict how soil structure influences soil microbial activity leading to different effects on the carbon cycle. Our first results of a chip inoculated with natural soil showed a succession of organisms colonizing channels leading to dead-end arenas, starting with a high presence of bacteria inside the chip during the first days. Fungal hyphae growth gradually inside the channels until it finally occupied the big majority of the spaces isolating bacteria which dramatically decreased in number. The structure inside the soil chip changes dynamically due to the creation of biofilms. Such changes alter the spatial distribution inside the chip gradually, to the point of getting significantly different from the original structures. Fungal hyphae, bacterial biofilms, and microbial necro mass accumulation where the components altering the chip structure. These findings suggest that a considerable part of the soil structure is microbial biomass. Using Lab-on-a-chip techniques leads to the creation of a much more realistic soil and ecosystem model, resembling spatial and chemical complexity in real soil structures at a micrometer scale, the scale relevant for soil organisms. Understanding small-scale processes in the soils is crucial to predict carbon and nutrient cycling, and to enable us to give recommendations for soil management in agriculture, horticulture and nature conservation. If parameterization of soil structure as a central determinant for carbon sequestration is possible, it will allow strong argumentation for management practices that conserve and foster soil structure, such as low-tillage, support of mycorrhizal fungi, and reduction of heavy machinery usage.

High Energy Moisture Characteristics: Linking Between Soil Physical Processes and Structure Stability

USDA-ARS?s Scientific Manuscript database

Water storage and flow in soils is usually complicated by the intricate nature of and changes in soil pore size distribution (PSD) due to modifications in soil structure following changes in agricultural management. The paper presents the Soil High Energy Moisture Characteristic (Soil-HEMC) method f...

A long-term soil structure observatory for post-compaction soil structure evolution: design and initial soil structure recovery observations

NASA Astrophysics Data System (ADS)

Keller, Thomas; Colombi, Tino; Ruiz, Siul; Grahm, Lina; Reiser, René; Rek, Jan; Oberholzer, Hans-Rudolf; Schymanski, Stanislaus; Walter, Achim; Or, Dani

2016-04-01

Soil compaction due to agricultural vehicular traffic alters the geometrical arrangement of soil constituents, thereby modifying mechanical properties and pore spaces that affect a range of soil hydro-ecological functions. The ecological and economic costs of soil compaction are dependent on the immediate impact on soil functions during the compaction event, and a function of the recovery time. In contrast to a wealth of soil compaction information, mechanisms and rates of soil structure recovery remain largely unknown. A long-term (>10-yr) soil structure observatory (SSO) was established in 2014 on a loamy soil in Zurich, Switzerland, to quantify rates and mechanisms of structure recovery of compacted arable soil under different post-compaction management treatments. We implemented three initial compaction treatments (using a two-axle agricultural vehicle with 8 Mg wheel load): compaction of the entire plot area (i.e. track-by-track), compaction in wheel tracks, and no compaction. After compaction, we implemented four post-compaction soil management systems: bare soil (BS), permanent grass (PG), crop rotation without mechanical loosening (NT), and crop rotation under conventional tillage (CT). BS and PG provide insights into uninterrupted natural processes of soil structure regeneration under reduced (BS) and normal biological activity (PG). The two cropping systems (NT and CT) enable insights into soil structure recovery under common agricultural practices with minimal (NT) and conventional mechanical soil disturbance (CT). Observations include periodic sampling and measurements of soil physical properties, earthworm abundance, crop measures, electrical resistivity and ground penetrating radar imaging, and continuous monitoring of state variables - soil moisture, temperature, CO2 and O2 concentrations, redox potential and oxygen diffusion rates - for which a network of sensors was installed at various depths (0-1 m). Initial compaction increased soil bulk density to about half a metre, decreased gas and water transport functions (air permeability, gas diffusivity, saturated hydraulic conductivity), and increased mechanical impedance. Water infiltration at the soil surface was initially reduced by three orders of magnitude, but significantly recovered within a year. However, within the soil profile, recovery of transport properties is much smaller. Air permeability tended to recover more than gas diffusivity, suggesting that initial post-compaction recovery is initiated by new macropores (e.g. biopores). Tillage recovered topsoil bulk density but not topsoil transport functions. Compaction changed grass species composition in PG, and significantly reduced grass biomass in PG and crop yields in NT and CT.

Analysis of Soil Structure Turnover with Garnet Particles and X-Ray Microtomography

PubMed Central

Vogel, Hans-Jörg

2016-01-01

Matter turnover in soil is tightly linked to soil structure which governs the heterogeneous distribution of habitats, reaction sites and pathways in soil. Thereby, the temporal dynamics of soil structure alteration is deemed to be important for essential ecosystem functions of soil but very little is known about it. A major reason for this knowledge gap is the lack of methods to study soil structure turnover directly at microscopic scales. Here we devise a conceptual approach and an image processing workflow to study soil structure turnover by labeling some initial state of soil structure with small garnet particles and tracking their fate with X-ray microtomography. The particles adhere to aggregate boundaries at the beginning of the experiment but gradually change their position relative to the nearest pore as structure formation progresses and pores are destructed or newly formed. A new metric based on the contact distances between particles and pores is proposed that allows for a direct quantification of soil structure turnover rates. The methodology is tested for a case study about soil compaction of a silty loam soil during stepwise increase of bulk density (ρ = {1.1, 1.3, 1.5} g/cm3). We demonstrate that the analysis of mean contact distances provides genuinely new insights about changing diffusion pathways that cannot be inferred neither from conventional pore space attributes (porosity, mean pore size, pore connectivity) nor from deformation analysis with digital image correlation. This structure labeling approach to quantify soil structure turnover provides a direct analogy to stable isotope labeling for the analysis of matter turnover and can be readily combined with each other. PMID:27453995

Soil compaction--indicators for the assessment of harmful changes to the soil in the context of the German Federal Soil Protection Act.

PubMed

Lebert, Matthias; Böken, Holger; Glante, Frank

2007-02-01

Soil compaction in agriculture induced by large-scale equipment is of growing concern. Heavy wheel loads used in arable cropping have the potential to cause irreversible damage to the subsoil structure and may lead to harmful soil compaction. In order to sustain or improve soil health or fitness on a sustainable basis, indicators are needed to assess the changes in the soil structure and the respective soil functions. This requires an adequate verification of methods for distinguishing between the impairment of soil structure and the disruption of soil functions, and for the respective subject of protection. In this article the link between existing models of soil physical prognosis, practical guidelines, and criteria for the identification of affected soil structure is demonstrated, and a viable concept to distinguish harmful changes to the soil is presented. The concept consists of methods for soil physical analysis such as "pre-compression stress" and "loading ratio", practical recommendations for best management practice, and an indicator-based model for the identification of harmful subsoil compaction derived from a research project for the German Federal Environmental Agency, making it possible to determine for a respective location the required level of action far beyond the common practice of precautions against harmful soil compaction.

Method for analyzing soil structure according to the size of structural elements

NASA Astrophysics Data System (ADS)

Wieland, Ralf; Rogasik, Helmut

2015-02-01

The soil structure in situ is the result of cropping history and soil development over time. It can be assessed by the size distribution of soil structural elements such as air-filled macro-pores, aggregates and stones, which are responsible for important water and solute transport processes, gas exchange, and the stability of the soil against compacting and shearing forces exerted by agricultural machinery. A method was developed to detect structural elements of the soil in selected horizontal slices of soil core samples with different soil structures in order for them to be implemented accordingly. In the second step, a fitting tool (Eureqa) based on artificial programming was used to find a general function to describe ordered sets of detected structural elements. It was shown that all the samples obey a hyperbolic function: Y(k) = A /(B + k) , k ∈ { 0 , 1 , 2 , … }. This general behavior can be used to develop a classification method based on parameters {A and B}. An open source software program in Python was developed, which can be downloaded together with a selection of soil samples.

Effects of drought on forest soil structure and hydrological soil functions

NASA Astrophysics Data System (ADS)

Gimbel, K.; Puhlmann, H.; Weiler, M.

2012-04-01

Climate change is predicted to severely affect precipitation patterns across central Europe. Soil structure is closely linked to the activity of soil microbiota and plant roots, which modify flow pathways along roots, organic matter and water repellence of soils. Through shrinkage and fracturing of soil aggregates, soil structure is also responding to changing climate (in particular drought) conditions. We investigate the possible effects on biogeochemical and hydropedological processes in response to predicted future reduced precipitation, and the interaction of these processes with the biodiversity of the forest understorey and soil biota. The hypotheses of this study are: (i) drought causes a change in soil structure, which affects hydrological soil functions (water infiltration, uptake and redistribution); (ii) changes in rooting patterns and microbial community composition, in response to drought, influence the hydrological soil functions. To test our hypotheses, we built adaptive roofing systems on nine sites in Germany, which allow a flexible reduction of precipitation in order to achieve the long-term minimum precipitation of a site. Here we present first measurements of our repeated measuring/sampling campaign, which will be conducted over a period of three years. The aim of our experiments is to analyze soil pore architecture and related flow and transport behaviour with dye tracer sprinkling experiments, soil column experiments with stable isotope (deuterium, oxygen-18) enriched water, computed tomography at soil monoliths (~70 l) and multi-step outflow experiments with 100 ml soil cores. Finally, we sketch our idea how to relate the observed temporal changes of soil structure and hydrological soil functions to the observed dynamics of hydrometeorological site conditions, soil moisture and desiccation as well as changes in rooting patterns, herb layer and soil microbiotic communities. The results of this study may help to assess future behavior of the plant-soil-water-microbiology-system and may help to adjust models to predict future response to different precipitation patterns as well as help coping with existing and future emerging challenges in forest management.

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

40 CFR 264.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2014 CFR

2014-07-01

... equipment, structures and soils. 264.114 Section 264.114 Protection of Environment ENVIRONMENTAL PROTECTION... of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soils must be properly disposed of or decontaminated unless otherwise specified in...

40 CFR 264.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2012 CFR

2012-07-01

... equipment, structures and soils. 264.114 Section 264.114 Protection of Environment ENVIRONMENTAL PROTECTION... of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soils must be properly disposed of or decontaminated unless otherwise specified in...

40 CFR 264.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2011 CFR

2011-07-01

... equipment, structures and soils. 264.114 Section 264.114 Protection of Environment ENVIRONMENTAL PROTECTION... of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soils must be properly disposed of or decontaminated unless otherwise specified in...

40 CFR 264.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2010 CFR

2010-07-01

... equipment, structures and soils. 264.114 Section 264.114 Protection of Environment ENVIRONMENTAL PROTECTION... of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soils must be properly disposed of or decontaminated unless otherwise specified in...

40 CFR 264.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2013 CFR

2013-07-01

... equipment, structures and soils. 264.114 Section 264.114 Protection of Environment ENVIRONMENTAL PROTECTION... of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soils must be properly disposed of or decontaminated unless otherwise specified in...

Soil structural quality assessment for soil protection regulation

NASA Astrophysics Data System (ADS)

Johannes, Alice; Boivin, Pascal

2017-04-01

Soil quality assessment is rapidly developing worldwide, though mostly focused on the monitoring of arable land and soil fertility. Soil protection regulations assess soil quality differently, focusing on priority pollutants and threshold values. The soil physical properties are weakly considered, due to lack of consensus and experimental difficulties faced with characterization. Non-disputable, easy to perform and inexpensive methods should be available for environmental regulation to be applied, which is unfortunately not the case. As a consequence, quantitative soil physical protection regulation is not applied, and inexpensive soil physical quality indicators for arable soil management are not available. Overcoming these limitations was the objective of a research project funded by the Swiss federal office for environment (FOEN). The main results and the perspectives of application are given in this presentation. A first step of the research was to characterize soils in a good structural state (reference soils) under different land use. The structural quality was assessed with field expertise and Visual Evaluation of the Soil Structure (VESS), and the physical properties were assessed with Shrinkage analysis. The relationships between the physical properties and the soil constituents were linear and highly determined. They represent the reference properties of the corresponding soils. In a second step, the properties of physically degraded soils were analysed and compared to the reference properties. This allowed defining the most discriminant parameters departing the different structure qualities and their threshold limits. Equivalent properties corresponding to these parameters but inexpensive and easy to determine were defined and tested. More than 90% of the samples were correctly classed with this method, which meets, therefore, the requirements for practical application in regulation. Moreover, result-oriented agri-environmental schemes for soil quality are now proposed to farmers based on these indicators.

Urbanization Effects on the Vertical Distribution of Soil Microbial Communities and Soil C Storage across Edge-to-Interior Urban Forest Gradients

NASA Astrophysics Data System (ADS)

Rosier, C. L.; Van Stan, J. T., II; Trammell, T. L.

2017-12-01

Urbanization alters environmental conditions such as temperature, moisture, carbon (C) and nitrogen (N) deposition affecting critical soil processes (e.g., C storage). Urban soils experience elevated N deposition (e.g., transportation, industry) and decreased soil moisture via urban heat island that can subsequently alter soil microbial community structure and activity. However, there is a critical gap in understanding how increased temperatures and pollutant deposition influences soil microbial community structure and soil C/N cycling in urban forests. Furthermore, canopy structural differences between individual tree species is a potentially important mechanism facilitating the deposition of pollutants to the soil. The overarching goal of this study is to investigate the influence of urbanization and tree species structural differences on the bacterial and fungal community and C and N content of soils experiencing a gradient of urbanization pressures (i.e., forest edge to interior; 150-m). Soil cores (1-m depth) were collected near the stem (< 0.5 meter) of two tree species with contrasting canopy and bark structure (Fagus grandifolia, vs. Liriodendron tulipifera), and evaluated for soil microbial structure via metagenomic analysis and soil C/N content. We hypothesize that soil moisture constraints coupled with increases in recalcitrant C will decrease gram negative bacteria (i.e., dependent on labile C) while increasing saprophytic fungal community abundance (i.e., specialist consuming recalcitrant C) within both surface and subsurface soils experiencing the greatest urban pressure (i.e., forest edge). We further expect trees located on the edge of forest fragments will maintain greater surface soil (< 20 cm) C concentrations due to decreased soil moisture constraining microbial activity (e.g., slower decay), and increased capture of recalcitrant C stocks from industrial/vehicle emission sources (e.g., black C). Our initial results support our hypotheses that urbanization alters soil microbial community composition via reduced soil moisture and carbon storage potential via deposition gradients. Further analyses will answer important questions regarding how individual tree species alters urban soil C storage, N retention, and microbial dynamics.

Modeling the Dynamics of Soil Structure and Water in Agricultural Soil

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2017-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

[Effects of Phyllostachys edulis cultivation on soil bacterial and fungal community structure and diversity].

PubMed

Zhao, Tian Xin; Mao, Xin Wei; Cheng, Min; Chen, Jun Hui; Qin, Hua; Li, Yong Chun; Liang, Chen Fei; Xu, Qiu Fang

2017-11-01

This study examined how soil bacterial and fungal communities responded to the cultivation history of Moso bamboo in Anji and Changxing counties, Huzhou, Zhejiang, China. Soil samples (0-20 and 20-40 cm) were taken from bamboo plantations subjected to different cultivation histories and analyzed the community structures of soil bacterial and fungal by PCR-DGGE methods. It was found that soil bacterial and fungal communities varied greatly with the development of bamboo plantations which converted from Masson pine forest or formed via invading adjacent broadleaf shrub forest. Soil bacterial community structures exhibited a greater response to bamboo cultivation time than fungal community, but bacteria structure of surface soil displayed an ability of resiliency to disturbance and the tendency to recover to the original state. The cultivation time, sampling site and soil layer significantly affected the biodiversity of soil bacteria and fungi, especially the latter two factors. Redundancy analysis (RDA) of soil properties and bacteria or fungi communities showed that there were no accordant factors to drive the alteration of microbial structure, and the first two axes explained less than 65.0% of variance for most of the sampling sites and soil layers, indicating there existed soil parameters besides the five examined that contributed to microbial community alteration.

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2010 CFR

2010-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2014 CFR

2014-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2012 CFR

2012-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2010 CFR

2010-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2011 CFR

2011-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2013 CFR

2013-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2012 CFR

2012-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2013 CFR

2013-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

40 CFR 265.114 - Disposal or decontamination of equipment, structures and soils.

Code of Federal Regulations, 2014 CFR

2014-07-01

... equipment, structures and soils. 265.114 Section 265.114 Protection of Environment ENVIRONMENTAL PROTECTION... decontamination of equipment, structures and soils. During the partial and final closure periods, all contaminated equipment, structures and soil must be properly disposed of, or decontaminated unless specified otherwise in...

40 CFR 267.116 - What must I do with contaminated equipment, structure, and soils?

Code of Federal Regulations, 2011 CFR

2011-07-01

... equipment, structure, and soils? 267.116 Section 267.116 Protection of Environment ENVIRONMENTAL PROTECTION..., structure, and soils? You must properly dispose of or decontaminate all contaminated equipment, structures, and soils during the partial and final closure periods. By removing any hazardous wastes or hazardous...

The physico-chemical properties and structural characteristics of artificial soil for cut slope restoration in Southwestern China

PubMed Central

Chen, Shunan; Ai, Xiaoyan; Dong, Tengyun; Li, Binbin; Luo, Ruihong; Ai, Yingwei; Chen, Zhaoqiong; Li, Chuanren

2016-01-01

Cut slopes are frequently generated by construction work in hilly areas, and artificial soil is often sprayed onto them to promote ecological rehabilitation. The artificial soil properties are very important for effective management of the slopes. This paper uses fractal and moment methods to characterize soil particle size distribution (PSD) and aggregates composition. The fractal dimension (D) showed linear relationships between clay, silt, and sand contents, with coefficients of determination from 0.843 to 0.875, suggesting that using of D to evaluate the PSD of artificial soils is reasonable. The bias (CS) and peak convex (CE) coefficients showed significant correlations with structure failure rate, moisture content, and total porosity, which validated the moment method to quantitatively describe soil structure. Railway slope (RS) soil has lower organic carbon and soil moisture, and higher pH than natural slope soil. Overall, RS exhibited poor soil structure and physicochemical properties, increasing the risk of soil erosion. Hence, more effective management measures should be adopted to promote the restoration of cut slopes. PMID:26883986

Vertical distribution of bacterial community is associated with the degree of soil organic matter decomposition in the active layer of moist acidic tundra.

PubMed

Kim, Hye Min; Lee, Min Jin; Jung, Ji Young; Hwang, Chung Yeon; Kim, Mincheol; Ro, Hee-Myong; Chun, Jongsik; Lee, Yoo Kyung

2016-11-01

The increasing temperature in Arctic tundra deepens the active layer, which is the upper layer of permafrost soil that experiences repeated thawing and freezing. The increasing of soil temperature and the deepening of active layer seem to affect soil microbial communities. Therefore, information on soil microbial communities at various soil depths is essential to understand their potential responses to climate change in the active layer soil. We investigated the community structure of soil bacteria in the active layer from moist acidic tundra in Council, Alaska. We also interpreted their relationship with some relevant soil physicochemical characteristics along soil depth with a fine scale (5 cm depth interval). The bacterial community structure was found to change along soil depth. The relative abundances of Acidobacteria, Gammaproteobacteria, Planctomycetes, and candidate phylum WPS-2 rapidly decreased with soil depth, while those of Bacteroidetes, Chloroflexi, Gemmatimonadetes, and candidate AD3 rapidly increased. A structural shift was also found in the soil bacterial communities around 20 cm depth, where two organic (upper Oi and lower Oa) horizons are subdivided. The quality and the decomposition degree of organic matter might have influenced the bacterial community structure. Besides the organic matter quality, the vertical distribution of bacterial communities was also found to be related to soil pH and total phosphorus content. This study showed the vertical change of bacterial community in the active layer with a fine scale resolution and the possible influence of the quality of soil organic matter on shaping bacterial community structure.

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.

Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

PubMed

Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

2015-09-01

Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions.

Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH.

PubMed

Pettersson, Marie; Bååth, Erland

2013-08-01

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.

Soil fungi colony growth and community dynamics

NASA Astrophysics Data System (ADS)

Falconer, Ruth E.; Kravchenko, Alexandra; Otten, Wilfred

2010-05-01

Fungi are a major player in soil functioning, they contribute to soil structure formation and shaping of plant communities through their role in nutrient cycling, pathogenesis and symbiosis. Theoretical approaches which have emerged over the years and improved considerably our understanding of above ground plant communities are still lacking below ground. A theoretical framework is needed, such that links soil physics, fungal biology and mathematical biology in order to understand fungal community dynamics and diversity in undisturbed soils. Such a framework is essential if we are to understand how environmental change or soil manipulation impacts biodiversity. Different land use and management practices significantly affect soil environmental characteristics crucial for fungal communities by contributing different quantities and qualities of biomass inputs, generating different levels of soil disturbance, influencing soil temperature and moisture regimes, and affecting structure and geometry of soil pore space. Differences in pore structures generated by long-term differences in land use and management are reflected in notable changes in soil physical and hydraulic properties, including soil porosity, hydraulic conductivity and water retention (Brye and Pirani, 2005). Changes in numbers, shapes, and distributions of soil macropores have been often observed (e.g., Pachepsky et al., 1996; Giménez et al., 1997; Udawatta et al., 2008). However, specific implications of these differences in pore structure and geometries for ability of pathogenic as well as non-pathogenic fungi to colonize soil have not yet been addressed. Recent advances in computed tomography and microscopy facilitate detailed examination of the inner pore structures of undisturbed soil samples as well as visualization of fungal mycelia. Such tools together with modelling generate a new level of understanding of the mechanisms governing fungal behaviour at microscopic scales, and for the first time allow us to examine species interactions in a 3D soil environment.

Topsoil structure stability in a restored floodplain: Impacts of fluctuating water levels, soil parameters and ecosystem engineers.

PubMed

Schomburg, A; Schilling, O S; Guenat, C; Schirmer, M; Le Bayon, R C; Brunner, P

2018-10-15

Ecosystem services provided by floodplains are strongly controlled by the structural stability of soils. The development of a stable structure in floodplain soils is affected by a complex and poorly understood interplay of hydrological, physico-chemical and biological processes. This paper aims at analysing relations between fluctuating groundwater levels, soil physico-chemical and biological parameters on soil structure stability in a restored floodplain. Water level fluctuations in the soil are modelled using a numerical surface-water-groundwater flow model and correlated to soil physico-chemical parameters and abundances of plants and earthworms. Causal relations and multiple interactions between the investigated parameters are tested through structural equation modelling (SEM). Fluctuating water levels in the soil did not directly affect the topsoil structure stability, but indirectly through affecting plant roots and soil parameters that in turn determine topsoil structure stability. These relations remain significant for mean annual days of complete and partial (>25%) water saturation. Ecosystem functioning of a restored floodplain might already be affected by the fluctuation of groundwater levels alone, and not only through complete flooding by surface water during a flood period. Surprisingly, abundances of earthworms did not show any relation to other variables in the SEM. These findings emphasise that earthworms have efficiently adapted to periodic stress and harsh environmental conditions. Variability of the topsoil structure stability is thus stronger driven by the influence of fluctuating water levels on plants than by the abundance of earthworms. This knowledge about the functional network of soil engineering organisms, soil parameters and fluctuating water levels and how they affect soil structural stability is of fundamental importance to define management strategies of near-natural or restored floodplains in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

Effects of different regulatory methods on improvement of greenhouse saline soils, tomato quality, and yield.

PubMed

Maomao, Hou; Xiaohou, Shao; Yaming, Zhai

2014-01-01

To identify effective regulatory methods scheduling with the compromise between the soil desalination and the improvement of tomato quality and yield, a 3-year field experiment was conducted to evaluate and compare the effect of straw mulching and soil structure conditioner and water-retaining agent on greenhouse saline soils, tomato quality, and yield. A higher salt removing rate of 80.72% in plough layer with straw mulching was obtained based on the observation of salt mass fraction in 0 ~ 20 cm soil layer before and after the experiment. Salts were also found to move gradually to the deeper soil layer with time. Straw mulching enhanced the content of soil organic matter significantly and was conductive to reserve soil available N, P, and K, while available P and K in soils of plough layer with soil structure conditioner decreased obviously; thus a greater usage of P fertilizer and K fertilizer was needed when applying soil structure conditioner. Considering the evaluation indexes including tomato quality, yield, and desalination effects of different regulatory methods, straw mulching was recommended as the main regulatory method to improve greenhouse saline soils in south China. Soil structure conditioner was the suboptimal method, which could be applied in concert with straw mulching.

Fertilization Shapes Bacterial Community Structure by Alteration of Soil pH.

PubMed

Zhang, Yuting; Shen, Hong; He, Xinhua; Thomas, Ben W; Lupwayi, Newton Z; Hao, Xiying; Thomas, Matthew C; Shi, Xiaojun

2017-01-01

Application of chemical fertilizer or manure can affect soil microorganisms directly by supplying nutrients and indirectly by altering soil pH. However, it remains uncertain which effect mostly shapes microbial community structure. We determined soil bacterial diversity and community structure by 454 pyrosequencing the V1-V3 regions of 16S rRNA genes after 7-years (2007-2014) of applying chemical nitrogen, phosphorus and potassium (NPK) fertilizers, composted manure or their combination to acidic (pH 5.8), near-neutral (pH 6.8) or alkaline (pH 8.4) Eutric Regosol soil in a maize-vegetable rotation in southwest China. In alkaline soil, nutrient sources did not affect bacterial Operational Taxonomic Unit (OTU) richness or Shannon diversity index, despite higher available N, P, K, and soil organic carbon in fertilized than in unfertilized soil. In contrast, bacterial OTU richness and Shannon diversity index were significantly lower in acidic and near-neutral soils under NPK than under manure or their combination, which corresponded with changes in soil pH. Permutational multivariate analysis of variance showed that bacterial community structure was significantly affected across these three soils, but the PCoA ordination patterns indicated the effect was less distinct among nutrient sources in alkaline than in acidic and near-neural soils. Distance-based redundancy analysis showed that bacterial community structures were significantly altered by soil pH in acidic and near-neutral soils, but not by any soil chemical properties in alkaline soil. The relative abundance (%) of most bacterial phyla was higher in near-neutral than in acidic or alkaline soils. The most dominant phyla were Proteobacteria (24.6%), Actinobacteria (19.7%), Chloroflexi (15.3%) and Acidobacteria (12.6%); the medium dominant phyla were Bacterioidetes (5.3%), Planctomycetes (4.8%), Gemmatimonadetes (4.5%), Firmicutes (3.4%), Cyanobacteria (2.1%), Nitrospirae (1.8%), and candidate division TM7 (1.0%); the least abundant phyla were Verrucomicrobia (0.7%), Armatimonadetes (0.6%), candidate division WS3 (0.4%) and Fibrobacteres (0.3%). In addition, Cyanobacteria and candidate division TM7 were more abundant in acidic soil, whereas Gemmatimonadetes, Nitrospirae and candidate division WS3 were more abundant in alkaline soil. We conclude that after 7-years of fertilization, soil bacterial diversity and community structure were shaped more by changes in soil pH rather than the direct effect of nutrient addition.

The effect of total carbon on microscopic soil properties and implications for crop production

USDA-ARS?s Scientific Manuscript database

Soil structure is a dynamic property affected by physical, chemical, and microbiological processes. Addition of organic matter to soils and the use of different management practices have been reported to impact soil structure and crop production. Moderation in soil temperature and increases in mic...

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.

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.

Response of soil biota to vineyard interrow soil cultivation can be altered by the surrounding landscape

NASA Astrophysics Data System (ADS)

Zaller, Johann; Buchholz, Jacob; Querner, Pascal; Paredes, Daniel; Kratschmer, Sophie; Schwantzer, Martina; Winter, Silvia; Strauss, Peter; Bauer, Thomas; Burel, Françoise; Guernion, Muriel; Scimia, Jennifer; Nicolai, Annegret; Cluzeau, Daniel

2017-04-01

Ecosystem services provided by viticultural landscapes result from interactions between management intensity, soil properties, organisms inhabiting these landscapes, and the diversity and structure of the surrounding landscape. However, there is actually very little known to what extent these different factors influence the abundance and diversity of various soil biota. In this study we examined (i) to what extent different soil management intensities of interrows affect the activity and diversity of soil biota (earthworms, Collembola, litter decomposition), (ii) the role of soil properties in influencing these effects and (iii) whether the surrounding landscape structure is altering these interactions. We collected data in 16 vineyards in Austria embedded in landscapes with varying structure (i.e. from structurally simple to complex) and assessed earthworms (hand sorting), Collembola (pitfall trapping and soil coring), litter decomposition (tea bag method). Additionally, soil physical (water infiltration, aggregate stability, porosity, bulk density, soil texture) and chemical (pH, soil carbon content, cation exchange capacity, potassium, phosphorus) parameters were assessed. The landscape surrounding our vineyards within a radius of 750 m was assessed by field mapping using a geographical information system. Results showed that different soil biota/processes are differently affected by soil cultivation intensity and soil properties. Parameters describing the surrounding landscape interacted more with the responses of Collembola to soil cultivation than with earthworms or litter decomposition. These investigations are part of the transdisciplinary BiodivERsA project VineDivers (www.vinedivers.eu) and will ultimately lead into management recommendations for various stakeholders.

[Soil microbial community structure of monoculture and mixed plantation stands of native tree species in south subtropical China].

PubMed

Luo, Da; Shi, Zuo-Min; Tang, Jing-Chao; Liu, Shi-Rong; Lu, Li-Hua

2014-09-01

The effects of three plantation stands, Erythrophleumf ordii (EF), Pinus massoniana (PM), and their mixed plantation (MP), on soil microbial biomass and microbial community structure in south subtropical China were studied by the method of phospholipid fatty acids (PLFAs) analysis. The results showed that the amounts of microbial total PLFAs and PLFAs of each microbial group in these three plantation stand soils were significantly higher in dry season than in rainy season. In dry season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and actinomycetes PLFAs were the highest in the PM soil, moderate in the MP soil, and the lowest in the EF soil. But in rainy season, the amounts of microbial total PLFAs, bacteria PLFAs, fungi PLFAs, and arbuscular mycorrhizal fungi (AMF) PLFAs in the EF soil were higher than in the MP soil, and were significantly higher than in the PM soil. Principal component analysis (PCA) indicated that the variations in soil microbial community structure composition were affected by both plantation types and seasons. Redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil temperature and moisture, pH, total nitrogen content, and ammonium nitrogen content had significant correlations with PLFA signatures. In addition, the ratio of fungi PLFAs to bacteria PLFAs in the MP soil was the highest among the three stand soils within the whole year, indicating that mixed plantation stands could facilitate the stability of the soil ecosystem.

Soil processes and functions across an international network of Critical Zone Observatories: Introduction to experimental methods and initial results

NASA Astrophysics Data System (ADS)

Banwart, Steven; Menon, Manoj; Bernasconi, Stefano M.; Bloem, Jaap; Blum, Winfried E. H.; Souza, Danielle Maia de; Davidsdotir, Brynhildur; Duffy, Christopher; Lair, Georg J.; Kram, Pavel; Lamacova, Anna; Lundin, Lars; Nikolaidis, Nikolaos P.; Novak, Martin; Panagos, Panos; Ragnarsdottir, Kristin Vala; Reynolds, Brian; Robinson, David; Rousseva, Svetla; de Ruiter, Peter; van Gaans, Pauline; Weng, Liping; White, Tim; Zhang, Bin

2012-11-01

Growth in human population and demand for wealth creates ever-increasing pressure on global soils, leading to soil losses and degradation worldwide. Critical Zone science studies the impact linkages between these pressures, the resulting environmental state of soils, and potential interventions to protect soil and reverse degradation. New research on soil processes is being driven by the scientific hypothesis that soil processes can be described along a life cycle of soil development. This begins with formation of new soil from parent material, development of the soil profile, and potential loss of the developed soil functions and the soil itself under overly intensive anthropogenic land use, thus closing the cycle. Four Critical Zone Observatories in Europe have been selected focusing research at sites that represent key stages along the hypothetical soil life cycle; incipient soil formation, productive use of soil for farming and forestry, and decline of soil due to longstanding intensive agriculture. Initial results from the research show that soil develops important biogeochemical properties on the time scale of decades and that soil carbon and the development of favourable soil structure takes place over similar time scales. A new mathematical model of soil aggregate formation and degradation predicts that set-aside land at the most degraded site studied can develop substantially improved soil structure with the accumulation of soil carbon over a period of several years. Further results demonstrate the rapid dynamics of soil carbon; how quickly it can be lost, and also demonstrate how data from the CZOs can be used to determine parameter values for models at catchment scale. A structure for a new integrated Critical Zone model is proposed that combines process descriptions of carbon and nutrient flows, a simplified description of the soil food web, and reactive transport; all coupled with a dynamic model for soil structure and soil aggregation. This approach is proposed as a methodology to analyse data along the soil life cycle and test how soil processes and rates vary within, and between, the CZOs representing different life cycle stages. In addition, frameworks are discussed that will help to communicate the results of this science into a more policy relevant format using ecosystem service approaches.

Modelling soil-water dynamics in the rootzone of structured and water-repellent soils

NASA Astrophysics Data System (ADS)

Brown, Hamish; Carrick, Sam; Müller, Karin; Thomas, Steve; Sharp, Joanna; Cichota, Rogerio; Holzworth, Dean; Clothier, Brent

2018-04-01

In modelling the hydrology of Earth's critical zone, there are two major challenges. The first is to understand and model the processes of infiltration, runoff, redistribution and root-water uptake in structured soils that exhibit preferential flows through macropore networks. The other challenge is to parametrise and model the impact of ephemeral hydrophobicity of water-repellent soils. Here we have developed a soil-water model, which is based on physical principles, yet possesses simple functionality to enable easier parameterisation, so as to predict soil-water dynamics in structured soils displaying time-varying degrees of hydrophobicity. Our model, WEIRDO (Water Evapotranspiration Infiltration Redistribution Drainage runOff), has been developed in the APSIM Next Generation platform (Agricultural Production Systems sIMulation). The model operates on an hourly time-step. The repository for this open-source code is https://github.com/APSIMInitiative/ApsimX. We have carried out sensitivity tests to show how WEIRDO predicts infiltration, drainage, redistribution, transpiration and soil-water evaporation for three distinctly different soil textures displaying differing hydraulic properties. These three soils were drawn from the UNSODA (Unsaturated SOil hydraulic Database) soils database of the United States Department of Agriculture (USDA). We show how preferential flow process and hydrophobicity determine the spatio-temporal pattern of soil-water dynamics. Finally, we have validated WEIRDO by comparing its predictions against three years of soil-water content measurements made under an irrigated alfalfa (Medicago sativa L.) trial. The results provide validation of the model's ability to simulate soil-water dynamics in structured soils.

The mechanics and energetics of soil bioturbation by earthworms and plant roots - Impacts on soil structure generation and maintenance

NASA Astrophysics Data System (ADS)

Or, Dani; Ruiz, Siul; Schymanski, Stanlislaus

2015-04-01

Soil structure is the delicate arrangement of solids and voids that facilitate numerous hydrological and ecological soil functions ranging from water infiltration and retention to gaseous exchange and mechanical anchoring of plant roots. Many anthropogenic activities affect soil structure, e.g. via tillage and compaction, and by promotion or suppression of biological activity and soil carbon pools. Soil biological activity is critical to the generation and maintenance of favorable soil structure, primarily through bioturbation by earthworms and root proliferation. The study aims to quantify the mechanisms, rates, and energetics associated with soil bioturbation, using a new biomechanical model to estimate stresses required to penetrate and expand a cylindrical cavity in a soil under different hydration and mechanical conditions. The stresses and soil displacement involved are placed in their ecological context (typical sizes, population densities, burrowing rates and behavior) enabling estimation of mechanical energy requirements and impacts on soil organic carbon pool (in the case of earthworms). We consider steady state plastic cavity expansion to determine burrowing pressures of earthworms and plant roots, akin to models of cone penetration representing initial burrowing into soil volumes. Results show that with increasing water content the strain energy decreases and suggest trade-offs between cavity expansion pressures and energy investment for different root and earthworm geometries and soil hydration. The study provides a quantitative framework for estimating energy costs of bioturbation in terms of soil organic carbon or the mechanical costs of soil exploration by plant roots as well as mechanical and hydration limits to such activities.

Impact of roots, mycorrhizas and earthworms on soil physical properties as assessed by shrinkage analysis

NASA Astrophysics Data System (ADS)

Milleret, R.; Le Bayon, R.-C.; Lamy, F.; Gobat, J.-M.; Boivin, P.

2009-07-01

SummarySoil biota such as earthworms, arbuscular mycorrhizal fungi (AMF) and plant roots are known to play a major role in engineering the belowground part of the terrestrial ecosystems, thus strongly influencing the water budget and quality on earth. However, the effect of soil organisms and their interactions on the numerous soil physical properties to be considered are still poorly understood. Shrinkage analysis allows quantifying a large spectrum of soil properties in a single experiment, with small standard errors. The objectives of the present study were, therefore, to assess the ability of the method to quantify changes in soil properties as induced by single or combined effects of leek roots ( Allium porrum), AMF ( Glomus intraradices) and earthworms ( Allolobophora chlorotica). The study was performed on homogenised soil microcosms and the experiments lasted 35 weeks. The volume of the root network and the external fungal hyphae was measured at the end, and undisturbed soil cores were collected. Shrinkage analysis allowed calculating the changes in soil hydro-structural stability, soil plasma and structural pore volumes, soil bulk density and plant available water, and structural pore size distributions. Data analysis revealed different impacts of the experimented soil biota on the soil physical properties. At any water content, the presence of A. chlorotica resulted in a decrease of the specific bulk volume and the hydro-structural stability around 25%, and in a significant increase in the bulk soil density. These changes went with a decrease of the structural pore volumes at any pore size, a disappearing of the thinnest structural pores, a decrease in plant available water, and a hardening of the plasma. On the contrary, leek roots decreased the bulk soil density up to 1.23 g cm -3 despite an initial bulk density of 1.15 g cm -3. This increase in volume was accompanied with a enhanced hydro-structural stability, a larger structural pore volume at any pore size, smaller structural pore radii and an increase in plant available water. Interestingly, a synergistic effect of leek roots and AMF in the absence of the earthworms was highlighted, and this synergistic effect was not observed in presence of earthworms. The structural pore volume generated by root and AMF growth was several orders of magnitude larger than the volume of the organisms. Root exudates as well as other AMF secretion have served as carbon source for bacteria that in turn would enhance soil aggregation and porosity, thus supporting the idea of a self-organization of the soil-plant-microbe complex previously described.

An examination of the earthquake behaviour of a retaining wall considering soil-structure interaction

NASA Astrophysics Data System (ADS)

Köktan, Utku; Demir, Gökhan; Kerem Ertek, M.

2017-04-01

The earthquake behavior of retaining walls is commonly calculated with pseudo static approaches based on Mononobe-Okabe method. The seismic ground pressure acting on the retaining wall by the Mononobe-Okabe method does not give a definite idea of the distribution of the seismic ground pressure because it is obtained by balancing the forces acting on the active wedge behind the wall. With this method, wave propagation effects and soil-structure interaction are neglected. The purpose of this study is to examine the earthquake behavior of a retaining wall taking into account the soil-structure interaction. For this purpose, time history seismic analysis of the soil-structure interaction system using finite element method has been carried out considering 3 different soil conditions. Seismic analysis of the soil-structure model was performed according to the earthquake record of "1971, San Fernando Pacoima Dam, 196 degree" existing in the library of MIDAS GTS NX software. The results obtained from the analyses show that the soil-structure interaction is very important for the seismic design of a retaining wall. Keywords: Soil-structure interaction, Finite element model, Retaining wall

Impact of rhizobial inoculation on Acacia senegal (L.) Willd. growth in greenhouse and soil functioning in relation to seed provenance and soil origin.

PubMed

Bakhoum, Niokhor; Ndoye, Fatou; Kane, Aboubacry; Assigbetse, Komi; Fall, Dioumacor; Sylla, Samba Ndao; Noba, Kandioura; Diouf, Diégane

2012-07-01

Rhizobial inoculation has a positive impact on plants growth; however, there is little information about its effect on soil microbial communities and their activity in the rhizosphere. It was therefore necessary to test the effect of inoculation of Acacia senegal (L.) Willd. seedlings with selected rhizobia on plant growth, structure and diversity of soil bacterial communities and soil functioning in relation to plant provenance and soil origin. In order to carry out this experiment, three A. senegal seeds provenance from Kenya, Niger, and Senegal were inoculated with selected rhizobial strains. They have been further grown during 4 months in greenhouse conditions in two non-disinfected soils, Dahra and Goudiry coming respectively from arid and semi-arid areas. The principal component analysis (ACP) showed an inoculation effect on plant growth, rhizospheric bacterial diversity and soil functioning. However, the performances of the rhizobial strains varied in relation to the seed provenance and the soil origin. The selected rhizobial strains, the A. senegal provenance and the soil origin have modified the structure and the diversity of soil bacterial communities as measured by principal component analysis/denaturing gradient gel electrophoresis analyses. It is interesting to note that bacterial communities of Dahra soil were highly structured according to A. senegal provenance, whereas they were structured in relation to rhizobial inoculation in Goudiry soil. Besides, the impact of inoculation on soil microbial activities measured by fluorescein diacetate analyses varied in relation to plant provenance and soil origin. Nevertheless, total microbial activity was about two times higher in Goudiry, arid soil than in Dahra, semi-arid soil. Our results suggest that the rhizobial inoculation is a suitable tool for improving plants growth and soil fertility. Yet, the impact is dependent on inoculants, plant provenance and soil origin. It will, therefore, be crucial to identify the appropriate rhizobial strains and plant provenance or species in relation to the soil type.

The Vertical Structure of Urban Soils and Their Convergence Across Cities

EPA Science Inventory

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is need...

76 FR 70057 - National Oil and Hazardous Substance Pollution Contingency Plan; National Priorities List...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... surface soils, subsurface soils, structures and groundwater within the boundaries of these parcels. In... soils, subsurface soils, structures and groundwater within the boundaries of the non-ETA part of PIN 05... additional contaminated groundwater and soil within the Site. On November 25, 2005 EPA partially deleted the...

Dynamic Effects of Biochar on the Bacterial Community Structure in Soil Contaminated with Polycyclic Aromatic Hydrocarbons.

PubMed

Song, Yang; Bian, Yongrong; Wang, Fang; Xu, Min; Ni, Ni; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

2017-08-16

Amending soil with biochar is an effective soil remediation strategy for organic contaminants. This study investigated the dynamic effects of wheat straw biochar on the bacterial community structure during remediation by high-throughput sequencing. The wheat straw biochar amended into the soil significantly reduced the bioavailability and toxicity of polycyclic aromatic hydrocarbons (PAHs). Biochar amendment helped to maintain the bacterial diversity in the PAH-contaminated soil. The relationship between the immobilization of PAHs and the soil bacterial diversity fit a quadratic model. Before week 12 of the incubation, the incubation time was the main factor contributing to the changes in the soil bacterial community structure. However, biochar greatly affected the bacterial community structure after 12 weeks of amendment, and the effects were dependent upon the biochar type. Amendment with biochar mainly facilitated the growth of rare bacterial genera (relative abundance of 0.01-1%) in the studied soil. Therefore, the application of wheat straw biochar into PAH-contaminated soil can reduce the environmental risks of PAHs and benefit the soil microbial ecology.

USDA-ARS?s Scientific Manuscript database

Ecosystems that maximize soil organic matter and good soil structure maintain high soil biological functioning, soil health and plant growth. Natural ecosystems such as prairies are valuable benchmarks for developing sustainable crop and soil management practices. Soil biological properties critical...

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.

Visual soil evaluation - future research requirements

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Ball, Bruce; Holden, Nick

2017-04-01

A review of Visual Soil Evaluation (VSE) techniques (Emmet-Booth et al., 2016) highlighted their established utility for soil quality assessment, though some limitations were identified; (1) The examination of aggregate size, visible intra-porosity and shape forms a key assessment criterion in almost all methods, thus limiting evaluation to structural form. The addition of criteria that holistically examine structure may be desirable. For example, structural stability can be indicated using dispersion tests or examining soil surface crusting, while the assessment of soil colour may indirectly indicate soil organic matter content, a contributor to stability. Organic matter assessment may also indicate structural resilience, along with rooting, earthworm numbers or shrinkage cracking. (2) Soil texture may influence results or impeded method deployment. Modification of procedures to account for extreme texture variation is desirable. For example, evidence of compaction in sandy or single grain soils greatly differs to that in clayey soils. Some procedures incorporate separate classification systems or adjust deployment based on texture. (3) Research into impacts of soil moisture content on VSE evaluation criteria is required. Criteria such as rupture resistance and shape may be affected by moisture content. It is generally recommended that methods are deployed on moist soils and quantification of influences of moisture variation on results is necessary. (4) Robust sampling strategies for method deployment are required. Dealing with spatial variation differs between methods, but where methods can be deployed over large areas, clear instruction on sampling is required. Additionally, as emphasis has been placed on the agricultural production of soil, so the ability of VSE for exploring structural quality in terms of carbon storage, water purification and biodiversity support also requires research. References Emmet-Booth, J.P., Forristal. P.D., Fenton, O., Ball, B.C. & Holden, N.M. 2016. A review of visual soil evaluation techniques for soil structure. Soil Use and Management, 32, 623-634.

State-Space Estimation of Soil Organic Carbon Stock

NASA Astrophysics Data System (ADS)

Ogunwole, Joshua O.; Timm, Luis C.; Obidike-Ugwu, Evelyn O.; Gabriels, Donald M.

2014-04-01

Understanding soil spatial variability and identifying soil parameters most determinant to soil organic carbon stock is pivotal to precision in ecological modelling, prediction, estimation and management of soil within a landscape. This study investigates and describes field soil variability and its structural pattern for agricultural management decisions. The main aim was to relate variation in soil organic carbon stock to soil properties and to estimate soil organic carbon stock from the soil properties. A transect sampling of 100 points at 3 m intervals was carried out. Soils were sampled and analyzed for soil organic carbon and other selected soil properties along with determination of dry aggregate and water-stable aggregate fractions. Principal component analysis, geostatistics, and state-space analysis were conducted on the analyzed soil properties. The first three principal components explained 53.2% of the total variation; Principal Component 1 was dominated by soil exchange complex and dry sieved macroaggregates clusters. Exponential semivariogram model described the structure of soil organic carbon stock with a strong dependence indicating that soil organic carbon values were correlated up to 10.8m.Neighbouring values of soil organic carbon stock, all waterstable aggregate fractions, and dithionite and pyrophosphate iron gave reliable estimate of soil organic carbon stock by state-space.

Soil cover of gas-bearing areas

NASA Astrophysics Data System (ADS)

Mozharova, N. V.

2010-08-01

Natural soils with disturbed functioning parameters compared to the background soils with conservative technogenic-pedogenic features were distinguished on vast areas above the artificial underground gas storages in the zones of spreading and predominant impact of hydrocarbon gases. The disturbance of the functioning parameters is related to the increase in the methane concentration, the bacterial oxidation intensity and destruction, and the complex microbiological and physicochemical synthesis of iron oxides. The technogenic-pedogenic features include neoformations of bacteriomorphic microdispersed iron oxides. The impurity components consist of elements typical for biogenic structures. New soil layers, horizons, specific anthropogenically modified soils, and soil-like structures were formed on small areas in the industrial zones of underground gas storages due to the mechanical disturbance, the deposition of drilling sludge, and the chemical contamination. Among the soils, postlithogenic formations were identified—chemotechnosols (soddy-podzolic soils and chernozems), as well as synlithogenic ones: strato-chemotechnosols and stratochemoembryozems. The soil-like bodies included postlithogenic soil-like structures (chemotechnozems) and synlithogenic ones (strato-chemotechnozems). A substantive approach was used for the soil diagnostics. The morphological and magnetic profiles and the physical, chemical, and physicochemical properties of the soils were analyzed. The micromorphological composition of the soil magnetic fraction was used as a magnetic label.

Effect of soil structure on the growth of bacteria in soil quantified using CARD-FISH

NASA Astrophysics Data System (ADS)

Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Otten, Wilfred

2014-05-01

It has been reported that compaction of soil due to use of heavy machinery has resulted in the reduction of crop yield. Compaction affects the physical properties of soil such as bulk density, soil strength and porosity. This causes an alteration in the soil structure which limits the mobility of nutrients, water and air infiltration and root penetration in soil. Several studies have been conducted to explore the effect of soil compaction on plant growth and development. However, there is scant information on the effect of soil compaction on the microbial community and its activities in soil. Understanding the effect of soil compaction on microbial community is essential as microbial activities are very sensitive to abrupt environmental changes in soil. Therefore, the aim of this work was to investigate the effect of soil structure on growth of bacteria in soil. The bulk density of soil was used as a soil physical parameter to quantify the effect of soil compaction. To detect and quantify bacteria in soil the method of catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used. This technique results in high intensity fluorescent signals which make it easy to quantify bacteria against high levels of autofluorescence emitted by soil particles and organic matter. In this study, bacterial strains Pseudomonas fluorescens SBW25 and Bacillus subtilis DSM10 were used. Soils of aggregate size 2-1mm were packed at five different bulk densities in polyethylene rings (4.25 cm3).The soil rings were sampled at four different days. Results showed that the total number of bacteria counts was reduced significantly (P

Effects of Rainfall-Induced Topsoil Structure Changes on Root-Zone Moisture Regime during the Dry Period

NASA Astrophysics Data System (ADS)

Wang, Feng; Chen, Jiazhou; Lin, Lirong

2018-01-01

Rainfall erosion and subsequent intermittent drought are serious barriers for agricultural production in the subtropical red soil region of China. Although it is widely recognized that rainfall-induced soil structure degradation reduced soil water storage and water-holding capacity, the effects of variation of the rainfall-induced topsoil structure on the subsequent soil water regime during the dry period is still rarely considered. The objective of this study was to ascertain the way of rainfall-induced topsoil structure changes on the subsequent soil water regime during the dry period. In a three-year-long experiment, six practices (CK, only crop; SM, straw mulching; PAM, polyacrylamide surface application; B, contour Bahia-grass strip; SPAM, straw mulching and polyacrylamide surface application; and BPAM, contour Bahia-grass strip and polyacrylamide surface application) were conducted at an 8° farmland with planting summer maize resulting in different topsoil structure and root-zone moisture, to establish and reveal the quantitatively relationship between the factors of topsoil structure and soil drought. Rainfall erosion significantly increased the soil crust coverage, and decreased the WSA 0.25, 0-30 mm soil porosity and mean pore size. There was no significant difference during the raining stage of root-zone water storage between CK and other practices. An index of soil drought intensity ( I) and degree ( D) was established using soil water loss rate and soil drought severity. The larger value of I means a higher rate of water loss. The larger value of D means more severe drought. During the dry period, I and D were significantly higher in CK than in other practices. I and D had significantly positively correlation with the crust size and crust coverage, and negatively with WSA 0.25, 15-30 mm soil porosity and mean pore size. Among of soil structure factors, the soil porosity had the largest effect on I and D. The rainfall-induced topsoil structure changes greatly deteriorated the root-zone regime during the dry period mainly due to significant increasing soil water loss but little improving the raining stage of soil water storage. Straw mulching had greater effects than other practices in alleviating rainfall-induced erosion and intermittent drought, and could be a better strategy applied for this region.

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

Soil structure characterized using computed tomographic images

Treesearch

Zhanqi Cheng; Stephen H. Anderson; Clark J. Gantzer; J. W. Van Sambeek

2003-01-01

Fractal analysis of soil structure is a relatively new method for quantifying the effects of management systems on soil properties and quality. The objective of this work was to explore several methods of studying images to describe and quantify structure of soils under forest management. This research uses computed tomography and a topological method called Multiple...

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.

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

PubMed Central

Skvortsova, Elena B.; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity. PMID:26010779

Universal spatial correlation functions for describing and reconstructing soil microstructure.

PubMed

Karsanina, Marina V; Gerke, Kirill M; Skvortsova, Elena B; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity.

Bacterial diversity of soil aggregates of different sizes in various land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Azida, Thakahova; Olga, Kutovaya

2014-05-01

The patterns of soil microbiome structure may be a universal and very sensitive indicator of soil quality (soil "health") used for optimization and biologization of agricultural systems. The understanding of how microbial diversity influenses, and is influenced by, the environment can only be attained by analyses at scales relevant to those at which processes influencing microbial diversity actually operate. The basic structural and functional unit of the soil is a soil aggregate, which is actually a microcosm of the associative co-existing groups of microorganisms that form characteristic ecological food chains. It is known that many important microbial processes occur in spatially segregated microenvironments in soil leading to a microscale biogeography. The Metagenomic library of typical chernozem in conditions of different land use systems was created. Total genomic DNA was extracted from 0.5 g of the frozen soil after mechanical destruction. Sample preparation and sequencing was performed on a GS Junior ("Roche»", Switzerland) according to manufacturer's recommendations, using the universal primers to the variable regions V4 gene 16S - rRNA - F515 (GTGCCAGCMGCCGCGGTAA) and R806 (GGACT-ACVSGGGTATCTAAT). It is shown that the system of land use is a stronger determinant of the taxonomic composition of the soil microbial community, rather than the size of the structural units. In soil samples from different land use systems the presence of accessory components was revealed. They may be used as indicators of processes of soil recovery, soil degradation or soil exhaustion processes occuring in the agroecosystems. The comparative analysis of microbial communities of chernozem aggregates investigated demonstrates the statistically valuable differences in the amount of bacterial phyla and Archean domain content as well as the species richness in aggregates of various size fractions. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates may indicate the presence of a certain size fraction in the structure of the investigated soil. The study of soils' metagenome is promising for the development of both soil microbiology, and for the soil processes trends in soils of anthropogenic origin.

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-10-01

Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions. Copyright © 2016. Published by Elsevier B.V.

Correlation of soil microbes and soil micro-environment under long-term safflower (Carthamus tinctorius L.) plantation in China.

PubMed

Lu, Shuang; Quan, Wang; Wang, Shao-Ming; Liu, Hong-Ling; Tan, Yong; Zeng, Guang-Ping; Zhang, Xia

2013-04-01

Microbial community structure and ecological functions are influenced by interactions between above and belowground biota. There is an urgent need for intensive monitoring of microbes feedback of soil micro-ecosystem for setting up a good agricultural practice. Recent researches have revealed that many soils characteristic can effect microbial community structure. In the present study factors affecting microbial community structure and soil in Carthamus tinctorius plantations in arid agricultural ecosystem of northern Xinjiang, China were identified. The result of the study revealed that soil type was the key factor in safflower yield; Unscientific field management resulted high fertility level (bacteria dominant) of soil to turn to low fertility level (fungi dominant), and Detruded Canonical Correspondence Analysis (DCCA) showed that soil water content, organic matter, available N, P and K were the dominant factors affecting distribution of microbial community. Soil water content showed a significant positive correlation with soil microbes quantity (P < 0.01), while others showed a significant quantity correlation with soil microbe quantity (P < 0.05).

[Soil microbial community structure in Picea asperata plantations with different ages in subalpine of western Sichuan, Southwest China.

PubMed

Luo, Da; Liu, Shun; Shi, Zuo Min; Feng, Qiu Hong; Liu, Qian Li; Zhang, Li; Huang, Quan; He, Jian She

2017-02-01

The effects of four Picea asperata plantations with different ages (50-, 38-, 27- and 20-year-old), in subalpine of western Sichuan, on the characteristics of soil microbial diversity and microbial community structure were studied by the method of phospholipid fatty acid (PLFA) profiles. The results showed that, with the increase of age, the contents of soil organic carbon and total nitrogen gradually improved, while Shannon's diversity index and Pielou's evenness index of soil microorganisms increased at first and then decreased. The amounts of microbial total PLFAs, bacterial PLFAs, fungal PLFAs, actinobacterial PLFAs, and arbuscular mycorrhizal fungal (AMF) PLFAs in soils consistently increased with increasing age. The principal component analysis (PCA) indicated that the soil microbial communities in different plantations were structurally distinct from each other. The first principal component (PC1) and the second principal component (PC2) together accounted for 66.8% of total variation of the soil microbial community structure. The redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil organic carbon, total nitrogen, total potassium, and fine root mass were the key determinants influencing the microbial community structure. Our study suggested that, with the extension of artificialafforestation time, the soil fertility and microbial biomass were enhanced, and the restoration processes of forest ecosystem were stable.

Future Carbon Dynamics of the Northern Rockies Ecoregion due to Climate Impacts and Fire Effects

NASA Astrophysics Data System (ADS)

Weller, U.; Lang, B.; Rabot, E.; Stössel, B.; Urbanski, L.; Vogel, H. J.; Wiesmeier, M.; Wollschlaeger, U.

2016-12-01

The impact of agricultural management on soil functions is manifold and severe. It has both positive and adverse influence. Our goal is to develop model tools quantifying the agricultural impact on soil functions based on a mechanistic understanding of soil processes to support farmers and decision makers. The modeling approach is based on defining relevant soil components, i.e. soil matrix, macropores, organisms, roots and organic matter. They interact and form the soil's macroscopic properties and functions including water and gas dynamics, and biochemical cycles. Based on existing literature information we derive functional interaction processes and combine them in a network of dynamic soil components. In agricultural soils, a major issue is linked to changes in soil structure and their influence on water dynamics. Compaction processes are well studied in literature, but for the resilience due to root growth and activity of soil organisms the information is scarcer. We implement structural dynamics into soil water and gas simulations using a lumped model that is both coarse enough to allow extensive model runs while still preserving some important, yet rarely modeled phenomenons like preferential flow, hysteretic and dynamic behavior. For simulating water dynamics, at each depth, the model assumes water at different binding energies depending on soil structure, i.e. the pore size distribution. Non-equilibrium is postulated, meaning that free water may occur even if the soil is not fully saturated. All energy levels are interconnected allowing water to move, both within a spatial node, and between neighboring nodes (adding gravity). Structure dynamics alters the capacity of this water compartments, and the conductance of its connections. Connections are switched on and off depending on whether their sources contain water or their targets have free capacity. This leads to piecewise linear system behavior that allows fast calculation for extended time steps. Based on this concept, the dynamics of soil structure can be directly linked to soil water dynamics as a main driver for other soil processes. Further steps will include integration of temperature and solute leaching as well as defining the feedback of the water regime on the structure forming processes.

Estimating soil erosion risk and evaluating erosion control measures for soil conservation planning at Koga watershed in the highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Molla, Tegegne; Sisheber, Biniam

2017-01-01

Soil erosion is one of the major factors affecting sustainability of agricultural production in Ethiopia. The objective of this paper is to estimate soil erosion using the universal soil loss equation (RUSLE) model and to evaluate soil conservation practices in a data-scarce watershed region. For this purpose, soil data, rainfall, erosion control practices, satellite images and topographic maps were collected to determine the RUSLE factors. In addition, measurements of randomly selected soil and water conservation structures were done at three sub-watersheds (Asanat, Debreyakob and Rim). This study was conducted in Koga watershed at upper part of the Blue Nile basin which is affected by high soil erosion rates. The area is characterized by undulating topography caused by intensive agricultural practices with poor soil conservation practices. The soil loss rates were determined and conservation strategies have been evaluated under different slope classes and land uses. The results showed that the watershed is affected by high soil erosion rates (on average 42 t ha-1 yr-1), greater than the maximum tolerable soil loss (18 t ha-1 yr-1). The highest soil loss (456 t ha-1 yr-1) estimated from the upper watershed occurred on cultivated lands of steep slopes. As a result, soil erosion is mainly aggravated by land-use conflicts and topographic factors and the rugged topographic land forms of the area. The study also demonstrated that the contribution of existing soil conservation structures to erosion control is very small due to incorrect design and poor management. About 35 % out of the existing structures can reduce soil loss significantly since they were constructed correctly. Most of the existing structures were demolished due to the sediment overload, vulnerability to livestock damage and intense rainfall. Therefore, appropriate and standardized soil and water conservation measures for different erosion-prone land uses and land forms need to be implemented in Koga watershed.

A process-based framework for soil ecosystem services study and management.

PubMed

Su, Changhong; Liu, Huifang; Wang, Shuai

2018-06-15

Soil provides various indispensable ecosystem services for human society. Soil's complex structure and property makes the soil ecological processes complicated and brings about tough challenges for soil ecosystem services study. Most of the current frameworks on soil services focus exclusively on services per se, neglecting the links and underlying ecological mechanisms. This article put forward a framework on soil services by stressing the underlying soil mechanisms and processes, which includes: 1) analyzing soil natural capital stock based on soil structure and property, 2) disentangling the underlying complex links and soil processes, 3) soil services valuation based on field investigation and spatial explicit models, and 4) enacting soil management strategy based on soil services and their driving factors. By application of this framework, we assessed the soil services of sediment retention, water yield, and grain production in the Upper-reach Fenhe Watershed. Based on the ecosystem services and human driving factors, the whole watershed was clustered into five groups: 1) municipal area, 2) typical coal mining area, 3) traditional farming area, 4) unsustainable urbanizing area, and 5) ecological conservation area. Management strategies on soils were made according to the clustering based soil services and human activities. Copyright © 2018 Elsevier B.V. All rights reserved.

Three Soil Quality Demonstrations for Educating Extension Clientele

ERIC Educational Resources Information Center

Hoorman, James J.

2014-01-01

There is a renewed interest in educating youth, Master Gardeners, and agricultural producers about soil quality. Three soil demonstrations show how soil organic matter increases water holding capacity, improves soil structure, and increases nutrient retention. Exercise one uses clay bricks and sponges to represent mineral soils and soil organic…

Soil and Water: Some Teaching Suggestions.

ERIC Educational Resources Information Center

Fischer, Richard B.

1987-01-01

Outlines six soil and water investigations that students can pursue outdoors, in nature centers, or in classrooms: soil characteristics; relationship between soil ph and plant life; what aggregates tell us; differences in soil structure; differences in rate of water absorption by soil; and soil exploration with a Berlesi funnel. (NEC)

Build your own soil: exploring microfluidics to create microbial habitat structures

PubMed Central

Aleklett, Kristin; Kiers, E Toby; Ohlsson, Pelle; Shimizu, Thomas S; Caldas, Victor EA; Hammer, Edith C

2018-01-01

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats. PMID:29135971

Pore-scale water dynamics during drying and the impacts of structure and surface wettability

NASA Astrophysics Data System (ADS)

Cruz, Brian C.; Furrer, Jessica M.; Guo, Yi-Syuan; Dougherty, Daniel; Hinestroza, Hector F.; Hernandez, Jhoan S.; Gage, Daniel J.; Cho, Yong Ku; Shor, Leslie M.

2017-07-01

Plants and microbes secrete mucilage into soil during dry conditions, which can alter soil structure and increase contact angle. Structured soils exhibit a broad pore size distribution with many small and many large pores, and strong capillary forces in narrow pores can retain moisture in soil aggregates. Meanwhile, contact angle determines the water repellency of soils, which can result in suppressed evaporation rates. Although they are often studied independently, both structure and contact angle influence water movement, distribution, and retention in soils. Here drying experiments were conducted using soil micromodels patterned to emulate different aggregation states of a sandy loam soil. Micromodels were treated to exhibit contact angles representative of those in bulk soil (8.4° ± 1.9°) and the rhizosphere (65° ± 9.2°). Drying was simulated using a lattice Boltzmann single-component, multiphase model. In our experiments, micromodels with higher contact angle surfaces took 4 times longer to completely dry versus micromodels with lower contact angle surfaces. Microstructure influenced drying rate as a function of saturation and controlled the spatial distribution of moisture within micromodels. Lattice Boltzmann simulations accurately predicted pore-scale moisture retention patterns within micromodels with different structures and contact angles.

[Effects of different fertilization treatments on soil humic acid structure characteristics].

PubMed

Zhao, Nan; Lü, Yi-Zhong

2012-07-01

The present article used soil humic acid as research object to study effects on the structure characteristics of soil humic acid under the condition of applying cake fertilizer, green manure, straw fertilizer with the same contents of nitrogen and phosphorus. It used element analysis, micro infrared, and solid 13C-NMR for structure analysis, the results indicated that: The chemical composition and structure characteristics of humic acids were similar, but they also had many obvious differences. (1) The atomic ratios of H/C, O/C, and C/N were all different for the humic acids, the soil humic acid of cake fertilizer processing had the highest contents of H and N, green manure processing of soil humic acid contained the highest content of O, while straw fertilizer processing of soil humic acid contained highest content of C. (2) Infrared analysis displayed that the three soil humic acids contained protein Cake fertilizer processing of soil humic acid contained the most amino compounds, green manure processing of soil humic acid contained the maximum contents of hydroxyl and aliphatic hydrocarbon, while straw fertilizer processing of soil humic acid contained the highest contents of alcohol and phenol. (3) Solid 13C-NMR data indicated that cake fertilizer processing of soil humic acid contained the most carboxyl carbon, green manure processing of soil humic acid contained the highest contents of alkyl carbon and carbonyl carbon, while straw fertilizer processing of soil humic acids had the most alkoxy carbon and aromatic carbon

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.

Soil compaction: Evaluation of stress transmission and resulting soil structure

NASA Astrophysics Data System (ADS)

Naveed, Muhammad; Schjønning, Per; Keller, Thomas; Lamande, Mathieu

2016-04-01

Accurate estimation of stress transmission and resultant deformation in soil profiles is a prerequisite for the development of predictive models and decision support tools for preventing soil compaction. Numerous studies have been carried out on the effects of soil compaction, whilst relatively few studies have focused on the cause (mode of stress transmission in the soil). We have coupled both cause and effects together in the present study by carrying out partially confined compression tests on (1) wet aggregates, (2) air dry aggregates, and (3) intact soils to quantify stress transmission and compaction-resulted soil structure at the same time. Stress transmission was quantified using both X-ray CT and Tactilus sensor mat, and soil-pore structure was quantified using X-ray CT. Our results imply that stress transmission through soil highly depends on the magnitude of applied load and aggregate strength. As soon as the applied load is lower than the aggregate strength, the mode of stress transmission is discrete as stresses were mainly transmitted through chain of aggregates. With increasing applied load soil aggregates start deforming that transformed heterogeneous soil into homogenous, as a result stress transmission mode was shifted from discrete towards more like a continuum. Continuum-like stress transmission mode was better simulated with Boussinesq (1885) model based on theory of elasticity compared to discrete. The soil-pore structure was greatly affected by increasing applied stresses. Total porosity was reduced 5-16% and macroporosity 50-85% at 620 kPa applied stress for the intact soils. Similarly, significant changes in the morphological indices of the macropore space were also observed with increasing applied stresses.

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

PubMed

Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

2016-02-01

Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences.

Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review.

PubMed

Zhu, Xiaomin; Chen, Baoliang; Zhu, Lizhong; Xing, Baoshan

2017-08-01

Biochars have attracted tremendous attention due to their effects on soil improvement; they enhance carbon storage, soil fertility and quality, and contaminant (organic and heavy metal) immobilization and transformation. These effects could be achieved by modifying soil microbial habitats and (or) directly influencing microbial metabolisms, which together induce changes in microbial activity and microbial community structures. This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars. In particular, we summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation. Special attention has been paid to biochar effects on the formation and protection of soil aggregates, biochar adsorption of contaminants, biochar-mediated transformation of soil contaminants by microorganisms, and biochar-facilitated electron transfer between microbial cells and contaminants and soil organic matter. Certain reactive organic compounds and heavy metals in biochar may induce toxicity to soil microorganisms. Adsorption and hydrolysis of signaling molecules by biochar interrupts microbial interspecific communications, potentially altering soil microbial community structures. Further research is urged to verify the proposed mechanisms involved in biochar-microbiota interactions for soil remediation and improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Correlation between soil physicochemical properties and vegetation parameters in secondary tropical forest in Sabal, Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Karyati, K.; Ipor, I. B.; Jusoh, I.; Wasli, M. E.

2018-04-01

The tree growth is influenced by soil morphological and physicochemical properties in the site. The purpose of this study was to describe correlation between soil properties under various stage secondary forests and vegetation parameters, such as floristic structure parameters and floristic diversity indices. The vegetation surveys were conducted in 5, 10, and 20 years old at secondary tropical forests in Sarawak, Malaysia. Nine sub plots sized 20 m × 20 m were established within each study site. The Pearson analysis showed that soil physicochemical properties were significantly correlated to floristic structure parameters and floristic diversity indices. The result of PCA clarified the correlation among most important soil properties, floristic structure parameters, and floristic diversity indices. The PC1 represented cation retention capacity and soil texture which were little affected by the fallow age and its also were correlated by floristic structure and diversity. The PC2 was linked to the levels of soil acidity. This property reflected the remnant effects of ash addition and fallow duration, and the significant correlation were showed among pH (H2O), floristic structure and diversity. The PC3 represented the soil compactness. The soil hardness could be influenced by fallow period and it was also correlated by floristic structure.

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

PubMed

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.

Agricultural management and labile carbon additions affect soil microbial community structure and interact with carbon and nitrogen cycling.

PubMed

Berthrong, Sean T; Buckley, Daniel H; Drinkwater, Laurie E

2013-07-01

We investigated how conversion from conventional agriculture to organic management affected the structure and biogeochemical function of soil microbial communities. We hypothesized the following. (1) Changing agricultural management practices will alter soil microbial community structure driven by increasing microbial diversity in organic management. (2) Organically managed soil microbial communities will mineralize more N and will also mineralize more N in response to substrate addition than conventionally managed soil communities. (3) Microbial communities under organic management will be more efficient and respire less added C. Soils from organically and conventionally managed agroecosystems were incubated with and without glucose ((13)C) additions at constant soil moisture. We extracted soil genomic DNA before and after incubation for TRFLP community fingerprinting of soil bacteria and fungi. We measured soil C and N pools before and after incubation, and we tracked total C respired and N mineralized at several points during the incubation. Twenty years of organic management altered soil bacterial and fungal community structure compared to continuous conventional management with the bacterial differences caused primarily by a large increase in diversity. Organically managed soils mineralized twice as much NO3 (-) as conventionally managed ones (44 vs. 23 μg N/g soil, respectively) and increased mineralization when labile C was added. There was no difference in respiration, but organically managed soils had larger pools of C suggesting greater efficiency in terms of respiration per unit soil C. These results indicate that the organic management induced a change in community composition resulting in a more diverse community with enhanced activity towards labile substrates and greater capacity to mineralize N.

Evolution of Pedostructure Parameters Under Tillage Practices

USDA-ARS?s Scientific Manuscript database

The pedostructure (PS) concept is a physically-based method of soil characterization that defines a soil based on its structure and the relationship between structure and soil water behavior. There are 15 unique pedostructure parameters that define the macropore and micropore soil water behavior fo...

Relationship between the erosion properties of soils and other parameters

USDA-ARS?s Scientific Manuscript database

Soil parameters are essential for erosion process prediction and ultimately improved model development, especially as they relate to dam and levee failure. Soil parameters including soil texture and structure, soil classification, soil compaction, moisture content, and degree of saturation can play...

Geotechnical centrifuge use at University of Cambridge Geotechnical Centre, August-September 1991

NASA Astrophysics Data System (ADS)

Gilbert, Paul A.

1992-01-01

A geotechnical centrifuge applies elevated acceleration to small-scale soil models to simulate body forces and stress levels characteristic of full-size soil structures. Since the constitutive behavior of soil is stress level development, the centrifuge offers considerable advantage in studying soil structures using models. Several experiments were observed and described in relative detail, including experiments in soil dynamics and liquefaction study, an experiment investigation leaning towers on soft foundations, and an experiment investigating migration of hot pollutants through soils.

Microbial community structure and activity in a Colorado Rocky Mountain forest soil scarred by slash pile burning

Treesearch

Aida E. Jimenez Esquilin; Mary E. Stromberger; William J. Massman; John M. Frank; Wayne D. Shepperd

2007-01-01

Tree thinning and harvesting produces large amounts of slash material which are typically disposed of by burning, often resulting in severe soil heating. We measured soil chemical properties and microbial community structure and function over time to determine effects of slash pile burning in a ponderosa pine forest soil. Real time data were collected for soil...

Humic Substances in Organic Wastes and their Effects on Amended Soils

NASA Astrophysics Data System (ADS)

Senesi, N.; Ciavatta, C.; Plaza, C.

2009-04-01

Soil humic substances (HS) are universally recognized to play a major role in a wide number of agronomic and environmental processes. For example, soil HS are able to bind mineral particles together, thus promoting a good soil structure, constitute an important source of nutrients for plants and microorganisms, contribute largely to the acid-base buffering capacity of soils, and exert a marked control on the biological availability, physico-chemical behavior, and environmental fate of toxic metal ions and xenobiotics. For these reasons, the knowledge of the short- and long-term effects of organic amendments on the status, quality, and reactivity of indigenous soil HS is of paramount importance. The objective of this presentation is to provide an overview of the chemical and physico-chemical data available in the literature for the evaluation of the effects of organic wastes of various origin and nature used as soil amendments on the composition, structure, and chemical reactivity of native soil HS. In general, HS-like components of organic wastes are typically characterized by a relatively larger presence of aliphatic, amide, and polysaccharide structures, simple structural components of wide molecular heterogeneity, smaller contents of oxygen, acidic functional groups, and organic free radicals, and smaller degrees of aromatic ring polycondensation, polymerization, and humification than native soil HS. Further, with respect to native soil HS, HS-like fractions from organic wastes generally exhibit smaller binding capacities and affinities for metal ions and organic xenobiotics. Appropriate treatment processes of raw organic wastes able to produce environmentally safe and agronomically efficient soil amendments, such as composting, yield HS-like fractions characterized by chemical and physico-chemical features that approach those of native soil HS. In general, aliphatic, polysaccharide, and lignin structures and S- and N-containing groups of the HS-like fractions of organic wastes can be partially incorporated into native soil HS determining modifications at various extents of their composition, structure, and chemistry. The changes occurred in amended soil HS are more evident when untreated organic materials are used. However, with increasing time after land application, the effects observed become less and less apparent with a clear trend to approach the molecular properties typical of native soil HS.

Assessing agricultural management effects on structure related soil hydraulic properties by tension infiltrometry

NASA Astrophysics Data System (ADS)

Bodner, G.; Loiskandl, W.; Kaul, H.-P.

2009-04-01

Soil structure is a dynamic property subject to numerous natural and human influences. It is recognized as fundamental for sustainable functioning of soil. Therefore knowledge of management impacts on the sensitive structural states of soil is decisive in order to avoid soil degradation. The stabilization of the soil's (macro)pore system and eventually the improvement of its infiltrability are essential to avoid runoff and soil erosion, particularly in view of an increasing probability of intense rainfall events. However structure-related soil properties generally have a high natural spatiotemporal variability that interacts with the potential influence of agricultural land use. This complicates a clear determination of management vs. environmental effects and requires adequate measurement methods, allowing a sufficient spatiotemporal resolution to estimate the impact of the targeted management factors within the natural dynamics of soil structure. A common method to assess structure-related soil hydraulic properties is tension infiltrometry. A major advantage of tension infiltrometer measurements is that no or only minimum soil disturbance is necessary and several structure-controlled water transmission properties can readily be derived. The method is more time- and cost-efficient compared to laboratory measurements of soil hydraulic properties, thus enabling more replications. Furthermore in situ measurements of hydraulic properties generally allow a more accurate reproduction of field soil water dynamics. The present study analyses the impact of two common agricultural management options on structure related hydraulic properties based on tension infiltrometer measurements. Its focus is the identification of the role of management within the natural spatiotemporal variability, particularly in respect to seasonal temporal dynamics. Two management approaches are analysed, (i) cover cropping as a "plant-based" agro-environmental measure, and (ii) tillage with different intensities including conventional tillage with a mouldboard plough, reduced tillage with a chisel plough and no-tillage. The results showed that the plant-based management measure of cover cropping had only minor influence on near-saturated hydraulic conductivity (kh) and flow weighted mean pore radius (λm). Substantial over-winter changes were found with a significant increase in kh and a reduction in the pore radius. A spatial trend in soil texture along the cover cropped slope resulted in a higher kh at lower pressure heads at the summit with higher fractions of coarse particles, while kh tended to be highest at the toeslope towards saturation. Cover crop management accounted for a maximum of 9.7% of the total variability in kh, with a decreasing impact towards the unsaturated range. A substantial difference to bare soil in the cover cropped treatments could be identified in relation to a stabilization of macro-pores over winter. The different tillage treatments had a substantial impact on near-saturated kh and pore radius. Although conventional tillage showed the highest values in kh and λm, settling of the soil after the ploughing event tended to reduce differences over time compared to the other tillage methods. The long-term no-tillage (10 years) however had the lowest values of kh at all measurement dates. The high contents of silt and fine sand probably resulted in soil densification that was not counterbalanced sufficiently by biological structure forming agents. The study could show that soil structure related hydraulic properties are subject to a substantial seasonal variability. A comprehensive assessment of agricultural measures such as tillage or cover cropping requires an estimate of these temporal dynamics and their interaction with the management strategies. Particularly for plant-based management measures such as cover cropping, which represent a less intense intervention in the structural states of the soil compared to tillage, this was evident, as the main mechanism revealed for this measure was structure stabilization over time. While spatial variability is mostly controlled in designed experiments, the role of temporal variability is often underestimated. From our study we concluded that (i) a proper understanding of processes involved in management effects on soil structure must take into consideration the dynamic nature of the respective soil properties, (ii) experimental planning for studies regarding management impacts on soil structure should allow an estimation of temporal variability, and (iii) for this purpose tension infiltrometry provides an efficient measurement tool to assess structure related soil hydraulic properties.

Faunal Drivers of Soil Flux Dynamics via Alterations in Crack Structure

NASA Astrophysics Data System (ADS)

DeCarlo, Keita; Caylor, Kelly

2016-04-01

Organismal activity, in addition to its role in ecological feedbacks, has the potential to serve as instigators or enhancers of atmospheric and hydrologic processes via alterations in soil structural regimes. We investigated the biomechanical effect of faunal activity on soil carbon dynamics via changes in soil crack structure, focusing on three dryland soil systems: bioturbated, biocompacted and undisturbed soils. Carbon fluxes were characterized using a closed-system respiration chamber, with CO2 concentration differences measured using an infrared gas analyzer (IRGA). Results show that faunal influences play a divergent biomechanics role in bulk soil cracking: bioturbation induced by belowground fauna creates "surficial" (shallow, large, well-connected) networks relative to the "systematic" (deep, moderate, poorly connected) networks created by aboveground fauna. The latter also shows a "memory" of past wetting/drying events in the consolidated soil through a crack layering effect. These morphologies further drive differences in soil carbon flux: under dry conditions, bioturbated and control soils show a persistently high and low mean carbon flux, respectively, while biocompacted soils show a large diurnal trend, with daytime lows and nighttime highs comparable to the control and bioturbated soils, respectively. Overall fluxes under wet conditions are considerably higher, but also more variable, though higher mean fluxes are observed in the biocompacted and bioturbated soils. Our results suggest that the increased surface area in the bioturbated soils create enhanced but constant diffusive processes, whereas the increased thermal gradient in the biocompacted soils create novel convective processes that create high fluxes that are diurnal in nature.

Soils and public health: the vital nexus

NASA Astrophysics Data System (ADS)

Pachepsky, Yakov

2015-04-01

Soils sustain life. They affect human health via quantity, quality, and safety of available food and water, and via direct exposure of individuals to soils. Throughout the history of civilization, soil-health relationships have inspired spiritual movements, philosophical systems, cultural exchanges, and interdisciplinary interactions, and provided medicinal substances of paramount impact. Given the climate, resource, and population pressures, understanding and managing the soil-health interactions becomes a modern imperative. We are witnessing a paradigm shift from recognizing and yet disregarding the 'soil-health' nexus complexity to parameterizing this complexity and identifying reliable controls. This becomes possible with the advent of modern research tools as a source of 'big data' on multivariate nonlinear soil systems and the multiplicity of health metrics. The phenomenon of suppression of human pathogens in soils and plants presents a recent example of these developments. Evidence is growing about the dependence of pathogen suppression on the soil microbial community structure which, in turn, is affected by the soil-plant system management. Soil eutrophication appears to create favorable conditions for pathogen survival. Another example of promising information-rich research considers links and feedbacks between the soil microbial community structure and structure of soil physical pore space. The two structures are intertwined and involved in the intricate self-organization that controls soil services to public health. This, in particular, affects functioning of soils as a powerful water filter and the capacity of this filter with respect to emerging contaminants in both 'green' and 'blue' waters. To evaluate effects of soil services to public health, upscaling procedures are needed for relating the fine-scale mechanistic knowledge to available coarse-scale information on soil properties and management. More needs to be learned about health effects of soils in organic agriculture that are often used for soil quality comparison and benchmarking. The influence of soil degradation and rehabilitation on public health has to be assessed in quantitative terms. Some links between soils and public health regarding, for example, immune maturation, antibiotic resistance development, and mental well-being, have been long hypothesized but remain to be examined. The data on soil-health relationships are scarce and very much disjointed, and a concerted international effort appears to be needed to encompass various economic and geographical settings. Current definitions of healthy soil broadly include aspects that are conducive for human health, and functional evaluation of soil quality with a focus on public health will have useful applications in public policies and perception. The 'soil-health' connection is complex in character, global in manifestation, and applicable to every human being.

Chemical evaluation of soil organic matter structure in diverse cropping systems

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) improves soil structure, nutrient and water retention, and biodiversity while reducing susceptibility to soil erosion. SOM also represents an important pool of C that can be increased to help mitigate global climate change. Our understanding of how agricultural management ...

Assessing the variation in bund structure design and its impact on soil physical properties and hydrology in Koga catchment, Highlands of Ethiopia

NASA Astrophysics Data System (ADS)

Lakew, Walle; Baartman, Jantiene; Fleskens, Luuk; Selassie, Yihenew; Ritsema, Coen

2017-04-01

Prolonged soil drying and severe moisture stress during the dry season, and soil saturation and erosion during the short rainy season are critical problems in the Ethiopian highlands. Large-scale implementation of bund structures has been used as soil and water management (SWM) strategy to fight these problems and establish a sustainable land management (SLM) system. However, many SWM practices are implemented with design flaws or without proper design and maintenance, and do not match conservation requirements. The quality of implementation and effects of bund structures on soil physical properties is not yet documented. Therefore, in this study, field investigations and laboratory analysis were carried out to evaluate the variation in bund structure design and its impact on soil-water retention, bulk density, porosity and soil depth. Results show that the dimensions and stability of bund structures, and consequently, the impacts of bunds varied widely. The widths and heights of bunds, and slope gradients were significantly correlated with infiltration rate and available soil-water content. Water holding capacity was 24% higher compared to that on untreated farms. Bunds with larger dimensions of top width (>85 cm) and height (>75 cm) showed 17 and 18% higher water holding capacity compared to fields with bunds having lower dimensions. In addition, results exhibited that the porosity and soil depth were significantly affected by the dimensions of bund structures and increased with increasing widths and heights of bunds. A 14.2% increase in porosity; a 41.2% increase in infiltration rate; and a 17.5% decrease in bulk density was found in soils of treated farms compared to those of untreated farm plots. Differences in particle size distribution and soil erodibility among widths of the bunds were low. It can be concluded that bund structure design varied substantially throughout the study area, which had impacted soil-water storage and soil physical properties. Bund structure design should be adapted to local biophysical settings at catchment level to enhance on- and offsite impacts.

Impacts of soil moisture content on visual soil evaluation

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Bondi, Giulia; Creamer, Rachel; Holden, Nick

2017-04-01

Visual Soil Examination and Evaluation (VSE) techniques offer tools for soil quality assessment. They involve the visual and tactile assessment of soil properties such as aggregate size and shape, porosity, redox morphology, soil colour and smell. An increasing body of research has demonstrated the reliability and utility of VSE techniques. However a number of limitations have been identified, including the potential impact of soil moisture variation during sampling. As part of a national survey of grassland soil quality in Ireland, an evaluation of the impact of soil moisture on two widely used VSE techniques was conducted. The techniques were Visual Evaluation of Soil Structure (VESS) (Guimarães et al., 2011) and Visual Soil Assessment (VSA) (Shepherd, 2009). Both generate summarising numeric scores that indicate soil structural quality, though employ different scoring mechanisms. The former requires the assessment of properties concurrently and the latter separately. Both methods were deployed on 20 sites across Ireland representing a range of soils. Additional samples were taken for soil volumetric water (θ) determination at 5-10 and 10-20 cm depth. No significant correlation was observed between θ 5-10 cm and either VSE technique. However, VESS scores were significantly related to θ 10-20 cm (rs = 0.40, sig = 0.02) while VSA scores were not (rs = -0.33, sig = 0.06). VESS and VSA scores can be grouped into quality classifications (good, moderate and poor). No significant mean difference was observed between θ 5-10 cm or θ 10-20 cm according to quality classification by either method. It was concluded that VESS scores may be affected by soil moisture variation while VSA appear unaffected. The different scoring mechanisms, where the separate assessment and scoring of individual properties employed by VSA, may limit soil moisture effects. However, moisture content appears not to affect overall structural quality classification by either method. References Guimarães, R.M.C., Ball, B.C. & Tormena, C.A. 2011. Improvements in the visual evaluation of soil structure, Soil Use and Management, 27, 3: 395-403 Shepherd, G.T. 2009. Visual Soil Assessment. Field guide for pastoral grazing and cropping on flat to rolling country. 2nd edn. Horizons regional council, New Zealand.

Model structures amplify uncertainty in predicted soil carbon responses to climate change.

PubMed

Shi, Zheng; Crowell, Sean; Luo, Yiqi; Moore, Berrien

2018-06-04

Large model uncertainty in projected future soil carbon (C) dynamics has been well documented. However, our understanding of the sources of this uncertainty is limited. Here we quantify the uncertainties arising from model parameters, structures and their interactions, and how those uncertainties propagate through different models to projections of future soil carbon stocks. Both the vertically resolved model and the microbial explicit model project much greater uncertainties to climate change than the conventional soil C model, with both positive and negative C-climate feedbacks, whereas the conventional model consistently predicts positive soil C-climate feedback. Our findings suggest that diverse model structures are necessary to increase confidence in soil C projection. However, the larger uncertainty in the complex models also suggests that we need to strike a balance between model complexity and the need to include diverse model structures in order to forecast soil C dynamics with high confidence and low uncertainty.

Soil respiration and bacterial structure and function after 17 years of a reciprocal soil transplant experiment

DOE PAGES

Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.; ...

2016-03-02

The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampledmore » the original 1994 soil transplants and controls, measuring CO 2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr -1precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. Lastly, these results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.« less

Physical-chemical and microbiological changes in Cerrado Soil under differing sugarcane harvest management systems

PubMed Central

2012-01-01

Background Sugarcane cultivation plays an important role in Brazilian economy, and it is expanding fast, mainly due to the increasing demand for ethanol production. In order to understand the impact of sugarcane cultivation and management, we studied sugarcane under different management regimes (pre-harvest burn and mechanical, unburnt harvest, or green cane), next to a control treatment with native vegetation. The soil bacterial community structure (including an evaluation of the diversity of the ammonia oxidizing (amoA) and denitrifying (nirK) genes), greenhouse gas flow and several soil physicochemical properties were evaluated. Results Our results indicate that sugarcane cultivation in this region resulted in changes in several soil properties. Moreover, such changes are reflected in the soil microbiota. No significant influence of soil management on greenhouse gas fluxes was found. However, we did find a relationship between the biological changes and the dynamics of soil nutrients. In particular, the burnt cane and green cane treatments had distinct modifications. There were significant differences in the structure of the total bacterial, the ammonia oxidizing and the denitrifying bacterial communities, being that these groups responded differently to the changes in the soil. A combination of physical and chemical factors was correlated to the changes in the structures of the total bacterial communities of the soil. The changes in the structures of the functional groups follow a different pattern than the physicochemical variables. The latter might indicate a strong influence of interactions among different bacterial groups in the N cycle, emphasizing the importance of biological factors in the structuring of these communities. Conclusion Sugarcane land use significantly impacted the structure of total selected soil bacterial communities and ammonia oxidizing and denitrifier gene diversities in a Cerrado field site in Central Brazil. A high impact of land use was observed in soil under the common burnt cane management. The green cane soil also presented different profiles compared to the control soil, but to at a lesser degree. PMID:22873209

Soil Respiration and Bacterial Structure and Function after 17 Years of a Reciprocal Soil Transplant Experiment.

PubMed

Bond-Lamberty, Ben; Bolton, Harvey; Fansler, Sarah; Heredia-Langner, Alejandro; Liu, Chongxuan; McCue, Lee Ann; Smith, Jeffrey; Bailey, Vanessa

2016-01-01

The effects of climate change on soil organic matter-its structure, microbial community, carbon storage, and respiration response-remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampled the original 1994 soil transplants and controls, measuring CO2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5°C monthly maximum air temperature, +50 mm yr-1 precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. These results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.

Forest canopy structural controls over throughfall affect soil microbial community structure in an epiphyte-laden maritime oak stand

NASA Astrophysics Data System (ADS)

Van Stan, J. T., II; Rosier, C. L.; Schrom, J. O.; Wu, T.; Reichard, J. S.; Kan, J.

2014-12-01

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to understanding of patterns in nutrient cycling and related ecological services. Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via the "throughfall" mechanism), is it possible changes in SMC structure variability could arise from modifications in canopy elements? Our study investigates this question by monitoring throughfall water and dissolved ion supply to soils beneath a continuum of canopy structure: from a large gap (0% cover) to heavy Tillandsia usneoides L. (Spanish moss) canopy (>90% cover). Throughfall water supply diminished with increasing canopy cover, yet increased washoff/leaching of Na+, Cl-, PO43-, and SO42- from the canopy to the soils (p < 0.01). Presence of T. usneoides diminished throughfall NO3-, but enhanced NH4+, concentrations supplied to subcanopy soils. The mineral soil horizon (0-10 cm) from canopy gaps, bare canopy, and T. usneoides-laden canopy significantly differed (p < 0.05) in soil chemistry parameters (pH, Ca2+, Mg2+, CEC). PCR-DGGE banding patterns beneath similar canopy covers (experiencing similar throughfall dynamics) also produced high similarities per ANalyses Of SIMilarity (ANO-SIM), and clustered together when analyzed by Nonmetric Multidimensional Scaling (NMDS). Correlation analysis of DGGE banding patterns, throughfall dynamics, and soil chemistry yielded significant correlations (p < 0.05) between fungal communities and soil chemical properties significantly differing between canopy cover types (pH: r2 = 0.50; H+ %-base saturation: r2 = 0.48; Ca2+ %-base saturation: r2 = 0.43). Bacterial community structure correlated with throughfall NO3-, NH4+, and Ca2+ concentrations (r2 = 0.37, p = 0.16). These results suggest that modifications of forest canopy structures are capable of affecting mineral-soil horizon SMC structure via the throughfall mechanism when canopies' biomass distribution is highly heterogeneous.

Distinct taxonomic and functional composition of soil microbiomes along the gradient forest-restinga-mangrove in southeastern Brazil.

PubMed

Mendes, Lucas William; Tsai, Siu Mui

2018-01-01

Soil microorganisms play crucial roles in ecosystem functioning, and the central goal in microbial ecology studies is to elucidate which factors shape community structure. A better understanding of the relationship between microbial diversity, functions and environmental parameters would increase our ability to set conservation priorities. Here, the bacterial and archaeal community structure in Atlantic Forest, restinga and mangrove soils was described and compared based on shotgun metagenomics. We hypothesized that each distinct site would harbor a distinct taxonomic and functional soil community, which is influenced by environmental parameters. Our data showed that the microbiome is shaped by soil properties, with pH, base saturation, boron and iron content significantly correlated to overall community structure. When data of specific phyla were correlated to specific soil properties, we demonstrated that parameters such as boron, copper, sulfur, potassium and aluminum presented significant correlation with the most number of bacterial groups. Mangrove soil was the most distinct site and presented the highest taxonomic and functional diversity in comparison with forest and restinga soils. From the total 34 microbial phyla identified, 14 were overrepresented in mangrove soils, including several archaeal groups. Mangrove soils hosted a high abundance of sequences related to replication, survival and adaptation; forest soils included high numbers of sequences related to the metabolism of nutrients and other composts; while restinga soils included abundant genes related to the metabolism of carbohydrates. Overall, our finds show that the microbial community structure and functional potential were clearly different across the environmental gradient, followed by functional adaptation and both were related to the soil properties.

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak.

PubMed

Pec, Gregory J; Karst, Justine; Taylor, D Lee; Cigan, Paul W; Erbilgin, Nadir; Cooke, Janice E K; Simard, Suzanne W; Cahill, James F

2017-01-01

Western North American landscapes are rapidly being transformed by forest die-off caused by mountain pine beetle (Dendroctonus ponderosae), with implications for plant and soil communities. The mechanisms that drive changes in soil community structure, particularly for the highly prevalent ectomycorrhizal fungi in pine forests, are complex and intertwined. Critical to enhancing understanding will be disentangling the relative importance of host tree mortality from changes in soil chemistry following tree death. Here, we used a recent bark beetle outbreak in lodgepole pine (Pinus contorta) forests of western Canada to test whether the effects of tree mortality altered the richness and composition of belowground fungal communities, including ectomycorrhizal and saprotrophic fungi. We also determined the effects of environmental factors (i.e. soil nutrients, moisture, and phenolics) and geographical distance, both of which can influence the richness and composition of soil fungi. The richness of both groups of soil fungi declined and the overall composition was altered by beetle-induced tree mortality. Soil nutrients, soil phenolics and geographical distance influenced the community structure of soil fungi; however, the relative importance of these factors differed between ectomycorrhizal and saprotrophic fungi. The independent effects of tree mortality, soil phenolics and geographical distance influenced the community composition of ectomycorrhizal fungi, while the community composition of saprotrophic fungi was weakly but significantly correlated with the geographical distance of plots. Taken together, our results indicate that both deterministic and stochastic processes structure soil fungal communities following landscape-scale insect outbreaks and reflect the independent roles tree mortality, soil chemistry and geographical distance play in regulating the community composition of soil fungi. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Land application of tylosin and chlortetracycline swine manure: Impacts to soil nutrients and soil microbial community structure.

PubMed

Stone, James J; Dreis, Erin K; Lupo, Christopher D; Clay, Sharon A

2011-01-01

The land application of aged chortetracycle (CTC) and tylosin-containing swine manure was investigated to determine associated impacts to soil microbial respiration, nutrient (phosphorus, ammonium, nitrate) cycling, and soil microbial community structure under laboratory conditions. Two silty clay loam soils common to southeastern South Dakota were used. Aerobic soil respiration results using batch reactors containing a soil-manure mixture showed that interactions between soil, native soil microbial populations, and antimicrobials influenced CO(2) generation. The aged tylosin treatment resulted in the greatest degree of CO(2) inhibition, while the aged CTC treatment was similar to the no-antimicrobial treatment. For soil columns in which manure was applied at a one-time agronomic loading rate, there was no significant difference in soil-P behavior between either aged CTC or tylosin and the no-antimicrobial treatment. For soil-nitrogen (ammonium and nitrate), the aged CTC treatment resulted in rapid ammonium accumulation at the deeper 40cm soil column depth, while nitrate production was minimal. The aged CTC treatment microbial community structure was different than the no-antimicrobial treatment, where amines/amide and carbohydrate chemical guilds utilization profile were low. The aged tylosin treatment also resulted in ammonium accumulation at 40 cm column depth, however nitrate accumulation also occurred concurrently at 10 cm. The microbial community structure for the aged tylosin was also significantly different than the no-antimicrobial treatment, with a higher degree of amines/amides and carbohydrate chemical guild utilization compared to the no-antimicrobial treatment. Study results suggest that land application of CTC and tylosin-containing manure appears to fundamentally change microbial-mediated nitrogen behavior within soil A horizons.

[Fractal features of soil aggregate structure in slope farmland with different de-farming patterns in South Sichuan Province of China].

PubMed

Wang, Jing-Yan; Hu, Ting-Xing; Gong, Wei; Gong, Yuan-Bo; Luo, Cheng-De

2010-06-01

By using fractal model, this paper studied the fractal dimension of soil aggregate structure (D) in the slope farmland (CK), its 5-year de-farmed Neosinocalamus affinis plantation (NAP), Bambusa pervariabilis x Dendrocalamopsis oldhami plantation (BDP), Alnus crenastogyne + Neosinocalamus affinis plantation (ANP), and abandoned farmland (AFL) in south Sichuan Province of China, and analyzed the relationships between the D and soil physical and chemical properties. In the de-farmed plantations and abandoned farmland, the contents of > 0.25 mm soil aggregates and water-stable aggregates were increased significantly, compared with those in the slope farmland. The D was 1.377-2.826, being in the order of NAP < BDP < ANP < AFL < CK, and decreased with the increasing contents of > 0.25 mm soil aggregates and water-stable aggregates. Comparing with CK, de-farming increased the soil natural water content, capillary porosity, and contents of soil organic matter, total N, alkali-hydrolysable N, total P, and total K, and decreased soil bulk density, non-capillary porosity, and aeration porosity. There were close relationships between the fractal dimension of soil aggregate structure and the soil physical and chemical properties. All the results suggested that the de-farming of slope farmland was beneficial to the increase of the contents of > 0.25 mm soil aggregates and water-stable aggregates, and the enhancement of soil structure stability. The D could be used as an ideal index to evaluate soil fertility, and planting Neosinocalamus affinis on the de-farming slope farmland was a good measure for the improvement of soil fertility in the research area.

Microbial community structure and activity in trace element-contaminated soils phytomanaged by Gentle Remediation Options (GRO).

PubMed

Touceda-González, M; Prieto-Fernández, Á; Renella, G; Giagnoni, L; Sessitsch, A; Brader, G; Kumpiene, J; Dimitriou, I; Eriksson, J; Friesl-Hanl, W; Galazka, R; Janssen, J; Mench, M; Müller, I; Neu, S; Puschenreiter, M; Siebielec, G; Vangronsveld, J; Kidd, P S

2017-12-01

Gentle remediation options (GRO) are based on the combined use of plants, associated microorganisms and soil amendments, which can potentially restore soil functions and quality. We studied the effects of three GRO (aided-phytostabilisation, in situ stabilisation and phytoexclusion, and aided-phytoextraction) on the soil microbial biomass and respiration, the activities of hydrolase enzymes involved in the biogeochemical cycles of C, N, P, and S, and bacterial community structure of trace element contaminated soils (TECS) from six field trials across Europe. Community structure was studied using denaturing gradient gel electrophoresis (DGGE) fingerprinting of Bacteria, α- and β-Proteobacteria, Actinobacteria and Streptomycetaceae, and sequencing of DGGE bands characteristic of specific treatments. The number of copies of genes involved in ammonia oxidation and denitrification were determined by qPCR. Phytomanagement increased soil microbial biomass at three sites and respiration at the Biogeco site (France). Enzyme activities were consistently higher in treated soils compared to untreated soils at the Biogeco site. At this site, microbial biomass increased from 696 to 2352 mg ATP kg -1 soil, respiration increased from 7.4 to 40.1 mg C-CO 2 kg -1 soil d -1 , and enzyme activities were 2-11-fold higher in treated soils compared to untreated soil. Phytomanagement induced shifts in the bacterial community structure at both, the total community and functional group levels, and generally increased the number of copies of genes involved in the N cycle (nirK, nirS, nosZ, and amoA). The influence of the main soil physico-chemical properties and trace element availability were assessed and eventual site-specific effects elucidated. Overall, our results demonstrate that phytomanagement of TECS influences soil biological activity in the long term. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

A radiosity-based model to compute the radiation transfer of soil surface

NASA Astrophysics Data System (ADS)

Zhao, Feng; Li, Yuguang

2011-11-01

A good understanding of interactions of electromagnetic radiation with soil surface is important for a further improvement of remote sensing methods. In this paper, a radiosity-based analytical model for soil Directional Reflectance Factor's (DRF) distributions was developed and evaluated. The model was specifically dedicated to the study of radiation transfer for the soil surface under tillage practices. The soil was abstracted as two dimensional U-shaped or V-shaped geometric structures with periodic macroscopic variations. The roughness of the simulated surfaces was expressed as a ratio of the height to the width for the U and V-shaped structures. The assumption was made that the shadowing of soil surface, simulated by U or V-shaped grooves, has a greater influence on the soil reflectance distribution than the scattering properties of basic soil particles of silt and clay. Another assumption was that the soil is a perfectly diffuse reflector at a microscopic level, which is a prerequisite for the application of the radiosity method. This radiosity-based analytical model was evaluated by a forward Monte Carlo ray-tracing model under the same structural scenes and identical spectral parameters. The statistics of these two models' BRF fitting results for several soil structures under the same conditions showed the good agreements. By using the model, the physical mechanism of the soil bidirectional reflectance pattern was revealed.

The vertical geography of urban soils and its convergence across cities

EPA Science Inventory

The theoretical patterns for vertical soil structure (e.g., A-B-C ordering of horizons) are a basis for research methods and our understanding of ecosystem structure and function in general. A general understanding of how urban soils differ from non-urban soils vertically is need...

Enhancing soil begins with soil biology and a stable soil microclimate

USDA-ARS?s Scientific Manuscript database

Protection of the soil resource from erosion requires reducing the surface impact from raindrop energy and maintaining soil structure and stability to allow more efficient infiltration of water into the soil column. These two processes are linked with practices associated with enhancing and maintain...

Soil properties impacting denitrifier community size, structure, and activity in New Zealand dairy-grazed pasture

NASA Astrophysics Data System (ADS)

Jha, Neha; Saggar, Surinder; Giltrap, Donna; Tillman, Russ; Deslippe, Julie

2017-09-01

Denitrification is an anaerobic respiration process that is the primary contributor of the nitrous oxide (N2O) produced from grassland soils. Our objective was to gain insight into the relationships between denitrifier community size, structure, and activity for a range of pasture soils. We collected 10 dairy pasture soils with contrasting soil textures, drainage classes, management strategies (effluent irrigation or non-irrigation), and geographic locations in New Zealand, and measured their physicochemical characteristics. We measured denitrifier abundance by quantitative polymerase chain reaction (qPCR) and assessed denitrifier diversity and community structure by terminal restriction fragment length polymorphism (T-RFLP) of the nitrite reductase (nirS, nirK) and N2O reductase (nosZ) genes. We quantified denitrifier enzyme activity (DEA) using an acetylene inhibition technique. We investigated whether varied soil conditions lead to different denitrifier communities in soils, and if so, whether they are associated with different denitrification activities and are likely to generate different N2O emissions. Differences in the physicochemical characteristics of the soils were driven mainly by soil mineralogy and the management practices of the farms. We found that nirS and nirK communities were strongly structured along gradients of soil water and phosphorus (P) contents. By contrast, the size and structure of the nosZ community was unrelated to any of the measured soil characteristics. In soils with high water content, the richnesses and abundances of nirS, nirK, and nosZ genes were all significantly positively correlated with DEA. Our data suggest that management strategies to limit N2O emissions through denitrification are likely to be most important for dairy farms on fertile or allophanic soils during wetter periods. Finally, our data suggest that new techniques that would selectively target nirS denitrifiers may be the most effective for limiting N2O emissions through denitrification across a wide range of soil types.

[Analysis of soil humus and components after 26 years' fertilization by infrared spectroscopy method].

PubMed

Zhang, Yu-Lan; Sun, Cai-Xia; Chen, Zhen-Hua; Li, Dong-Po; Liu, Xing-Bin; Chen, Li-Jun; Wu, Zhi-Jie; Du, Jian-Xiong

2010-05-01

The infrared spectrum was used to discuss structure change of soil humus and components of chemical groups in soil humic acids (HA) and fulvic acids (FA) isolated from soils in different fertilization treatment after 26 year's fertilization. The result indicated that using the infrared spectroscopy method for the determination of humus, humus fractions (HA and FA) and their structure is feasible. Fertilization affected the structure and content of soil humus and aromatization degree. After 26 years' fertilization, the infrared spectrum shapes with different treatments are similar, but the characteristic peak intensity is obviously different, which reflects the effects of different fertilization treatments on the structure and amounts of soil humus or functional groups. Compared with no fertilization, little molecule saccharides decreased and aryl-groups increased under application of inorganic fertilizer or combined application of organic and chemical fertilizer. The effect was greater in Treatment NPK and M+NPK than in Treatment M1 N and M2 N. Organic and NPK fertilizer increased the development of soil and increased soil quality to a certain extent. Results showed that organic fertilization increased aromatization degree of soil humus and humus fractions distinctly. The authors could estimate soil humus evolvement of different fertilization with infrared spectroscopy.

The interactive effects of soil transplant into colder regions and cropping on soil microbiology and biogeochemistry.

PubMed

Liu, Shanshan; Wang, Feng; Xue, Kai; Sun, Bo; Zhang, Yuguang; He, Zhili; Van Nostrand, Joy D; Zhou, Jizhong; Yang, Yunfeng

2015-03-01

Soil transplant into warmer regions has been shown to alter soil microbiology. In contrast, little is known about the effects of soil transplant into colder regions, albeit that climate cooling has solicited attention in recent years. To address this question, we transplanted bare fallow soil over large transects from southern China (subtropical climate zone) to central (warm temperate climate zone) and northern China (cold temperate climate zone). After an adaptation period of 4 years, soil nitrogen components, microbial biomass and community structures were altered. However, the effects of soil transplant on microbial communities were dampened by maize cropping, unveiling a negative interaction between cropping and transplant. Further statistical analyses with Canonical correspondence analysis and Mantel tests unveiled annual average temperature, relative humidity, aboveground biomass, soil pH and NH4 (+) -N content as environmental attributes closely correlated with microbial functional structures. In addition, average abundances of amoA-AOA (ammonia-oxidizing archaea) and amoA-AOB (ammonia-oxidizing bacteria) genes were significantly (P < 0.05) correlated with soil nitrification capacity, hence both AOA and AOB contributed to the soil functional process of nitrification. These results suggested that the soil nitrogen cycle was intimately linked with microbial community structure, and both were subjected to disturbance by soil transplant to colder regions and plant cropping. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand.

PubMed

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch ( Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N 2 O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity.

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand

PubMed Central

Truu, Marika; Ostonen, Ivika; Preem, Jens-Konrad; Lõhmus, Krista; Nõlvak, Hiie; Ligi, Teele; Rosenvald, Katrin; Parts, Kaarin; Kupper, Priit; Truu, Jaak

2017-01-01

Soil microbes play a fundamental role in forest ecosystems and respond rapidly to changes in the environment. Simultaneously with the temperature increase the climate change scenarios also predict an intensified hydrological cycle for the Baltic Sea runoff region. The aim of this study was to assess the effect of elevated air humidity on the top soil microbial community structure of a silver birch (Betula pendula Roth.) stand by using a free air humidity manipulation facility (FAHM). The bacterial community structures of bulk soil and birch rhizosphere were analyzed using high-throughput sequencing of bacteria-specific16S rRNA gene fragments and quantification of denitrification related genes. The increased air humidity altered both bulk soil and rhizosphere bacterial community structures, and changes in the bacterial communities initiated by elevated air humidity were related to modified soil abiotic and biotic variables. Network analysis revealed that variation in soil bacterial community structural units is explained by altered abiotic conditions such as increased pH value in bulk soil, while in rhizosphere the change in absorptive root morphology had a higher effect. Among root morphological traits, the absorptive root diameter was strongest related to the bacterial community structure. The changes in bacterial community structures under elevated air humidity are associated with shifts in C, N, and P turnover as well as mineral weathering processes in soil. Increased air humidity decreased the nir and nosZ gene abundance in the rhizosphere bacterial community. The potential contribution of the denitrification to the N2O emission was not affected by the elevated air humidity in birch stand soil. In addition, the study revealed a strong link between the bacterial community structure, abundance of denitrification related genes, and birch absorptive root morphology in the ecosystem system adaptation to elevated air humidity. PMID:28421053

Effects of imidacloprid on soil microbial communities in different saline soils.

PubMed

Zhang, Qingming; Xue, Changhui; Wang, Caixia

2015-12-01

The effects of imidacloprid in the soil environment are a worldwide concern. However, the impact of imidacloprid on soil microorganisms under salt stress is almost unknown. Therefore, an indoor incubation test was performed, and the denaturing gradient gel electrophoresis (DGGE) approach was used to determine the response of different saline soil bacterial and fungal community structures to the presence of imidacloprid (0.4, 2, 10 mg kg(-1)). The results showed that the soil bacterial diversity slightly declined with increasing imidacloprid concentration in soils with low salinity. In moderately saline soils, a new band in the DGGE profile suggested that imidacloprid could improve the soil bacterial diversity to some degree. An analysis of variance indicated that the measured soil bacterial diversity parameters were significantly affected by dose and incubation time. Compared with the control, the soil fungal community structure showed no obvious changes in low and moderately saline soils treated with imidacloprid. The results of these observations provide a basic understanding of the potential ecological effects of imidacloprid on different microorganisms in saline soils.

Bioindication in Urban Soils in Switzerland

NASA Astrophysics Data System (ADS)

Amossé, J.; Le Bayon, C.; Mitchell, E. A. D.; Gobat, J. M.

2012-04-01

Urban development leads to profound changes in ecosystem structure (e.g. biodiversity) and functioning (e.g. ecosystem services). While above-ground diversity is reasonably well studied much less is known about soil diversity, soil processes and more generally soil health in urban settings. Soil invertebrates are key actors of soil processes at different spatial and temporal scales and provide essential ecosystem services. These functions may be even more vital in stressed environments such as urban ecosystems. Despite the general recognition of the importance of soil organisms in ecosystems, soil trophic food webs are still poorly known and this is especially the case in urban settings. As urban soils are characterised by high fragmentation and stress (e.g. drought, pollution) the structure and functioning of soil communities is likely to be markedly different from that of natural soils. It is for example unclear if earthworms, whose roles in organic matter transformation and soil structuration is well documented in natural and semi-natural soils, are also widespread and active in urban soils. Bioindication is a powerful tool to assess the quality of the environment. It is complementary to classical physicochemical soil analysis or can be used as sole diagnostic tool in cases where these analyses cannot be performed. However little is known about the potential use of bioindicators in urban settings and especially it is unclear if methods developped in agriculture can be applied to urban soils. The development of reliable methods for assessing the quality of urban soils has been identified as a priority for policy making and urban management in Switzerland, a high-urbanized country. We therefore initiated a research project (Bioindication in Urban Soil - BUS). The project is organised around four parts: (i) typology of urban soils in a study Region (Neuchâtel), (ii) sampling of soil fauna and analysis of soil physicochemical properties, (iii) comparison of the functionality of urban soils and alluvial soils, used as a natural reference because of their regular physical perturbation by flooding and associated erosion/sedimentation, (iv) evaluation of soil bioindicators (e.g. earthworm, enchytraeid and testate amoebae) for urban soils. The application objective of my research is to introduce bioindicators and their limit values for the future revision of the legal Ordonnance on soils (OSol), and to develop guidelines to improve or to build urban soils with the aim of reaching a sustainable urban ecosystem development.

SITE AMPLIFICATION OF EARTHQUAKE GROUND MOTION.

USGS Publications Warehouse

Hays, Walter W.

1986-01-01

When analyzing the patterns of damage in an earthquake, physical parameters of the total earthquake-site-structure system are correlated with the damage. Soil-structure interaction, the cause of damage in many earthquakes, involves the frequency-dependent response of both the soil-rock column and the structure. The response of the soil-rock column (called site amplification) is controversial because soil has strain-dependent properties that affect the way the soil column filters the input body and surface seismic waves, modifying the amplitude and phase spectra and the duration of the surface ground motion.

Soil physical land degradation processes

NASA Astrophysics Data System (ADS)

Horn, Rainer

2017-04-01

According to the European Soil Framework Directive (2006) soil compaction is besides water and wind erosion one of the main physical reasons and threats of soil degradation. It is estimated, that 32% of the subsoils in Europe are highly degraded and 18% moderately vulnerable to compaction. The problem is not limited to crop land or forest areas (especially because of non-site adjusted harvesting machines) but is also prevalent in rangelands and grassland, and even in so called natural non-disturbed systems. The main reasons for an intense increase in compacted agricultural or forested regions are the still increasing masses of the machines as well the increased frequency of wheeling under non favorable site conditions. Shear and vibration induced soil deformation enhances the deterioration of soil properties especially if the soil water content is very high and the internal soil strength very low. The same is true for animal trampling in combination with overgrazing of moist to wet pastures which subsequently causes a denser (i.e. reduced proportion of coarse pores with smaller continuity) but still structured soil horizons and will finally end in a compacted platy structure. In combination with high water content and shearing due to trampling therefore results in a complete muddy homogeneous soil with no structure at all. (Krümmelbein et al. 2013) Site managements of arable, forestry or horticulture soils requires a sufficiently rigid pore system which guarantees water, gas and heat exchange, nutrient transport and adsorption as well as an optimal rootability in order to avoid subsoil compaction. Such pore system also guarantees a sufficient microbial activity and composition in order to also decompose the plant etc. debris. It is therefore essential that well structured horizons dominate in soils with at best subangular blocky structure or in the top A- horizons a crumbly structure due to biological activity. In contrast defines the formation of a platy structure down to deeper depth and/or in combination with the deterioration of a continuous pore system an intensely degraded soil. A dominating anisotropy of pore functions causes a lateral soil and water movement. Doerner and Horn (2006), documented the increasing effect of stress and shear affected horizontal anisotropy on the hydraulic and gas permeability which coincides with a retarded gas exchange and an increased proportion of e.g. CO2 or even CH4 in soil pores and hinders the normal population growth. If the internal soil strength is exceeded the microbial composition and activity is converted to anoxia and even results in the emission of CH4 (Haas et al. 2016). Furthermore, the accessibility of nutrient adsorption places as well as connection between the pores within the compacted soils is decreased and results in a retarded ion mass flow and diffusion within the plats and /or in between the soil horizons. How to overcome these negative effects and how to deal with soils adequately according to their internal strength will be presented in the lecture - we need to improve the food production at an preserved land area for growing population. Literature Haas,C., Holthusen,D., Mordhorst,A., Lipiec,J., Horn, R. 2016. Elastic and plastic soil deformation and its influence on emission of greenhouse gases. Int. Agrophys., 30, 173-184 Krümmelbein, J., R.Horn 2013: Cycle of Soil Structure. Soil Degradation 183-198, Advances in Geoecology, 42, Catena Verlag, ISBN: 978-3-923381-59-3

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.

Environmental impacts of different crop rotations in terms of soil compaction.

PubMed

Götze, Philipp; Rücknagel, Jan; Jacobs, Anna; Märländer, Bernward; Koch, Heinz-Josef; Christen, Olaf

2016-10-01

Avoiding soil compaction caused by agricultural management is a key aim of sustainable land management, and the soil compaction risk should be considered when assessing the environmental impacts of land use systems. Therefore this project compares different crop rotations in terms of soil structure and the soil compaction risk. It is based on a field trial in Germany, in which the crop rotations (i) silage maize (SM) monoculture, (ii) catch crop mustard (Mu)_sugar beet (SB)-winter wheat (WW)-WW, (iii) Mu_SM-WW-WW and (iv) SB-WW-Mu_SM are established since 2010. Based on the cultivation dates, the operation specific soil compaction risks and the soil compaction risk of the entire crop rotations are modelled at two soil depths (20 and 35 cm). To this end, based on assumptions of the equipment currently used in practice by a model farm, two scenarios are modelled (100 and 50% hopper load for SB and WW harvest). In addition, after one complete rotation, in 2013 and in 2014, the physical soil parameters saturated hydraulic conductivity (kS) and air capacity (AC) were determined at soil depths 2-8, 12-18, 22-28 and 32-38 cm in order to quantify the soil structure. At both soil depths, the modelled soil compaction risks for the crop rotations including SB (Mu_SB-WW-WW, SB-WW-Mu_SM) are higher (20 cm: medium to very high risks; 35 cm: no to medium risks) than for those without SB (SM monoculture, Mu_SM-WW-WW; 20 cm: medium risks; 35 cm: no to low risks). This increased soil compaction risk is largely influenced by the SB harvest in years where soil water content is high. Halving the hopper load and adjusting the tyre inflation pressure reduces the soil compaction risk for the crop rotation as a whole. Under these conditions, there are no to low soil compaction risks for all variants in the subsoil (soil depth 35 cm). Soil structure is mainly influenced in the topsoil (2-8 cm) related to the cultivation of Mu as a catch crop and WW as a preceding crop. Concerning kS, Mu_SB-WW-WW (240 cm d(-1)) and Mu_SM-WW-WW (196 cm d(-1)) displayed significantly higher values than the SM monoculture (67 cm d(-1)), indicating better structural stability and infiltration capacity. At other soil depths, and for the parameter AC, there are no systematic differences in soil structure between the variants. Under the circumstances described, all crop rotations investigated are not associated with environmental impacts caused by soil compaction. Copyright © 2016 Elsevier Ltd. All rights reserved.

Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

USGS Publications Warehouse

Cartwright, Jennifer M.; Advised by Dzantor, E. Kudjo

2015-01-01

Stress factors quantified by this research include shallow soil (depth to bedrock ranging from 2.4 to 22.6 cm), volumetric soil water content levels seasonally ranging from xeric (below 5%) to saturated (above 50%), and seasonally extreme ground-surface temperatures (above 48°C). Findings from this research indicate that spatial and temporal heterogeneity exists in limestone cedar glades in terms of abiotic stress factors and soil physical and chemical properties. Several such soil properties (e.g. soil depth, organic matter levels, pH, and particle size distribution) are spatially correlated. These soil properties were statistically related to ecological structures and functions such as vegetation patterns, soil respiration, the density of culturable heterotrophic microbes in soil and metabolic diversity of soil microbial community profiles. In general, zones within limestone cedar glades that had relatively shallow soil, alkaline pH, low levels of organic matter and high levels of silt also tended to have depressed rates of soil respiration and reduced densities and metabolic diversity of culturable heterotrophic soil microbes. Additionally, seasonally-relevant stress factors including soil water content and temperatures at or near the soil surface were related to the same set of ecological structures and functions.

Pyrosequencing of microbial community of typical chernozem in contrast land use conditions

NASA Astrophysics Data System (ADS)

Ivanova, Ekaterina; Olga, Kutovaya; Azida, Tkhakakhova

2015-04-01

Chernozems are the principal soil resourse of Russia, so the sustainable use of these fertile soils in the intensive agriculturural production is of great importance, especially in terms of agro-ecological security of the country. The increase in agricultural inputs - intensive cropping, soil fallowing application accompanied with high frequency of mechanical treatment, result in decrease in soil organic matter content as well as soil structure degradation and, finally, lead to the loss of soil fertility. Soil microorganisms can serve as bioindicators of anthropogenic stress experienced by the soil during its agricultural use, so they may be universal indicators of soil quality (soil health) used for optimization and biologization of agricultural systems. The way to study the relationship between the structural status of the soil, its microbial communities and the organic matter content is the comparative analysis of soil aggregates in conditions of different land use practices. The objects of our research were soil samples of soil with permanent wheat cropping (50 years), continuous dead fallow (50 years) soil, and recovering soil (for 18 years under native steppe vegetation, fallowed in previous). The analysis of 16 S rRNA gene amplicon libraries of typical chernozem in conditions of different land use systems revealed that the way of agricultural use is a strong determinant of soil microbiome taxonomic composition. It was shown that the continuous «dead fallowing» application (for 50 years) lead to the establishment of olygothrophic components of microbial community, including spore-forming members of phylum Firmicutes. The increase of Acidobacteria lineages in this variant may be an indicator of some acidification of soil during long-time fallowing application. The variant of continuous wheat cropping lead to increasing in Proteobacteria lineages. The variant of soil under native steppe vegetation was characterized by the highest values of biodiversity indices - species richness and eveness, which can indicate the occurrence of soil recovering. This variant was also characterized by the maximum content of agricultural valuable aggregate fraction of 2-5 mm size. In soil samples from different aggregate fractions the presence of accessory components was revealed. It was determined that Actinobacteria lineages preferred microaggregates (less than 0.25 mm) rather than coarse aggregate fractions (more than 7 mm). The opposite trend was determined for Proteobacteria: the amount was maximum in aggregates more than 7 mm in diameter. The occurrence of specific components in the taxonomic structure of micro-and macro-aggregates may indicate the presence of a certain size fraction in the structure of the investigated soil. The study of soils' metagenome is promising for the development of both soil microbiology, and for the soil processes trends in soils of anthropogenic origin. The study was supported by Russian Scientific Fund (14-26-00079 and 14-26-00094)

Using synthetic polymers to reduce soil erosion after forest fires in Mediterranean soils

NASA Astrophysics Data System (ADS)

Lado, Marcos; Ben-Hur, Meni; Inbar, Assaf

2010-05-01

Forest fires are a major environmental problem in the Mediterranean region because they result in a loss of vegetation cover, changes in biodiversity, increases in greenhouse gasses emission and a potential increase of runoff and soil erosion. The large increases in runoff and sediment yields after high severity fires have been attributed to several factors, among them: increase in soil water repellency; soil sealing by detached particles and by ash particles, and the loss of a surface cover. The presence of a surface cover increases infiltration, and decreases runoff and erosion by several mechanisms which include: rainfall interception, plant evapotranspiration, preservation of soil structure by increasing soil organic matter, and increasing surface roughness. The loss of vegetation cover as a result of fire leaves the surface of the soil exposed to the direct impact of the raindrops, and therefore the sensitivity of the soil to runoff generation and soil loss increases. In this work, we propose a new method to protect soils against post-fire erosion based on the application of synthetic polymers to the soil. Laboratory rainfall simulations and field runoff plots were used to analyze the suitability of the application of synthetic polymers to reduce soil erosion and stabilize soil structure in Mediterranean soils. The combination of these two processes will potentially favor a faster recovery of the vegetation structure. This method has been successfully applied in arable land, however it has not been tested in burnt forests. The outcome of this study may provide important managerial tools for forest management following fires.

Agriculturization in the Argentinean Northern Humid Pampas: the Impact on Soil Structure and Runoff

NASA Astrophysics Data System (ADS)

Sasal, M. C.; Léonard, J.; Andriulo, A.; Wilson, M. G.

2012-04-01

Argentina is among the countries with the largest cropped area under no-tillage (NT). No tillage was adopted in the northern Humid Pampas to reduce the widespread soil degradation by water erosion. With the advent of genetically modified soybean varieties, NT has developed exponentially. This evolution, combined with the influence of the international market trend, has resulted in large changes in crop sequence composition toward the disappearance of pastures and the expansion of soybean monoculture. The aim of this work was to evaluate the long-term consequences of these changes on the topsoil structure and the way in which the evolution of soil structure relates to the simplification of the crop sequence and to runoff at a regional scale. We analyzed the topsoil structure of 25 sites with Argiudolls having 4 to 29 consecutive years of NT using the cultural profile approach. An intensification sequence index (ISI) was calculated as the ratio between the length of the growth period and the length of the year. Fifteen natural-rainfall runoff plots (100 m2) with 3.5% slope were used to analyze the relationship between soil structural state, crop sequence and runoff for four years. Four types of soil structures were identified and a general pattern of vertical soil structure organization was revealed. The top centimeters of 72% of the sites were dominated by a granular structure. Platy soil structure development was omnipresent: all sites exhibited a horizontal platy structure (<10 cm thick) developing either directly from the soil surface or from below the granular structure. Below the platy structure layer, a gamma soil structure (with visible structural porosity) was observed in all sites (30-75% of the A horizon), while compacted delta soil structure was detected in localized zones. A significant parabolic relationship (R2=0.60) was found between the number of consecutive years under NT and the proportion of platy structure in the A horizon. The proportion of platy structure increased during the first 15 years of NT, and then the extension of platy structure tended to stabilize and even to decrease after 20 to 25 years. The development of platy soil structure was negatively related to the ISI (R2=0.57) and runoff increased as the proportion of platy structure increased and the proportion of granular structure decreased (R2=0.85). We concluded that high soybean frequency in cropping systems under NT favors the extension of platy soil structure and increases runoff. More than 70% of the agricultural area of the northern Humid Pampas region is currently covered by soybean cultivation, mostly as a single annual crop (ISI=0.38). Our results thus suggest that promoting management practices such as the expansion of wheat/soybean double crop (ISI=0.83) could limit soil structure degradation and reduce runoff and the associated environmental risks.

Dullgren extraction of soil mites (Acarina): Effect of refrigeration time on extraction efficiency

Treesearch

Michelle B. Lakly; D.A. Crossley

2000-01-01

Soil microarthropods constitute one of the most species rich communities in . forest ecosystems (Crossley & Blair, 1991). The effects of soil fauna in these systems on decomposition rates, nutrient regeneration and soil structure have been well documented; however, dependable estimates of population size and community structure largely depend upon adequate sampling...

Single application of Sewage Sludge to an Alluvial Agricultural Soil - impacts on Soil Quality

NASA Astrophysics Data System (ADS)

Suhadolc, M.; Graham, D. B.; Hagn, A.; Doerfler, U.; Schloter, M.; Schroll, R.; Munch, J. C.; Lobnik, F.

2009-04-01

Limited information exists on the effects of sewage sludge on soil quality with regard to their ability to maintain soil functions. We studied effects of sewage sludge amendment on soil chemical properties, microbial community structure and microbial degradation of the herbicide glyphosate. Three months soil column leaching experiment has been conducted using alluvial soils (Eutric Fluvisol) with no prior history of sludge application. The soil was loamy with pH 7,4 and organic matter content of 3,5%. Soil material in the upper 2 cm of columns was mixed with dehydrated sewage sludge which was applied in amounts corresponding to the standards governing the use of sewage sludge for agricultural land. Sludge did increase some nutrients (total N, NH4+, available P and K, organic carbon) and some heavy metals contents (Zn, Cu, Pb) in soil. However, upper limits for heavy metals in agricultural soils were not exceeded. Results of heavy metal availability in soil determined by sequential extraction will be also presented. Restriction fragment length polymorphism (RFLP) analyses of 16s/18s rDNA, using universal fungal and bacterial primers, revealed clear shifts in bacterial and fungal community structure in the upper 2 cm of soils after amendment. Fungal fingerprints showed greater short term effects of sewage sludge, whereas sewage sludge seems to have prolonged effects on soil bacteria. Furthermore, sewage sludge amendment significantly increased glyphosate degradation from 21.6±1% to 33.6±1% over a 2 months period. The most probable reasons for shifts in microbial community structure and increased degradation of glyphosate are beneficial alterations to the physical-chemical characteristics of the soil. Negative effects of potentially toxic substances present in the sewage sludge on soil microbial community functioning were not observed with the methods used in our study.

Evaluating the importance of characterizing soil structure and horizons in parameterizing a hydrologic process model

USGS Publications Warehouse

Mirus, Benjamin B.

2015-01-01

Incorporating the influence of soil structure and horizons into parameterizations of distributed surface water/groundwater models remains a challenge. Often, only a single soil unit is employed, and soil-hydraulic properties are assigned based on textural classification, without evaluating the potential impact of these simplifications. This study uses a distributed physics-based model to assess the influence of soil horizons and structure on effective parameterization. This paper tests the viability of two established and widely used hydrogeologic methods for simulating runoff and variably saturated flow through layered soils: (1) accounting for vertical heterogeneity by combining hydrostratigraphic units with contrasting hydraulic properties into homogeneous, anisotropic units and (2) use of established pedotransfer functions based on soil texture alone to estimate water retention and conductivity, without accounting for the influence of pedon structures and hysteresis. The viability of this latter method for capturing the seasonal transition from runoff-dominated to evapotranspiration-dominated regimes is also tested here. For cases tested here, event-based simulations using simplified vertical heterogeneity did not capture the state-dependent anisotropy and complex combinations of runoff generation mechanisms resulting from permeability contrasts in layered hillslopes with complex topography. Continuous simulations using pedotransfer functions that do not account for the influence of soil structure and hysteresis generally over-predicted runoff, leading to propagation of substantial water balance errors. Analysis suggests that identifying a dominant hydropedological unit provides the most acceptable simplification of subsurface layering and that modified pedotransfer functions with steeper soil-water retention curves might adequately capture the influence of soil structure and hysteresis on hydrologic response in headwater catchments.

[Diversity of uncultured actinomycetes in saline-alkali soil from Jiuquan area of Hexi Corridor].

PubMed

Li, Hai-yun; Niu, Shi-quan; Kong, Wei-bao; Yan, Wei-ru; Geng, Hui; Han, Cai-hong; Da, Wen-yan; Zhang, Ai-mei; Zhu, Xue-tai

2015-09-01

In order to more accurately understand community structure and diversity of actinomycetes in saline-alkali soil from Jiuquan area of Hexi Corridor, the community structure and diversity from three kinds of soil samples (primary, secondary saline alkali soil and farmland soil) were analyzed using uncultured methods. The results showed that the 16S rDNA clone library of actinomycetales from the primary saline-alkali soil belonged to 19 OTUs, Micrococcineae, Propionibacterineae, Corynebacterineae, Frankineae, Pseudonocardineae and unknown groups of Actinomycetales; the 16S r DNA clone library of actinomycetales from the secondary saline-alkali soil belonged to 14 OTUs, Micrococcineae, Propionibacterineae, Corynebacterineae, Frankineae, Pseudonocardineae and unknown groups of Actinomycetales; the 16S rDNA clone library of farmland soil belonged to 7 OTUs, Micrococcineae, Propionibacterineae, Corynebacterineae, Frankineae, Pseudonocardineae and unknown groups of Actinomycetales; Micrococcineae was the common population in the three soils, and also was the dominant population in primary saline alkali soil and farmland soil. The diversity index and rarefaction curves analysis showed that actinomycetes species richness was in order of primary saline-alkali soil > secondary saline-alkali soil > farmland soil. The dilution curves of primary saline-alkali soil and secondary saline-alkali soil were not leveled off, which indicated the actinomycetes diversity in saline-alkali soil was more enriched than the actual. The rich and diverse actinomycetes resources in saline-alkali soil from Jiuquan area of Hexi Corridor provide important data on the actinomycetes ecology distribution research, exploitation and utilization in saline-alkali soil.

Spatial variability structure of soil CO2 emission and soil physical and chemical properties characterized by fractal dimension in sugarcane areas

NASA Astrophysics Data System (ADS)

Bicalho, E. S.; Teixeira, D. B.; Panosso, A. R.; Perillo, L. I.; Iamaguti, J. L.; Pereira, G. T.; La Scala, N., Jr.

2012-04-01

Soil CO2 emission (FCO2) is influenced by chemical, physical and biological factors that affect the production of CO2 in the soil and its transport to the atmosphere, varying in time and space depending on environmental conditions, including the management of agricultural area. The aim of this study was to investigate the structure of spatial variability of FCO2 and soil properties by using fractal dimension (DF), derived from isotropic variograms at different scales, and construction of fractograms. The experimental area consisted of a regular grid of 60 × 60 m on sugarcane area under green management, containing 141 points spaced at minimum distances ranging from 0.5 to 10 m. Soil CO2 emission, soil temperature and soil moisture were evaluated over a period of 7 days, and soil chemical and physical properties were determined by sampling at a depth of 0.0 to 0.1 m. FCO2 showed an overall average of 1.51 µmol m-2 s-1, correlated significantly (p < 0.05) with soil physical factors such as soil bulk density, air-filled pore space, macroporosity and microporosity. Significant DF values were obtained in the characterization of FCO2 in medium and large scales (from 20 m). Variations in DF with the scale, which is the fractogram, indicate that the structure of FCO2 variability is similar to that observed for the soil temperature and total pore volume, and reverse for the other soil properties, except for macroporosity, sand content, soil organic matter, carbon stock, C/N ratio and CEC, which fractograms were not significantly correlated to the FCO2 fractogram. Thus, the structure of spatial variability for most soil properties, characterized by fractogram, presents a significant relationship with the structure of spatial variability of FCO2, generally with similar or dissimilar behavior, indicating the possibility of using the fractogram as tool to better observe the behavior of the spatial dependence of the variables along the scale.

Soil microbial community successional patterns during forest ecosystem restoration.

PubMed

Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.

Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

PubMed Central

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890

Green roof soil system affected by soil structural changes: A project initiation

NASA Astrophysics Data System (ADS)

Jelínková, Vladimíra; Dohnal, Michal; Šácha, Jan; Šebestová, Jana; Sněhota, Michal

2014-05-01

Anthropogenic soil systems and structures such as green roofs, permeable or grassed pavements comprise appreciable part of the urban watersheds and are considered to be beneficial regarding to numerous aspects (e.g. carbon dioxide cycle, microclimate, reducing solar absorbance and storm water). Expected performance of these systems is significantly affected by water and heat regimes that are primarily defined by technology and materials used for system construction, local climate condition, amount of precipitation, the orientation and type of the vegetation cover. The benefits and potencies of anthropogenic soil systems could be considerably threatened in case when exposed to structural changes of thin top soil layer in time. Extensive green roof together with experimental green roof segment was established and advanced automated monitoring system of micrometeorological variables was set-up at the experimental site of University Centre for Energy Efficient Buildings as an interdisciplinary research facility of the Czech Technical University in Prague. The key objectives of the project are (i) to characterize hydraulic and thermal properties of soil substrate studied, (ii) to establish seasonal dynamics of water and heat in selected soil systems from continuous monitoring of relevant variables, (iii) to detect structural changes with the use of X-ray Computed Tomography, (iv) to identify with the help of numerical modeling and acquired datasets how water and heat dynamics in anthropogenic soil systems are affected by soil structural changes. Achievements of the objectives will advance understanding of the anthropogenic soil systems behavior in conurbations with the temperate climate.

Improvements of the Profil Cultural Method for a better Low-tech Field Assessment of Soil Structure under no-till

NASA Astrophysics Data System (ADS)

Roger-Estrade, Jean; Boizard, Hubert; Peigné, Josephine; Sasal, Maria Carolina; Guimaraes, Rachel; Piron, Denis; Tomis, Vincent; Vian, Jean-François; Cadoux, Stephane; Ralisch, Ricardo; Filho, Tavares; Heddadj, Djilali; de Battista, Juan; Duparque, Annie

2016-04-01

In France, agronomists have studied the effects of cropping systems on soil structure, using a field method based on a visual description of soil structure. The "profil cultural" method (Manichon and Gautronneau, 1987) has been designed to perform a field diagnostic of the effects of tillage and compaction on soil structure dynamics. This method is of great use to agronomists improving crop management for a better preservation of soil structure. However, this method was developed and mainly used in conventional tillage systems, with ploughing. As several forms of reduced, minimum and no tillage systems are expanding in many parts of the world, it is necessary to re-evaluate the ability of this method to describe and interpret soil macrostructure in unploughed situations. In unploughed fields, soil structure dynamics of untilled layers is mainly driven by compaction and regeneration by natural agents (climatic conditions, root growth and macrofauna) and it is of major importance to evaluate the importance of these natural processes on soil structure regeneration. These concerns have led us to adapt the standard method and to propose amendments based on a series of field observations and experimental work in different situations of cropping systems, soil types and climatic conditions. We improved the description of crack type and we introduced an index of biological activity, based on the visual examination of clods. To test the improved method, a comparison with the reference method was carried out and the ability of the "profil cultural" method to make a diagnosis was tested on five experiments in France, Brazil and Argentina. Using the improved method, the impact of cropping systems on soil functioning was better assessed when natural processes were integrated into the description.

Beech cupules as keystone structures for soil fauna.

PubMed

Melguizo-Ruiz, Nereida; Jiménez-Navarro, Gerardo; Moya-Laraño, Jordi

2016-01-01

Facilitative or positive interactions are ubiquitous in nature and play a fundamental role in the configuration of ecological communities. In particular, habitat modification and niche construction, in which one organism locally modifies abiotic conditions and favours other organisms by buffering the effects of adverse environmental factors, are among the most relevant facilitative interactions. In line with this, 'keystone structures', which provide resources, refuge, or advantageous services decisive for other species, may allow the coexistence of various species and thus considerably contribute to diversity maintenance. Beech cupules are woody husks harbouring beech fruits that remain in the forest soil for relatively long periods of time. In this study, we explored the potential role of these cupules in the distribution and maintenance of the soil fauna inhabiting the leaf litter layer. We experimentally manipulated cupule availability and soil moisture in the field to determine if such structures are limiting and can provide moist shelter to soil animals during drought periods, contributing to minimize desiccation risks. We measured invertebrate abundances inside relative to outside the cupules, total abundances in the leaf litter and animal body sizes, in both dry and wet experimental plots. We found that these structures are preferentially used by the most abundant groups of smaller soil animals-springtails, mites and enchytraeids-during droughts. Moreover, beech cupules can be limiting, as an increase in use was found with higher cupule densities, and are important resources for many small soil invertebrates, driving the spatial structure of the soil community and promoting higher densities in the leaf litter, probably through an increase in habitat heterogeneity. We propose that fruit woody structures should be considered 'keystone structures' that contribute to soil community maintenance. Therefore, beech trees may indirectly facilitate soil fauna activities through their decaying fruit husks, hence acting as ecosystem engineers.

Land-use and soil depth affect resource and microbial stoichiometry in a tropical mountain rainforest region of southern Ecuador.

PubMed

Tischer, Alexander; Potthast, Karin; Hamer, Ute

2014-05-01

Global change phenomena, such as forest disturbance and land-use change, significantly affect elemental balances as well as the structure and function of terrestrial ecosystems. However, the importance of shifts in soil nutrient stoichiometry for the regulation of belowground biota and soil food webs have not been intensively studied for tropical ecosystems. In the present account, we examine the effects of land-use change and soil depth on soil and microbial stoichiometry along a land-use sequence (natural forest, pastures of different ages, secondary succession) in the tropical mountain rainforest region of southern Ecuador. Furthermore, we analyzed (PLFA-method) whether shifts in the microbial community structure were related to alterations in soil and microbial stoichiometry. Soil and microbial stoichiometry were affected by both land-use change and soil depth. After forest disturbance, significant decreases of soil C:N:P ratios at the pastures were followed by increases during secondary succession. Microbial C:N ratios varied slightly in response to land-use change, whereas no fixed microbial C:P and N:P ratios were observed. Shifts in microbial community composition were associated with soil and microbial stoichiometry. Strong positive relationships between PLFA-markers 18:2n6,9c (saprotrophic fungi) and 20:4 (animals) and negative associations between 20:4 and microbial N:P point to land-use change affecting the structure of soil food webs. Significant deviations from global soil and microbial C:N:P ratios indicated a major force of land-use change to alter stoichiometric relationships and to structure biological systems. Our results support the idea that soil biotic communities are stoichiometrically flexible in order to adapt to alterations in resource stoichiometry.

Throughfall-mediated alterations to soil microbial community structure in a forest plot of homogenous soil texture, litter, and plant species composition

NASA Astrophysics Data System (ADS)

Van Stan, John; Rosier, Carl; Moore, Leslie; Gay, Trent; Reichard, James; Wu, Tiehang; Kan, Jinjun

2015-04-01

Identifying spatiotemporal influences on soil microbial community (SMC) structure is critical to our understanding of patterns in biogeochemical cycling and related ecological services (e.g., plant community structure, water quality, response to environmental change). Since forest canopy structure alters the spatiotemporal patterning of precipitation water and solute supplies to soils (via "throughfall"), is it possible that changes in SMC structure could arise from modifications in canopy elements? Our study investigates this question by monitoring throughfall water and dissolved ion supply to soils beneath a continuum of canopy structure: from large gaps (0% cover), to bare Quercus virginiana Mill. (southern live oak) canopy (~50-70%), to heavy Tillandsia usneoides L. (Spanish moss) canopy (>90% cover). Throughfall water supply diminished with increasing canopy cover, yet increased washoff/leaching of Na+, Cl-, PO43-, and SO42- from the canopy to the soils. Presence of T. usneoides diminished throughfall NO3-, but enhanced NH4+, concentrations supplied to subcanopy soils. The mineral soil horizon (0-10 cm) sampled in triplicate from locations receiving throughfall water and solutes from canopy gaps, bare canopy, and T. usneoides-laden canopy significantly differed in soil chemistry parameters (pH, Ca2+, Mg2+, CEC). Polymerase Chain Reaction-Denaturant Gradient Gel Electrophoresis (PCR-DGGE) banding patterns beneath similar canopy covers (experiencing similar throughfall dynamics) also produced high similarities per ANalyses Of SIMilarity (ANO-SIM), and clustered together when analyzed by Nonmetric Multidimensional Scaling (NMDS). These results suggest that modifications of forest canopy structures are capable of affecting mineral-soil horizon SMC structure via throughfall when canopies' biomass distribution is highly heterogeneous. As SMC structure, in many instances, relates to functional diversity, we suggest that future research seek to identify functional diversity shifts (e.g., nitrogen transformation) in response to canopy structural alterations of throughfall water/solute concentration

Short-term C mineralization (aka the flush of CO2) as an indicator of soil biological health

USDA-ARS?s Scientific Manuscript database

Soil biological activity is a key component of soil health assessments, as it (a) indicates soil nutrient cycling capacity from various organic matter sources to inorganic availability, (b) relates to soil structural conditions, (c) informs about the potential to harbor biodiversity in soil, and (d)...

Mapping of Soil-Ecological Conditions of a Medium-Size Industrial City (Birobidzhan City, Jewish Autonomous Oblast, FarEast of Russia as an Example)

NASA Astrophysics Data System (ADS)

Kalmanova, V. B.; Matiushkina, L. A.

2018-01-01

The authors analyze soil relations with other elements of the city ecosystem (the position in the landscape, soil-forming rocks and lithology, vegetation and its state) to develop the legend and map of soils in the City of Birobidzhan (scale 1:25 000). The focus of study is the morphological structure of urban soils with different degree of disturbance of these relations under the impact of technical effects, economic and recreational activities of the city population. The soil cover structure is composed of four large ecological groups of soils: natural untransformed, natural with a disturbed surface, anthropogenic soils and technogenic surface formations. Using cartometry of the mapped soil contours the authors created the scheme of soil-ecological city zoning, which in a general way depicts the state of soil ecological functions in the city as well as identified zones of soils with preserved, partially and fully distured ecological functions and zones of local geochemical anomalies at the initial formation stage (environmental risk zones).

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau

PubMed Central

Li, Yuntao; Adams, Jonathan; Shi, Yu; Wang, Hao; He, Jin-Sheng; Chu, Haiyan

2017-01-01

Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem. PMID:28401921

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Li, Yuntao; Adams, Jonathan; Shi, Yu; Wang, Hao; He, Jin-Sheng; Chu, Haiyan

2017-04-01

Global change may be a severe threat to natural and agricultural systems, partly through its effects in altering soil biota and processes, due to changes in water balance. We studied the potential influence of changing soil water balance on soil biota by comparing existing sites along a natural water balance gradient in the Qinghai-Tibetan Plateau. In this study, the community structure of bacteria, archaea and eukaryotes differed between the different soil water conditions. Soil moisture was the strongest predictor of bacterial and eukaryotic community structure, whereas C/N ratio was the key factor predicting variation in the archaeal community. Bacterial and eukaryotic diversity was quite stable among different soil water availability, but archaeal diversity was dramatically different between the habitats. The auxotype of methanogens also varied significantly among different habitats. The co-varying soil properties among habitats shaped the community structure of soil microbes, with archaea being particularly sensitive in terms of community composition, diversity and functional groups. Bacterial and archaeal phylogenetic community turnover was mainly driven by deterministic processes while stochastic processes had stronger effects on eukaryotic phylogenetic community turnover. Our work provides insight into microbial community, functional group and phylogenetic turnover under different soil conditions in low-latitude alpine ecosystem.

Jatropha curcas L. Root Structure and Growth in Diverse Soils

PubMed Central

Valdés-Rodríguez, Ofelia Andrea; Sánchez-Sánchez, Odilón; Pérez-Vázquez, Arturo; Caplan, Joshua S.; Danjon, Frédéric

2013-01-01

Unlike most biofuel species, Jatropha curcas has promise for use in marginal lands, but it may serve an additional role by stabilizing soils. We evaluated the growth and structural responsiveness of young J. curcas plants to diverse soil conditions. Soils included a sand, a sandy-loam, and a clay-loam from eastern Mexico. Growth and structural parameters were analyzed for shoots and roots, although the focus was the plasticity of the primary root system architecture (the taproot and four lateral roots). The sandy soil reduced the growth of both shoot and root systems significantly more than sandy-loam or clay-loam soils; there was particularly high plasticity in root and shoot thickness, as well as shoot length. However, the architecture of the primary root system did not vary with soil type; the departure of the primary root system from an index of perfect symmetry was 14 ± 5% (mean ± standard deviation). Although J. curcas developed more extensively in the sandy-loam and clay-loam soils than in sandy soil, it maintained a consistent root to shoot ratio and root system architecture across all types of soil. This strong genetic determination would make the species useful for soil stabilization purposes, even while being cultivated primarily for seed oil. PMID:23844412

Jatropha curcas L. root structure and growth in diverse soils.

PubMed

Valdés-Rodríguez, Ofelia Andrea; Sánchez-Sánchez, Odilón; Pérez-Vázquez, Arturo; Caplan, Joshua S; Danjon, Frédéric

2013-01-01

Unlike most biofuel species, Jatropha curcas has promise for use in marginal lands, but it may serve an additional role by stabilizing soils. We evaluated the growth and structural responsiveness of young J. curcas plants to diverse soil conditions. Soils included a sand, a sandy-loam, and a clay-loam from eastern Mexico. Growth and structural parameters were analyzed for shoots and roots, although the focus was the plasticity of the primary root system architecture (the taproot and four lateral roots). The sandy soil reduced the growth of both shoot and root systems significantly more than sandy-loam or clay-loam soils; there was particularly high plasticity in root and shoot thickness, as well as shoot length. However, the architecture of the primary root system did not vary with soil type; the departure of the primary root system from an index of perfect symmetry was 14 ± 5% (mean ± standard deviation). Although J. curcas developed more extensively in the sandy-loam and clay-loam soils than in sandy soil, it maintained a consistent root to shoot ratio and root system architecture across all types of soil. This strong genetic determination would make the species useful for soil stabilization purposes, even while being cultivated primarily for seed oil.

Effects of Manure Compost Application on Soil Microbial Community Diversity and Soil Microenvironments in a Temperate Cropland in China

PubMed Central

Zhen, Zhen; Liu, Haitao; Wang, Na; Guo, Liyue; Meng, Jie; Ding, Na; Wu, Guanglei; Jiang, Gaoming

2014-01-01

The long-term application of excessive chemical fertilizers has resulted in the degeneration of soil quality parameters such as soil microbial biomass, communities, and nutrient content, which in turn affects crop health, productivity, and soil sustainable productivity. The objective of this study was to develop a rapid and efficient solution for rehabilitating degraded cropland soils by precisely quantifying soil quality parameters through the application of manure compost and bacteria fertilizers or its combination during maize growth. We investigated dynamic impacts on soil microbial count, biomass, basal respiration, community structure diversity, and enzyme activity using six different treatments [no fertilizer (CK), N fertilizer (N), N fertilizer + bacterial fertilizer (NB), manure compost (M), manure compost + bacterial fertilizer (MB), and bacterial fertilizer (B)] in the plowed layer (0–20 cm) of potted soil during various maize growth stages in a temperate cropland of eastern China. Denaturing gradient electrophoresis (DGGE) fingerprinting analysis showed that the structure and composition of bacterial and fungi communities in the six fertilizer treatments varied at different levels. The Shannon index of bacterial and fungi communities displayed the highest value in the MB treatments and the lowest in the N treatment at the maize mature stage. Changes in soil microorganism community structure and diversity after different fertilizer treatments resulted in different microbial properties. Adding manure compost significantly increased the amount of cultivable microorganisms and microbial biomass, thus enhancing soil respiration and enzyme activities (p<0.01), whereas N treatment showed the opposite results (p<0.01). However, B and NB treatments minimally increased the amount of cultivable microorganisms and microbial biomass, with no obvious influence on community structure and soil enzymes. Our findings indicate that the application of manure compost plus bacterial fertilizers can immediately improve the microbial community structure and diversity of degraded cropland soils. PMID:25302996

[Effects of grape-replanting on soil bacterial and fungal populations].

PubMed

Li, Kun; Guo, Xiu-wu; Sun, Ying-ni; Zhang, Li-heng; Hu, Xi-xi

2009-12-01

Rhizosphere and non-rhizosphere soil samples were collected from the vineyards having been planted for 3 and 30 years, and PCR-DGGE technique was adopted to study the effects of grape-replanting on the population structure and diversity of soil bacteria and fungi. The bacterial and fungal diversities were higher in 30-year-planted vineyard than in 3-year-planted vineyard, and higher in rhizosphere soil than in non-rhizosphere soil. After 30 years replanting, the population structure of bacteria and fungi approached the same in rhizosphere soil and non-rhizosphere soil but differed from that in fallow soil; while in the 3-year-planted vineyard, the population structure in rhizosphere soil was different from that in non-rhizosphere soil and fallow soil. Comparing with that in 3-year-planted vineyard, the rhizosphere soil microbial population in 30-year-planted vineyard had a greater change. In bacterial population, Flavobacterium sp. (DQ339585) and Bacillus sp. (AY039821) decreased while Pedobacter sp. (AJ871084) increased; in fungal population, Omphalina farinolens (EF413029) appeared, Pestalotiopsis sp. (DQ657877, DQ657875, DQ657871), Phacidium lacerum (DQ470976), and Lecythophora decumbens (AF353597) decreased, while Pilidium acerinum voucher (AY48709) increased. Bacillus sp., Flavobacterium sp. , and Pestalotiopsis sp. had antagonism to pathogen, and their decrease reduced the resistance of grape against pathogen. The increase of Pilidium acerinum voucher might relate to the severe disease after grape-replanting.

Vertical variation of a black soil's properties in response to freeze-thaw cycles and its links to shift of microbial community structure.

PubMed

Han, Ziming; Deng, Mingwen; Yuan, Anqi; Wang, Jiahui; Li, Hao; Ma, Jincai

2018-06-01

Soil freeze-thaw cycles (FTCs) change soil physical, chemical, and biological properties, however information regarding their vertical variations in response to FTCs is limited. In this work, black soil (silty loam) packed soil columns were exposed to 8 FTCs, and soil properties were determined for each of vertical layer of soil columns. The results revealed that after FTCs treatment, moisture and electrical conductivity (EC) salinity tended to increase in upper soil layers. Increments of ammonium nitrogen (NH 4 + -N) and nitrate nitrogen (NO 3 - -N) in top layers (0-10cm) were greater than those in other layers, and increments of water soluble organic carbon (WSOC) and decrease of microbial biomass carbon (MBC) in middle layers (10-20cm) were greater than those in both ends. Overall, microbial community structure was mainly influenced by soil physical properties (moisture and EC) and chemical properties (pH and WSOC). For bacterial (archaeal) and fungal communities, soil physical properties, chemical properties and their interaction explained 79.73% and 82.66% of total variation, respectively. Our results provided insights into the vertical variation of soil properties caused by FTCs, and such variation had a major impact on the change of structure and composition of soil bacterial and fungal communities. Copyright © 2017 Elsevier B.V. All rights reserved.

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan

NASA Astrophysics Data System (ADS)

Pershina, E. V.; Ivanova, E. A.; Nagieva, A. G.; Zhiengaliev, A. T.; Chirak, E. L.; Andronov, E. E.; Sergaliev, N. Kh.

2016-06-01

The goal of this study was to determine the relationships between the structure of the soil microbiome and the agroecological state of soils by the example of natural undisturbed (steppe areas) and anthropogenically disturbed (pastures, croplands, fallows) areas in the territory of northwestern Kazakhstan. The highest abundance of proteobacteria was found in the anthropogenically disturbed of fallows and in undisturbed soils; in other cases, actinobacteria and representatives of the Firmicutes phylum predominated. Different kinds of anthropogenic impacts resulted in the decrease in the portions of bacteria from the Acidobacteria, Gemmatimonadetes, and Firmicutes phyla. In the disturbed soils, the portions of bacteria from the Erysipelothrix, Mycobacterium, Methylibium, Skermanella, Ralstonia, Lactococcus, Bdellovibrio, Candidatus nitrososphaera, Catellatospora, Cellulomonas, Stenotrophomonas, and Steroidobacter genera increased. Bacteria of the Erysipelothrix and Methylibium genera occurred only in the undisturbed soils. The anthropogenically disturbed and undisturbed soils differed significantly in the taxonomic structure of their microbiomes forming two separate clusters, which confirms the efficiency of using the data on the structure of soil microbiomes when assessing the agroecological status of soils.

The Role of Teak Leaves (Tectona grandis), Rhizobium, and Vesicular-Arbuscular Mycorrhizae on Improving Soil Structure and Soil Nutrition

NASA Astrophysics Data System (ADS)

Yuliani; Rahayu, Y. S.

2018-01-01

Calcium is the largest mineral in calcareous soils. High levels of calcium carbonate lead to phosphate deposition. Nutrient deficiencies in calcareous soil (mainly Phosphate and Nitrogen) resulted only certain crops with a wide range of tolerances that can grow. Meanwhile, dynamics nutrient in calcareous soils also depend on the topography and decomposition of the litter in the growing vegetation. The purpose of this study was to describe the pattern of nutrient enhancement and soil-texture structures on calcareous soils after littering the teak leaves, Rhizobium and Vesicular Arbuscular Mycorrhiza. The research parameters were the concentration of N, P, K; C/N ratio, humid acid content, and soil structure, which measured at days 30, 60, and 85 of soil decomposition process. The results showed that at days 30, the texture and structure of the soil tend to be stable (porosity 31.2, DMR 1.93, moisture content 0.36, sandy clay) while at days 85 has been very stable (porosity 49.8; Water content 0.28, sandy clay). While C and N organic, N and K concentration at days 30 showed low value (C organic 1.03, N 0.12, K 0.49, C / N ratio 9). This condition is almost unchanged at days 85. While the P value shows very high value (60.53) at days 30 although after 60 days the P content showed a decrease.

[Effects of biochar application on the abundance and structure of ammonia-oxidizer communities in coal-mining area.

PubMed

Liu, Yuan; Zhu, Ji Rong; Wu, Yu Chen; Shu, Liang Zuo

2017-10-01

As a new type of soil amendment, biochar can effectively improve soil fertility, structure and soil nitrogen transformation. We studied the effects of biochar application on soil properties, abundance and community structure of ammonia oxidizer in coal-mining area. The results showed that the biochar application significantly increased contents of soil NH4+-N, total nitrogen, available phosphorus and potassium. Compared with the control, no change in the abundance of ammonia-oxidizing archaea (AOA) was found under biochar treatment, but there was a significant increase in the abundance of ammonia-oxidizing bacteria (AOB). The analysis of T-RFLP profiles showed that biochar significantly increased the diversity indexes of AOA and AOB, and altered the community structure of both AOA and AOB. Improved soil nutrients as well as increased abundance and diversity of ammonia-oxidizing community to some extent indicated the potential of biochar application in reclamation of coal-mining area soil.

3D soil structure characterization of Biological Soil Crusts from Alpine Tarfala Valley

NASA Astrophysics Data System (ADS)

Mele, Giacomo; Gargiulo, Laura; Zucconi, Laura; D'Acqui, Luigi; Ventura, Stefano

2017-04-01

Cyanobacteria filaments, microfungal hyphae, lichen rhizinae and anchoring rhizoids of bryophytes all together contribute to induce formation of structure in the thin soil layer beneath the Biological Soil Crusts (BSCs). Quantitative assessment of the soil structure beneath the BSCs is primarily hindered by the fragile nature of the crusts. Therefore, the role of BSCs in affecting such soil physical property has been rarely addressed using direct measurements. In this work we applied non-destructive X-ray microtomography imaging on five different samples of BSCs collected in the Alpine Tarfala Valley (northern Sweden), which have already been characterized in terms of fungal biodiversity in a previous work. We obtained images of the 3D spatial organization of the soil underneath the BSCs and characterized its structure by applying procedures of image analysis allowing to determine pore size distribution, pore connectivity and aggregate size distribution. Results has then been correlated with the different fungal assemblages of the samples.

Soil mixing design methods and construction techniques for use in high organic soils.

DOT National Transportation Integrated Search

2015-06-01

Organic soils present a difficult challenge for roadway designers and construction due to the high : compressibility of the soil structure and the often associated high water table and moisture content. For : other soft or loose inorganic soils, stab...

The effects of vegetation and soil hydraulic properties on passive microwave sensing of soil moisture: Data report for the 1982 fiels experiments

NASA Technical Reports Server (NTRS)

Oneill, P.; Jackson, T.; Blanchard, B. J.; Vandenhoek, R.; Gould, W.; Wang, J.; Glazar, W.; Mcmurtrey, J., III

1983-01-01

Field experiments to (1) study the biomass and geometrical structure properties of vegetation canopies to determine their impact on microwave emission data, and (2) to verify whether time series microwave data can be related to soil hydrologic properties for use in soil type classification. Truck mounted radiometers at 1.4 GHz and 5 GHz were used to obtain microwave brightness temperatures of bare vegetated test plots under different conditions of soil wetness, plant water content and canopy structure. Observations of soil moisture, soil temperature, vegetation biomass and other soil and canopy parameters were made concurrently with the microwave measurements. The experimental design and data collection procedures for both experiments are documented and the reduced data are presented in tabular form.

Deciphering biodegradable chelant-enhanced phytoremediation through microbes and nitrogen transformation in contaminated soils.

PubMed

Fang, Linchuan; Wang, Mengke; Cai, Lin; Cang, Long

2017-06-01

Biodegradable chelant-enhanced phytoremediation offers an alternative treatment technique for metal contaminated soils, but most studies to date have addressed on phytoextraction efficiency rather than comprehensive understanding of the interactions among plant, soil microbes, and biodegradable chelants. In the present study, we investigated the impacts of biodegradable chelants, including nitrilotriacetate, S,S-ethylenediaminedisuccinic acid (EDDS), and citric acid on soil microbes, nitrogen transformation, and metal removal from contaminated soils. The EDDS addition to soil showed the strongest ability to promote the nitrogen cycling in soil, ryegrass tissue, and microbial metabolism in comparison with other chelants. Both bacterial community-level physiological profiles and soil mass specific heat rates demonstrated that soil microbial activity was inhibited after the EDDS application (between day 2 and 10), but this effect completely vanished on day 30, indicating the revitalization of microbial activity and community structure in the soil system. The results of quantitative real-time PCR revealed that the EDDS application stimulated denitrification in soil by increasing nitrite reductase genes, especially nirS. These new findings demonstrated that the nitrogen release capacity of biodegradable chelants plays an important role in accelerating nitrogen transformation, enhancing soil microbial structure and activity, and improving phytoextraction efficiency in contaminated soil.

The Microbiome Structure of Oklahoma Cropland and Prairie Soils and its Response to Seasonal Forcing and Management Practices

NASA Astrophysics Data System (ADS)

Cornell, C. R.; Peterson, B.; Zhou, J.; Xiao, X.; Wawrik, B.

2017-12-01

Greenhouse gases (GHG) emissions from soils are primarily the consequence of microbial processes. Agricultural management of soils is known to affect the structure of microbial communities, and it is likely that dominant GHG emitting microbial activities are impacted via requisite practices. To gain better insight into the impact of seasonal forcing and management practices on the microbiome structure in Oklahoma agricultural soils, a seasonal study was conducted. Over a year period, samples were collected bi-weekly during wet months, and monthly during dry months from two grassland and two managed agricultural sites in El Reno, Oklahoma. Microbial community structure was determined in quadruplicate for each site and time point via 16S rRNA gene sequencing. Measures of soil water content, subsoil nitrate, ammonium, organic matter, total nitrogen, and biomass were also taken for each time point. Data analysis revealed several important trends, indicating greater microbial diversity in native grassland and distinct microbial community changes in response to management practices. The native grassland soils also contained greater microbial biomass than managed soils and both varied in response to rainfall events. Native grassland soils harbor more diverse microbial communities, with the diversity and biomass decreasing along a gradient of agricultural management intensity. These data indicate that microbial community structure in El Reno soils occurs along a continuum in which native grasslands and highly managed agricultural soils (tilling and manure application) form end members. Integration with measurements from eddy flux towers into modelling efforts using the DeNitrification-DeComposition (DNDC) model is currently being explored to improve predictions of GHG emissions from grassland soils.

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

Bond-Lamberty, Benjamin; Bolton, Harvey; Fansler, Sarah J.

The effects of climate change on soil organic matter—its structure, microbial community, carbon storage, and respiration response—remain uncertain and widely debated. In addition, the effects of climate changes on ecosystem structure and function are often modulated or delayed, meaning that short-term experiments are not sufficient to characterize ecosystem responses. This study capitalized on a long-term reciprocal soil transplant experiment to examine the response of dryland soils to climate change. The two transplant sites were separated by 500 m of elevation on the same mountain slope in eastern Washington state, USA, and had similar plant species and soil types. We resampledmore » the original 1994 soil transplants and controls, measuring CO 2 production, temperature response, enzyme activity, and bacterial community structure after 17 years. Over a laboratory incubation of 100 days, reciprocally transplanted soils respired roughly equal cumulative amounts of carbon as non-transplanted controls from the same site. Soils transplanted from the hot, dry, lower site to the cooler and wetter (difference of -5 °C monthly maximum air temperature, +50 mm yr -1precipitation) upper site exhibited almost no respiratory response to temperature (Q10 of 1.1), but soils originally from the upper, cooler site had generally higher respiration rates. The bacterial community structure of transplants did not differ significantly from that of untransplanted controls, however. Slight differences in local climate between the upper and lower Rattlesnake locations, simulated with environmental control chambers during the incubation, thus prompted significant differences in microbial activity, with no observed change to bacterial structure. Lastly, these results support the idea that environmental shifts can influence soil C through metabolic changes, and suggest that microbial populations responsible for soil heterotrophic respiration may be constrained in surprising ways, even as shorter- and longer-term soil microbial dynamics may be significantly different under changing climate.« less

pH dependence and unsuitability of fluorescein dye as a tracer for pesticide mobility studies in acid soil

Treesearch

Chris Peterson

2009-01-01

The mobility of fluorescein and bromide used as tracers in packed soil columns was investigated.Five different soils were used in two application methods: soil surface application and soil incorporation, both of which simulate accepted methods of soil application of termiticides to prevent structural infestation. The...

Response of soil microbial and invertebrate communities to tracked vehicle disturbance in tallgrass prairie

Treesearch

P.S. Althoff; T.C. Todd; S.J. Thien; M.A. Callaham

2009-01-01

Soil biota drive fundamental ecosystem processes such as decomposition, nutrient cycling, and maintenance of soil structure. They are especially active in grassland ecosystems such as the tallgrass by heterotrophic soil organisms. Because both soil microbes and soil fauna display perturbation responses that integrate the physical, chemical, and biological changes to...

Response of soil microbial activities and microbial community structure to vanadium stress.

PubMed

Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

2017-08-01

High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.

Prototype reinforced soil embankment for reconstruction of US route 62 slope failure in Chickasha, OK.

DOT National Transportation Integrated Search

2015-01-01

One of the main concerns in internal stability of reinforced soil structures constructed with fine-grained or : marginal quality soils is the change in shear strength of the soil-reinforcement interface when the soil gravimetric water : content (GWC)...

Prototype reinforced soil embankment for reconstruction of US 62 slope failure in Chickasha, OK.

DOT National Transportation Integrated Search

2013-05-01

One of the main concerns in internal stability of reinforced soil structures constructed with fine-grained or marginal quality soils is the change in shear strength of the soil-reinforcement interface when the soil gravimetric water content (GWC) inc...

Effects of biochar blends on microbial community composition in two coastal plain soils

EPA Science Inventory

The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

Plant diversity and root traits benefit physical properties key to soil function in grasslands.

PubMed

Gould, Iain J; Quinton, John N; Weigelt, Alexandra; De Deyn, Gerlinde B; Bardgett, Richard D

2016-09-01

Plant diversity loss impairs ecosystem functioning, including important effects on soil. Most studies that have explored plant diversity effects belowground, however, have largely focused on biological processes. As such, our understanding of how plant diversity impacts the soil physical environment remains limited, despite the fundamental role soil physical structure plays in ensuring soil function and ecosystem service provision. Here, in both a glasshouse and a long-term field study, we show that high plant diversity in grassland systems increases soil aggregate stability, a vital structural property of soil, and that root traits play a major role in determining diversity effects. We also reveal that the presence of particular plant species within mixed communities affects an even wider range of soil physical processes, including hydrology and soil strength regimes. Our results indicate that alongside well-documented effects on ecosystem functioning, plant diversity and root traits also benefit essential soil physical properties. © 2016 The Authors Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Copper pollution decreases the resistance of soil microbial community to subsequent dry-rewetting disturbance.

PubMed

Li, Jing; Wang, Jun-Tao; Hu, Hang-Wei; Ma, Yi-Bing; Zhang, Li-Mei; He, Ji-Zheng

2016-01-01

Dry-rewetting (DW) disturbance frequently occurs in soils due to rainfall and irrigation, and the frequency of DW cycles might exert significant influences on soil microbial communities and their mediated functions. However, how microorganisms respond to DW alternations in soils with a history of heavy metal pollution remains largely unknown. Here, soil laboratory microcosms were constructed to explore the impacts of ten DW cycles on the soil microbial communities in two contrasting soils (fluvo-aquic soil and red soil) under three copper concentrations (zero, medium and high). Results showed that the fluctuations of substrate induced respiration (SIR) decreased with repeated cycles of DW alternation. Furthermore, the resistance values of substrate induced respiration (RS-SIR) were highest in non-copper-stressed (zero) soils. Structural equation model (SEM) analysis ascertained that the shifts of bacterial communities determined the changes of RS-SIR in both soils. The rate of bacterial community variance was significantly lower in non-copper-stressed soil compared to the other two copper-stressed (medium and high) soils, which might lead to the higher RS-SIR in the fluvo-aquic soil. As for the red soil, the substantial increase of the dominant group WPS-2 after DW disturbance might result in the low RS-SIR in the high copper-stressed soil. Moreover, in both soils, the bacterial diversity was highest in non-copper-stressed soils. Our results revealed that initial copper stress could decrease the resistance of soil microbial community structure and function to subsequent DW disturbance. Copyright © 2015. Published by Elsevier B.V.

Rhizosphere biophysics and root water uptake

NASA Astrophysics Data System (ADS)

Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

2016-04-01

The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its low unsaturated conductivity, failed to compensate root water uptake. We conclude that root hairs are functional to increase the contact area between the roots and the soil structures and mucilage maintains wet the soil region between root hairs. These observations demonstrate the importance of the biophysical processes in the rhizosphere in modulating root water uptake.

[Distribution characteristics of soil nematodes in reclaimed land of copper-mine-tailings in different plant associations].

PubMed

Zhu, Yong-heng; Li, Ke-zhong; Zhang, Heng; Han, Fei; Zhou, Ju-hua; Gao, Ting-ting

2015-02-01

A survey was carried out to investigate soil nematode communities in the plant associations of gramineae (Arthraxon lanceolatus, AL; Imperata cylindrica, IC) and leguminosae (Glycine soja, GS) in reclaimed land of copper-mine-tailings and in the plant associations of gramineae (Digitaria chrysoblephara, DC-CK) of peripheral control in Fenghuang Mountain, Tongling City. A total of 1277 nematodes were extracted and sorted into 51 genera. The average individual density of the nematodes was 590 individuals · 100 g(-1) dry soil. In order to analyze the distribution character- istics of soil nematode communities in reclaimed land of copper-mine-tailings, Shannon community diversity index and soil food web structure indices were applied in the research. The results showed that the total number of nematode genus and the Shannon community diversity index of soil nematode in the three plant associations of AL, IC and GS were less than that in the plant associations of DC-CK. Compared with the ecological indices of soil nematode communities among the different plant associations in reclaimed land of copper-mine-tailings and peripheral natural habitat, we found that the structure of soil food web in the plant associations of GS was more mature, with bacterial decomposition being dominant in the soil organic matter decomposition, and that the soil ecosystem in the plant associations of GS was not stable with low interference. This indicated that the soil food web in the plant associations of leguminosae had a greater development potential to improve the ecological stability of the reclaimed land of copper-mine-tailings. On the other hand, the structure of soil food web in the plant associations of AL and IC were relatively stable in a structured state with fungal decomposition being dominant in the decomposition of soil organic matter. This indicated that the soil food web in the plant associations of gramineae was at a poor development level.

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

Land-use and land-management change: relationships with earthworm and fungi communities and soil structural properties.

PubMed

Spurgeon, David J; Keith, Aidan M; Schmidt, Olaf; Lammertsma, Dennis R; Faber, Jack H

2013-12-01

Change in land use and management can impact massively on soil ecosystems. Ecosystem engineers and other functional biodiversity in soils can be influenced directly by such change and this in turn can affect key soil functions. Here, we employ meta-analysis to provide a quantitative assessment of the effects of changes in land use and land management across a range of successional/extensification transitions (conventional arable → no or reduced tillage → grassland → wooded land) on community metrics for two functionally important soil taxa, earthworms and fungi. An analysis of the relationships between community change and soil structural properties was also included. Meta-analysis highlighted a consistent trend of increased earthworm and fungal community abundances and complexity following transitions to lower intensity and later successional land uses. The greatest changes were seen for early stage transitions, such as introduction of reduced tillage regimes and conversion to grassland from arable land. Not all changes, however, result in positive effects on the assessed community metrics. For example, whether woodland conversion positively or negatively affects community size and complexity depends on woodland type and, potentially, the changes in soil properties, such as pH, that may occur during conversion. Alterations in soil communities tended to facilitate subsequent changes in soil structure and hydrology. For example, increasing earthworm abundances and functional group composition were shown to be positively correlated with water infiltration rate (dependent on tillage regime and habitat characteristics); while positive changes in fungal biomass measures were positively associated with soil microaggregate stability. These findings raise the potential to manage landscapes to increase ecosystem service provision from soil biota in relation to regulation of soil structure and water flow.

Slow reaction of soil structure to conservation agriculture practices in Veneto silty soils (North-Easter Italy)

NASA Astrophysics Data System (ADS)

Piccoli, Ilaria; Camarotto, Carlo; Lazzaro, Barbara; Furlan, Lorenzo; Morari, Francesco

2017-04-01

Soil structure plays a pivotal role in soil functioning and can inform of the degradation of the soil ecosystem. Intensive and repeated tillage operations have been known to negatively affect the soil structure characteristics while conservation agriculture (CA) practices were demonstrated to improve soil structure and related ecosystem services. The aim of this study is to evaluate the effect of conservation agriculture practices on total porosity, pore size distribution, pore architecture and morphology on silty soils of Veneto low-lying plain (North-Eastern Italy). Experimental design was established in 2010 on 4 farms in North-Eastern Italy to compare conventional intensive tillage system "IT" versus conservation agriculture "CA" (no-tillage, cover-crop and residue retention). 96 samples were collected in 2015 at four depths down to 50 cm depth, and investigated for porosity from micro to macro by coupling mercury intrusion porosimetry (MIP) (0.0074-100 µm) and x-ray computed microtomography (µCT) (>26 µm). Pore morphology and architecture were studied from 3D images analysis and MIP pore size curve. Ultramicroporosity class (0.1-5 μm) positively responded to CA after 5-yr of practices adoption while no significant effects were observed in the x-ray µCT domain (> 26 µm). Silty soils of Veneto plain showed a slow reaction to conservation agriculture because of the low soil organic carbon content and poor aggregate stability. Nevertheless the positive influence of CA on ultramicroporosity, which is strictly linked to soil organic carbon (SOC) stabilization, indicated that a virtuous cycle was initiated between SOC and porosity, hopefully leading to well-developed macropore systems and, in turn, enhanced soil functions and ecosystem services.

Similar soil microbial community structure across different environments after long-term succession: evidence from volcanoes of different ages.

PubMed

Xu, Shangqi; Zhang, Jianfeng; Luo, Shasha; Zhou, Xue; Shi, Shaohua; Tian, Chunjie

2018-06-08

Soil microbes play critical roles in global biogeochemical cycles, but their succession patterns across long temporal scales have rarely been studied. In this study, soil samples were collected from three volcanoes in Wudalianchi, northeastern China: Laoheishan (LH, approximately 240 years old), Dongjiaodebushan (DJ, 0.45-0.6 million years old), and Nangelaqiushan (NG, 0.8-1.3 million years old). For each volcano, both southern (S) and northern (N) slope aspects were sampled. Soil microbial communities were analyzed using phospholipid fatty acid analysis (PLFA). The results showed that soil properties and microbial biomass changed perceptibly among different volcanoes and different slope aspects. Almost all of the detected soil nutrient contents of LH were lowest, and total microbial biomass of LH was 40 and 36% lower than those of NG and DJ, respectively. LH was significantly different from NG and DJ in soil microbial community structure with a higher relative abundance of fungi and a lower relative abundance of actinomycetes and bacteria. However, for the two ancient volcanoes (NG and DJ), soil microbial community structures were highly similar among different ages and different slope aspects. No difference was detected in any of the measured microbial indices, including richness, evenness, Shannon's diversity, Simpson's diversity and the relative abundance of different microbial groups. The results indicated that while soil microbial biomass may change across different soil environments after long-term succession, soil microbial community structure can remain relatively stable. The results further indicated that soil microbes may show different successional patterns in different stages of succession. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Using semi-variogram analysis for providing spatially distributed information on soil surface condition for land surface modeling

NASA Astrophysics Data System (ADS)

Croft, Holly; Anderson, Karen; Kuhn, Nikolaus J.

2010-05-01

The ability to quantitatively and spatially assess soil surface roughness is important in geomorphology and land degradation studies. Soils can experience rapid structural degradation in response to land cover changes, resulting in increased susceptibility to erosion and a loss of Soil Organic Matter (SOM). Changes in soil surface condition can also alter sediment detachment, transport and deposition processes, infiltration rates and surface runoff characteristics. Deriving spatially distributed quantitative information on soil surface condition for inclusion in hydrological and soil erosion models is therefore paramount. However, due to the time and resources involved in using traditional field sampling techniques, there is a lack of spatially distributed information on soil surface condition. Laser techniques can provide data for a rapid three dimensional representation of the soil surface at a fine spatial resolution. This provides the ability to capture changes at the soil surface associated with aggregate breakdown, flow routing, erosion and sediment re-distribution. Semi-variogram analysis of the laser data can be used to represent spatial dependence within the dataset; providing information about the spatial character of soil surface structure. This experiment details the ability of semi-variogram analysis to spatially describe changes in soil surface condition. Soil for three soil types (silt, silt loam and silty clay) was sieved to produce aggregates between 1 mm and 16 mm in size and placed evenly in sample trays (25 x 20 x 2 cm). Soil samples for each soil type were exposed to five different durations of artificial rainfall, to produce progressively structurally degraded soil states. A calibrated laser profiling instrument was used to measure surface roughness over a central 10 x 10 cm plot of each soil state, at 2 mm sample spacing. The laser data were analysed within a geostatistical framework, where semi-variogram analysis quantitatively represented the change in soil surface structure during crusting. The laser data were also used to create digital surface models (DSM) of the soil states for visual comparison. This research has shown that aggregate breakdown and soil crusting can be shown quantitatively by a decrease in sill variance (silt soil: 11.67 (control) to 1.08 (after 90 mins rainfall)). Features present within semi-variograms were spatially linked to features at the soil surface, such as soil cracks, tillage lines and areas of deposition. Directional semi-variograms were used to provide a spatially orientated component, where the directional sill variance associated with a soil crack was shown to increase from 7.95 to 19.33. Periodicity within semi-variogram was also shown to quantify the spatial scale of soil cracking networks and potentially surface flowpaths; an average distance between soil cracks of 37 mm closely corresponded to the distance of 38 mm shown in the semi-variogram. The results provide a strong basis for the future retrieval of spatio-temporal variations in soil surface condition. Furthermore, the presence of process-based information on hydrological pathways within semi-variograms may work towards an inclusion of geostatisically-derived information in land surface models and the understanding of complex surface processes at different spatial scales.

Impact of land-use and long-term (>150 years) charcoal accumulation on microbial activity, biomass and community structure in temperate soils (Belgium).

NASA Astrophysics Data System (ADS)

Hardy, Brieuc; Cornelis, Jean-Thomas; Dufey, Joseph E.

2015-04-01

In the last decade, biochar has been increasingly investigated as a soil amendment for long-term soil carbon sequestration while improving soil fertility. On the short term, biochar application to soil generally increases soil respiration as well as microbial biomass and activity and affects significantly the microbial community structure. However, such effects are relatively short-term and tend to vanish over time. In our study, we investigated the long-term impact of charcoal accumulation and land-use on soil biota in temperate haplic Luvisols developed in the loess belt of Wallonia (Belgium). Charcoal-enriched soils were collected in the topsoil of pre-industrial (>150 years old) charcoal kilns in forest (4 sites) and cropland (5 sites). The topsoil of the adjacent charcoal-unaffected soils was sampled in a comparable way. Soils were characterized (pH, total, organic and inorganic C, total N, exchangeable Ca, Mg, K, Na, cation exchange capacity and available P) and natural soil organic matter (SOM) and black carbon (BC) contents were determined by differential scanning calorimetry. After rewetting at pF 2.5, soils were incubated during 140 days at 20 °C. At 70 days of incubation, 10 g of each soil were freeze dried in order to measure total microbial biomass and community structure by PLFA analysis. The PLFA dataset was analyzed by principal component analysis (PCA) while soil parameters were used as supplementary variables. For both agricultural and forest soils, the respiration rate is highly related to the total microbial biomass (R²=0.90). Both soil respiration and microbial biomass greatly depend on the SOM content, which indicates that the BC pool is relatively inert microbiologically. Land-use explains most of the variance in the PLFA dataset, largely governing the first principal component of the ACP. In forest soils, we observe a larger proportion of gram + bacteria, actinomycetes and an increased bacteria:fungi ratio compared to cropland, where gram - bacteria, arbuscular mycorrhizal fungi and 18:2 and 18:3 fungi are more present. BC is quite well represented (R=-0.765) by the third principal component of the PCA, representing 12.2 % of the total variance. It has limited impact on the community structure, particularly in cropland. However, in forest BC is negatively correlated (R=-0.785) with 18:1 fungi. The more pronounced effect of BC on community structure under forest could result from modified trophic conditions at kiln site (e.g. higher pH, lower available P content, …) while cultivation practices attenuated such differences over time in cropland. In conclusion, our survey tends to confirm that the influence of BC on the soil microbiological parameters is governed by indirect effects on trophic conditions. On the other hand, land-use affects dramatically soil microbial community structure.

Farm-scale variation of soil quality indices and association with edaphic properties

USDA-ARS?s Scientific Manuscript database

Soil organisms are indicators of dynamic soil quality because their community structure and population density are sensitive to management changes. However, edaphic properties can also affect soil organisms and high spatial variability can confound their utility for soil evaluation. In the present...

Fall cover crops boost soil arbuscular mycorrhizal fungi which can lead to reduced inputs

USDA-ARS?s Scientific Manuscript database

Fall cover crops provide multiple benefits to producers. These benefits include pathogen and pest protection, drought protection, weed control, reduced soil erosion, nutrient acquisition and retention, increased soil organic matter, and conservation of soil water by improvement of soil structure th...

Development and assessment of transparent soil and particle image velocimetry in dynamic soil-structure interaction

DOT National Transportation Integrated Search

2007-02-01

This research combines Particle Image Velocimetry (PIV) and transparent soil to investigate the dynamic rigid block and soil interaction. In order to get a low viscosity pore fluid for the transparent soil, 12 different types of chemical solvents wer...

Assessing the performance of structure-from-motion photogrammetry and terrestrial lidar 1 at reconstructing soil surface microtopography of naturally vegetated plots

USDA-ARS?s Scientific Manuscript database

Soil microtopography or soil roughness is a property of critical importance in many earth surface processes but is often difficult to measure. Advances in computer vision technologies have made image-based 3D depiction of the soil surface or Structure-from-Motion (SfM) available to many scientists ...

The soil carbon/nitrogen ratio and moisture affect microbial community structures in alkaline permafrost-affected soils with different vegetation types on the Tibetan plateau.

PubMed

Zhang, Xinfang; Xu, Shijian; Li, Changming; Zhao, Lin; Feng, Huyuan; Yue, Guangyang; Ren, Zhengwei; Cheng, Guogdong

2014-01-01

In the Tibetan permafrost region, vegetation types and soil properties have been affected by permafrost degradation, but little is known about the corresponding patterns of their soil microbial communities. Thus, we analyzed the effects of vegetation types and their covariant soil properties on bacterial and fungal community structure and membership and bacterial community-level physiological patterns. Pyrosequencing and Biolog EcoPlates were used to analyze 19 permafrost-affected soil samples from four principal vegetation types: swamp meadow (SM), meadow (M), steppe (S) and desert steppe (DS). Proteobacteria, Acidobacteria, Bacteroidetes and Actinobacteria dominated bacterial communities and the main fungal phyla were Ascomycota, Basidiomycota and Mucoromycotina. The ratios of Proteobacteria/Acidobacteria decreased in the order: SM>M>S>DS, whereas the Ascomycota/Basidiomycota ratios increased. The distributions of carbon and nitrogen cycling bacterial genera detected were related to soil properties. The bacterial communities in SM/M soils degraded amines/amino acids very rapidly, while polymers were degraded rapidly by S/DS communities. UniFrac analysis of bacterial communities detected differences among vegetation types. The fungal UniFrac community patterns of SM differed from the others. Redundancy analysis showed that the carbon/nitrogen ratio had the main effect on bacteria community structures and their diversity in alkaline soil, whereas soil moisture was mainly responsible for structuring fungal communities. Thus, microbial communities and their functioning are probably affected by soil environmental change in response to permafrost degradation. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Environmental factors shaping the community structure of ammonia-oxidizing bacteria and archaea in sugarcane field soil.

PubMed

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers' fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers' sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 10(5)-9.2 × 10(6) and 1.7 × 10(6)-5.3 × 10(7) gene copies g dry soil(-1), respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields.

Freeze-Thaw Cycles Effects on Soil Compaction in a Clay Loam

NASA Astrophysics Data System (ADS)

Jabro, J.; Evans, R.; Iversen, W.

2012-04-01

Inappropriate soil management practices and heavier farm machinery and equipment have led to an increase in soil compaction in the last two decades prompting increased global concern regarding the impact of soil compaction on crop production and soil quality in modern mechanized agriculture. A 3-yr comprehensive study was established to evaluate the dynamic of freeze-thaw cycles on soil compaction in a clay loam soil. Plots of frozen soils were compared with plots where soils were prevented from freezing with electrically heated blankets commonly used on concrete. Results showed that frequent freeze-thaw cycles over the winter alleviated a majority of soil compaction at the 0 - 20 cm depth. Soil penetration resistance in compacted soils was reduced by 73 and 68% over the winter at the 0 - 10 and 10 - 20 cm depths, respectively, due to dynamic effects of freeze-thaw cycles on soil structure and particles configuration. In unfrozen compacted soils, the penetration resistance was also reduced by 50 and 60% over winter at the 0 - 10 and 10 - 20 cm depths, respectively, due to the biology of soil, microbial activity, and disruptive effects of shrink-swell cycles. These results have demonstrated of how repeated freeze-thaw cycles can alleviate soil compaction, alter soil physical quality and create optimal soil conditions required for profitable growth of agricultural crops. The results from this study will save growers considerable time, money and energy currently required to alleviate soil compaction using other methods such as sub-soiling and deep tillage. We believe that Mother Nature provides ways to reverse soil compaction and improve soil structure and aggregation through the dynamic of freeze-thaw cycles that soils in Montana and other parts of the country go through each year. We concluded that the Mother Nature is the most effective and cheapest way to alleviate soil compaction.

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.

Designing sustainable soils in Earth's critical zone

NASA Astrophysics Data System (ADS)

Banwart, Steven Allan; de Souza, Danielle Maia; Menon, Manoj; Nikolaidis, Nikolaos; Panagos, Panos; Vala Ragnardsdottir, Kristin; Rousseva, Svelta; van Gaans, Pauline

2014-05-01

The demographic drivers of increasing human population and wealth are creating tremendous environmental pressures from growing intensity of land use, resulting in soil and land degradation worldwide. Environmental services are provided through multiple soil functions that include biomass production, water storage and transmission, nutrient transformations, contaminant attenuation, carbon and nitrogen storage, providing habitat and maintaining the genetic diversity of the land environment. One of the greatest challenges of the 21st century is to identify key risks to soil, and to design mitigation strategies to manage these risks and to enhance soil functions that can last into the future. The scientific study of Earth's Critical Zone (CZ), the thin surface layer that extends vertically from the top of the tree canopy to the bottom of aquifers, provides an essential integrating scientific framework to study, protect and enhance soil functions. The research hypothesis is that soil structure, the geometric architecture of solids, pores and biomass, is a critical indicator and essential factor of productive soil functions. The experimental design selects a network of Critical Zone Observatories (CZOs) as advanced field research sites along a gradient of land use intensity in order to quantify soil structure and soil processes that dictate the flows and transformations of material and energy as soil functions. The CZOs focus multidisciplinary expertise on soil processes, field observation and data interpretation, management science and ecological economics. Computational simulation of biophysical processes provides a quantitative method of integration for the range of theory and observations that are required to quantify the linkages between changes in soil structure and soil functions. Key results demonstrate that changes in soil structure can be quantified through the inputs of organic carbon and nitrogen from plant productivity and microbial activity, coupled with particle aggregation dynamics and organic matter mineralization. Simulation results show that soil structure is highly dynamic and is sensitive to organic matter production and minearlisation rates as influenced by vegetation, tillage and organic carbon amendments. These results point to a step-change in the capability to design soil management and land use through computational simulation. This approach of "sustainability by design" describes the mechanistic process linkages that exist between the above-ground inputs to the CZ and the internal processes that produce soil functions. This approach provides a rational, scientific approach to selecting points of intervention with the CZ in order to design methods to mitigate soil threats and to enhance and sustain vital soil functions. Furthermore, this approach provides a successful pilot study to the use of international networks of CZOs as a planetary-scale laboratory to test the response of CZ process rates along gradients of global environmental change - and to test adaptation strategies to manage the risks arising from the CZ impacts. Acknowledgements. The authors acknowledge the substantial contributions of the entire team of investigators and funding of the SoilTrEC project (EC FP7, agreement no. 244118; www.soiltrec.eu).

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2014 CFR

2014-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2010 CFR

2010-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2012 CFR

2012-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2013 CFR

2013-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

40 CFR 267.191 - What are the required design and construction standards for new tank systems or components?

Code of Federal Regulations, 2011 CFR

2011-07-01

... of the tank system will be in contact with the soil or with water, a determination by a corrosion expert of: (1) Factors affecting the potential for corrosion, such as: (i) Soil moisture content. (ii) Soil pH. (iii) Soil sulfides level. (iv) Soil resistivity. (v) Structure to soil potential. (vi...

Surface soil root response to season of repeated fire in a young longleaf pine plantation

Treesearch

Mary Anne Sword Sayer; James D. Haywood

2012-01-01

The potential exists for interaction between naturally high soil bulk density and low soil water content to create root-growth limiting soil strengths. This problem is commonly remedied by soil structural attributes, old root channels and other perturbations, and periods of wetness during which soil strength is favorable for root elongation. Because the application and...

[Priming effect of biochar on the minerialization of native soil organic carbon and the mechanisms: A review.

PubMed

Chen, Ying; Liu, Yu Xue; Chen, Chong Jun; Lyu, Hao Hao; Wa, Yu Ying; He, Li Li; Yang, Sheng Mao

2018-01-01

In recent years, studies on carbon sequestration of biochar in soil has been in spotlight owing to the specific characteristics of biochar such as strong carbon stability and well developed pore structure. However, whether biochar will ultimately increase soil carbon storage or promote soil carbon emissions when applied into the soil? This question remains controversial in current academic circles. Further research is required on priming effect of biochar on mineralization of native soil organic carbon and its mechanisms. Based on the analysis of biochar characteristics, such as its carbon composition and stability, pore structure and surface morphology, research progress on the priming effect of biochar on the decomposition of native soil organic carbon was reviewed in this paper. Furthermore, possible mechanisms of both positive and negative priming effect, that is promoting and suppressing the mineralization, were put forward. Positive priming effect is mainly due to the promotion of soil microbial activity caused by biochar, the preferential mineralization of easily decomposed components in biochar, and the co-metabolism of soil microbes. While negative priming effect is mainly based on the encapsulation and adsorption protection of soil organic matter due to the internal pore structure and the external surface of biochar. Other potential reasons for negative priming effect can be the stabilization resulted from the formation of organic-inorganic complex promoted by biochar in the soil, and the inhibition of activity of soil microbes and its enzymes by biochar. Finally, future research directions were proposed in order to provide theoretical basis for the application of biochar in soil carbon sequestration.

Principles of control automation of soil compacting machine operating mechanism

NASA Astrophysics Data System (ADS)

Anatoly Fedorovich, Tikhonov; Drozdov, Anatoly

2018-03-01

The relevance of the qualitative compaction of soil bases in the erection of embankment and foundations in building and structure construction is given.The quality of the compactible gravel and sandy soils provides the bearing capability and, accordingly, the strength and durability of constructed buildings.It has been established that the compaction quality depends on many external actions, such as surface roughness and soil moisture; granulometry, chemical composition and degree of elasticity of originalfilled soil for compaction.The analysis of technological processes of soil bases compaction of foreign and domestic information sources showed that the solution of such important problem as a continuous monitoring of soil compaction actual degree in the process of machine operation carry out only with the use of modern means of automation. An effective vibrodynamic method of gravel and sand material sealing for the building structure foundations for various applications was justified and suggested.The method of continuous monitoring the soil compaction by measurement of the amplitudes and frequencies of harmonic oscillations on the compactible surface was determined, which allowed to determine the basic elements of facilities of soil compacting machine monitoring system of operating, etc. mechanisms: an accelerometer, a bandpass filter, a vibro-harmonics, an on-board microcontroller. Adjustable parameters have been established to improve the soil compaction degree and the soil compacting machine performance, and the adjustable parameter dependences on the overall indexhave been experimentally determined, which is the soil compaction degree.A structural scheme of automatic control of the soil compacting machine control mechanism and theoperation algorithm has been developed.

Native soil organic matter conditions the response of microbial communities to organic inputs with different stability

NASA Astrophysics Data System (ADS)

Yanardaǧ, Ibrahim H.; Zornoza, Raúl; Bastida, Felipe; Büyükkiliç-Yanardaǧ, Asuman; Acosta, Jose A.; García, Carlos; Faz, Ángel; Mermut, Ahmet R.

2017-04-01

The response of soil microbial communities from soils with different soil organic matter (SOM) content to organic inputs with different stability is still poorly understood. Thus, an incubation experiment was designed to study how the addition of pig slurry (PS), its manure (M) and its biochar (BC) affect soil microbial community and activity in three soils differing in SOM content (Regosol, Luvisol and Kastanozem). The evolution of different C and N fractions, microbial biomass C and N, enzyme activities and microbial community structure by the use of phospholipid fatty acid (PLFA) analysis was assessed for 60 days. Results showed that the different amendments had different effect on microbial properties depending on the soil type. The addition of M caused the highest increase in all microbial properties in the three soils, followed by PS. These changes were more intense in the soil with the lowest SOM (Regosol). The addition of M and PS caused changes in the microbial community structure in all soils, which were more related to the presence of available sources of N than to the labile fractions of C. The addition of BC was followed by increases in the proportions of fungi and Gram positive bacteria in the Regosol, while enhanced the proportion of actinobacteria in all soil types, related to increments in pH and soil C recalcitrance. Thus, native SOM determined the response of microbial communities to external inputs with different stability, soils with low SOM being more prone to increase microbial biomass and activity and change microbial community structure.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem.

PubMed

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-03-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models.

Differential controls on soil carbon density and mineralization among contrasting forest types in a temperate forest ecosystem

PubMed Central

You, Ye-Ming; Wang, Juan; Sun, Xiao-Lu; Tang, Zuo-Xin; Zhou, Zhi-Yong; Sun, Osbert Jianxin

2016-01-01

Understanding the controls on soil carbon dynamics is crucial for modeling responses of ecosystem carbon balance to global change, yet few studies provide explicit knowledge on the direct and indirect effects of forest stands on soil carbon via microbial processes. We investigated tree species, soil, and site factors in relation to soil carbon density and mineralization in a temperate forest of central China. We found that soil microbial biomass and community structure, extracellular enzyme activities, and most of the site factors studied varied significantly across contrasting forest types, and that the associations between activities of soil extracellular enzymes and microbial community structure appeared to be weak and inconsistent across forest types, implicating complex mechanisms in the microbial regulation of soil carbon metabolism in relation to tree species. Overall, variations in soil carbon density and mineralization are predominantly accounted for by shared effects of tree species, soil, microclimate, and microbial traits rather than the individual effects of the four categories of factors. Our findings point to differential controls on soil carbon density and mineralization among contrasting forest types and highlight the challenge to incorporate microbial processes for constraining soil carbon dynamics in global carbon cycle models. PMID:26925871

Soil microbial community response to land use change in an agricultural landscape of western Kenya.

PubMed

Bossio, D A; Girvan, M S; Verchot, L; Bullimore, J; Borelli, T; Albrecht, A; Scow, K M; Ball, A S; Pretty, J N; Osborn, A M

2005-01-01

Tropical agroecosystems are subject to degradation processes such as losses in soil carbon, nutrient depletion, and reduced water holding capacity that occur rapidly resulting in a reduction in soil fertility that can be difficult to reverse. In this research, a polyphasic methodology has been used to investigate changes in microbial community structure and function in a series of tropical soils in western Kenya. These soils have different land usage with both wooded and agricultural soils at Kakamega and Ochinga, whereas at Ochinga, Leuro, Teso, and Ugunja a replicated field experiment compared traditional continuous maize cropping against an improved N-fixing fallow system. For all sites, principal component analysis of 16S rRNA gene denaturing gradient gel electrophoresis (DGGE) profiles revealed that soil type was the key determinant of total bacterial community structure, with secondary variation found between wooded and agricultural soils. Similarly, phospholipid fatty acid (PLFA) analysis also separated wooded from agricultural soils, primarily on the basis of higher abundance of monounsaturated fatty acids, anteiso- and iso-branched fatty acids, and methyl-branched fatty acids in the wooded soils. At Kakamega and Ochinga wooded soils had between five 5 and 10-fold higher levels of soil carbon and microbial biomass carbon than agricultural soils from the same location, whereas total enzyme activities were also lower in the agricultural sites. Soils with woody vegetation had a lower percentage of phosphatase activity and higher cellulase and chitinase activities than the agricultural soils. BIOLOG analysis showed woodland soils to have the greatest substrate diversity. Throughout the study the two functional indicators (enzyme activity and BIOLOG), however, showed lower specificity with respect to soil type and land usage than did the compositional indicators (DGGE and PLFA). In the field experiment comparing two types of maize cropping, both the maize yields and total microbial biomass were found to increase with the fallow system. Moreover, 16S rRNA gene and PLFA analyses revealed shifts in the total microbial community in response to the different management regimes, indicating that deliberate management of soils can have considerable impact on microbial community structure and function in tropical soils.

Effects of Spatial Variability of Soil Properties on the Triggering of Rainfall-Induced Shallow Landslides

NASA Astrophysics Data System (ADS)

Fan, Linfeng; Lehmann, Peter; Or, Dani

2015-04-01

Naturally-occurring spatial variations in soil properties (e.g., soil depth, moisture, and texture) affect key hydrological processes and potentially the mechanical response of soil to hydromechanical loading (relative to the commonly-assumed uniform soil mantle). We quantified the effects of soil spatial variability on the triggering of rainfall-induced shallow landslides at the hillslope- and catchment-scales, using a physically-based landslide triggering model that considers interacting soil columns with mechanical strength thresholds (represented by the Fiber Bundle Model). The spatial variations in soil properties are represented as Gaussian random distributions and the level of variation is characterized by the coefficient of variation and correlation lengths of soil properties (i.e., soil depth, soil texture and initial water content in this study). The impacts of these spatial variations on landslide triggering characteristics were measured by comparing the times to triggering and landslide volumes for heterogeneous soil properties and homogeneous cases. Results at hillslope scale indicate that for spatial variations of an individual property (without cross correlation), the increasing of coefficient of variation introduces weak spots where mechanical damage is accelerated and leads to earlier onset of landslide triggering and smaller volumes. Increasing spatial correlation length of soil texture and initial water content also induces early landslide triggering and small released volumes due to the transition of failure mode from brittle to ductile failure. In contrast, increasing spatial correlation length of soil depth "reduces" local steepness and postpones landslide triggering. Cross-correlated soil properties generally promote landslide initiation, but depending on the internal structure of spatial distribution of each soil property, landslide triggering may be reduced. The effects of cross-correlation between initial water content and soil texture were investigated in detail at the catchment scale by incorporating correlations of both variables with topography. Results indicate that the internal structure of the spatial distribution of each soil property together with their interplays determine the overall performance of the coupled spatial variability. This study emphasizes the importance of both the randomness and spatial structure of soil properties on landslide triggering and characteristics.

Microbiomes structure and diversity in different horizons of full soil profiles

NASA Astrophysics Data System (ADS)

Chernov, Timofey; Tkhakakhova, Azida; Zhelezova, Alena; Semenov, Mikhail; Kutovaya, Olga

2017-04-01

Topsoil is a most common object for soil metagenomic studies; sometimes soil profile is being formally split in layers by depth. However, Russian Soil Science School formulated the idea of soil profile as a complex of soil horizons, which can differ in their properties and genesis. In this research we analyzed 57 genetic soil horizons of 8 different soils from European part of Russia: Albeluvisol, Greyzemic Phaeozem, three Chermozems (different land use - till, fallow, wind-protecting tree line), Rhodic Cambisol, Haplic Kastanozem and Salic Solonetz (WRB classification). Sampling was performed from all genetic horizons in each soil profile starting from topsoil until subsoil. Total DNA was extracted and 16S rRNA sequencing was provided together with chemical analysis of soil (pH measurement, C and N contents, etc.). Structure and diversity of prokaryotic community are significantly different in those soil horizons, which chemical properties and processes of origin are contrasting with nearest horizons: Na-enriched horizon of Solonetz, eluvial horizon of Albeluvisol, plough pan of Agrochernozem. Actinobacteria were abundant in top horizons of soils in warm and dry climate, while Acidobacteria had the highest frequency in soils of moist and cold regions. Concerning Archaea, Thaumarchaeota prevailed in all studied soils. Their rate was higher in microbiomes of upper horizons of steppe soils and it was reducing with depth down the profile. Prokaryotic communities in Chernozems were clustered by soil horizons types: microbiomes of A (organic topsoil) and B (mineral) horizons formed non-overlapping clusters by principal component analysis, cluster formed by prokaryotic communities of transitional soil horizons (AB) take place between clusters of A and B horizons. Moreover, prokaryotic communities of A horizons differ from each other strongly, while microbiomes of B horizons formed a narrow small cluster. It must be explaned by more diverse conditions in upper A horizons. Thus, ecological differences between soil horizons are important factor of differentiation of prokaryotic communities in soil profile; their structure can be specific for horizon type. This study was supported by Russian Science Foundation, project no. 14-26-00079

Spatial and seasonal variations in mercury methylation and microbial community structure in a historic mercury mining area, Yolo County, California

USGS Publications Warehouse

Holloway, J.M.; Goldhaber, M.B.; Scow, K.M.; Drenovsky, R.E.

2009-01-01

The relationships between soil parent lithology, nutrient concentrations, microbial biomass and community structure were evaluated in soils from a small watershed impacted by historic Hg mining. Upland and wetland soils, stream sediments and tailings were collected and analyzed for nutrients (DOC, SO4=, NO3-), Hg, MeHg, and phospholipid fatty acids (PLFA). Stream sediment was derived from serpentinite, siltstone, volcanic rocks and mineralized serpentine with cinnabar, metacinnabar and other Hg phases. Soils from different parent materials had distinct PLFA biomass and community structures that are related to nutrient concentrations and toxicity effects of trace metals including Hg. The formation of MeHg appears to be most strongly linked to soil moisture, which in turn has a correlative relationship with PLFA biomass in wetland soils. The greatest concentrations of MeHg (> 0.5??ng g- 1 MeHg) were measured in wetland soils and soil with a volcanic parent (9.5-37????g g- 1 Hg). Mercury methylation was associated with sulfate-reducing bacteria, including Desulfobacter sp. and Desulfovibrio sp., although these organisms are not exclusively responsible for Hg methylation. Statistical models of the data demonstrated that soil microbial communities varied more with soil type than with season.

Increased Electron-Accepting and Decreased Electron-Donating Capacities of Soil Humic Substances in Response to Increasing Temperature.

PubMed

Tan, Wenbing; Xi, Beidou; Wang, Guoan; Jiang, Jie; He, Xiaosong; Mao, Xuhui; Gao, Rutai; Huang, Caihong; Zhang, Hui; Li, Dan; Jia, Yufu; Yuan, Ying; Zhao, Xinyu

2017-03-21

The electron transfer capacities (ETCs) of soil humic substances (HSs) are linked to the type and abundance of redox-active functional moieties in their structure. Natural temperature can affect the chemical structure of natural organic matter by regulating their oxidative transformation and degradation in soil. However, it is unclear if there is a direct correlation between ETC of soil HS and mean annual temperature. In this study, we assess the response of the electron-accepting and -donating capacities (EAC and EDC) of soil HSs to temperature by analyzing HSs extracted from soil set along glacial-interglacial cycles through loess-palaeosol sequences and along natural temperature gradients through latitude and altitude transects. We show that the EAC and EDC of soil HSs increase and decrease, respectively, with increasing temperature. Increased temperature facilitates the prevalence of oxidative degradation and transformation of HS in soils, thus potentially promoting the preferentially oxidative degradation of phenol moieties of HS or the oxidative transformation of electron-donating phenol moieties to electron-accepting quinone moieties in the HS structure. Consequently, the EAC and EDC of HSs in soil increase and decrease, respectively. The results of this study could help to understand biogeochemical processes, wherein the redox functionality of soil organic matter is involved in the context of increasing temperature.

Impact of monovalent cations on soil structure. Part II. Results of two Swiss soils

NASA Astrophysics Data System (ADS)

Farahani, Elham; Emami, Hojat; Keller, Thomas

2018-01-01

In this study, we investigated the impact of adding solutions with different potassium and sodium concentrations on dispersible clay, water retention characteristics, air permeability, and soil shrinkage behaviour using two agricultural soils from Switzerland with different clay content but similar organic carbon to clay ratio. Three different solutions (including only Na, only K, and the combination of both) were added to soil samples at three different cation ratio of soil structural stability levels, and the soil samples were incubated for one month. Our findings showed that the amount of readily dispersible clay increased with increasing Na concentrations and with increasing cation ratio of soil structural stability. The treatment with the maximum Na concentration resulted in the highest water retention and in the lowest shrinkage capacity. This was was associated with high amounts of readily dispersible clay. Air permeability generally increased during incubation due to moderate wetting and drying cycles, but the increase was negatively correlated with readily dispersible clay. Readily dispersible clay decreased with increasing K, while readily dispersible clay increased with increasing K in Iranian soil (Part I of our study). This can be attributed to the different clay mineralogy of the studied soils (muscovite in Part I and illite in Part II).

75 FR 16202 - Office of New Reactors; Interim Staff Guidance on Ensuring Hazard-Consistent Seismic Input for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-31

... Staff Guidance on Ensuring Hazard-Consistent Seismic Input for Site Response and Soil Structure...-Consistent Seismic Input for Site Response and Soil Structure Interaction Analyses,'' (Agencywide Documents... Soil Structure Interaction Analyses,'' (ADAMS Accession No. ML092230455) to solicit public and industry...

Reflecting on the structure of soil classification systems: insights from a proposal for integrating subsoil data into soil information systems

NASA Astrophysics Data System (ADS)

Dondeyne, Stefaan; Juilleret, Jérôme; Vancampenhout, Karen; Deckers, Jozef; Hissler, Christophe

2017-04-01

Classification of soils in both World Reference Base for soil resources (WRB) and Soil Taxonomy hinges on the identification of diagnostic horizons and characteristics. However as these features often occur within the first 100 cm, these classification systems convey little information on subsoil characteristics. An integrated knowledge of the soil, soil-to-substratum and deeper substratum continuum is required when dealing with environmental issues such as vegetation ecology, water quality or the Critical Zone in general. Therefore, we recently proposed a classification system of the subsolum complementing current soil classification systems. By reflecting on the structure of the subsoil classification system which is inspired by WRB, we aim at fostering a discussion on some potential future developments of WRB. For classifying the subsolum we define Regolite, Saprolite, Saprock and Bedrock as four Subsolum Reference Groups each corresponding to different weathering stages of the subsoil. Principal qualifiers can be used to categorize intergrades of these Subsoil Reference Groups while morphologic and lithologic characteristics can be presented with supplementary qualifiers. We argue that adopting a low hierarchical structure - akin to WRB and in contrast to a strong hierarchical structure as in Soil Taxonomy - offers the advantage of having an open classification system avoiding the need for a priori knowledge of all possible combinations which may be encountered in the field. Just as in WRB we also propose to use principal and supplementary qualifiers as a second level of classification. However, in contrast to WRB we propose to reserve the principal qualifiers for intergrades and to regroup the supplementary qualifiers into thematic categories (morphologic or lithologic). Structuring the qualifiers in this manner should facilitate the integration and handling of both soil and subsoil classification units into soil information systems and calls for paying attention to these structural issues in future developments of WRB.

Differential effects of fine root morphology on water dynamics in the root-soil interface

NASA Astrophysics Data System (ADS)

DeCarlo, K. F.; Bilheux, H.; Warren, J.

2017-12-01

Soil water uptake form plants, particularly in the rhizosphere, is a poorly understood question in the plant and soil sciences. Our study analyzed the role of belowground plant morphology on soil structural and water dynamics of 5 different plant species (juniper, grape, maize, poplar, maple), grown in sandy soils. Of these, the poplar system was extended to capture drying dynamics. Neutron radiography was used to characterize in-situ dynamics of the soil-water-plant system. A joint map of root morphology and soil moisture was created for the plant systems using digital image processing, where soil pixels were connected to associated root structures via minimum distance transforms. Results show interspecies emergent behavior - a sigmoidal relationship was observed between root diameter and bulk/rhizosphere soil water content difference. Extending this as a proxy for extent of rhizosphere development with root age, we observed a logistic growth pattern for the rhizosphere: minimal development in the early stages is superceded by rapid onset of rhizosphere formation, which then stabilizes/decays with the likely root suberization. Dynamics analysis of water content differences between the root/rhizosphere, and rhizosphere/bulk soil interface highlight the persistently higher water content in the root at all water content and root size ranges. At the rhizosphere/bulk soil interface, we observe a shift in soil water dynamics by root size: in super fine roots, we observe that water content is primarily lower in the rhizosphere under wetter conditions, which then gradually increases to a relatively higher water content under drier conditions. This shifts to a persistently higher rhizosphere water content relative to bulk soil in both wet/dry conditions with increased root size, suggesting that, by size, the finest root structures may contribute the most to total soil water uptake in plants.

Impact of Hydrologic Variability on Ecosystem Dynamics and the Sustainable Use of Soil and Water Resources

NASA Astrophysics Data System (ADS)

Porporato, A. M.

2013-05-01

We discuss the key processes by which hydrologic variability affects the probabilistic structure of soil moisture dynamics in water-controlled ecosystems. These in turn impact biogeochemical cycling and ecosystem structure through plant productivity and biodiversity as well as nitrogen availability and soil conditions. Once the long-term probabilistic structure of these processes is quantified, the results become useful to understand the impact of climatic changes and human activities on ecosystem services, and can be used to find optimal strategies of water and soil resources management under unpredictable hydro-climatic fluctuations. Particular applications regard soil salinization, phytoremediation and optimal stochastic irrigation.

Soil physical conditions as livestock treading effect in tropical Agroecosystem of dryland and strategies to mitigate desertification risk

NASA Astrophysics Data System (ADS)

Florentino, A.; Torres, D.; Ospina, A.; Contreras, J.; Palma, Z.; Silvera, J.

2012-04-01

Soil degradation in natural ecosystem of arid and semi-arid zones of Venezuela due to livestock treading (goats) it is an important problem that affect their environment functions; increase soil erodibility, bulk density, water losses and reduce porosity, water infiltration rate and soil structural stability. The presence of biological crust (BSC) in this type of soil it is very common. The objective of this study was to evaluate the soil surface physical quality through the use of selected indicators, mainly some of that related to structural stability, infiltrability and the prediction of soil erosion risk in two zones of Lara state: 1) Quíbor (QUI) and 2) Humocaro Bajo (HB). The study was conducted on two selected plots (30 m x 20 m) in each zone, with natural vegetation and BSC cover, with areas affected by different degree of compaction due to treading in the paths where the goats are moving. Five sites per plot (50 cm x 50 cm) under vegetation cover and five sites over the path with bare soil were sampled (0-7,5 and 7,5-15 cm depth). The results showed that soil macroaggregate stability (equivalent diameter of aggregates >0,25 mm) was significantly higher (p<0,05 %) in soil with vegetation cover and BSC compared with bare soil. Sealing index, as a measure of aggregate stability, determined in laboratory under simulated rain and expressed as hydraulic conductivity of soil surface sealing (Kse), decreased with decreasing soil vegetation cover and the presence of BSC. However, Ksei (i: inicial) and Ksef (f: final) were significantly greater in soil with more than 75 % of BSC in comparison to bare soils. The sealing index it is used to for to estimate changes in soil water losses. As the sealing index increases, the susceptibility of the soil to undergo surface sealing or slaking decrease. These results suggested that soil physical properties are potential indicators of soil quality with regard to soil erodibility and showed that soils under vegetation cover had higher quality level than bare soils. Some predictive regression equation had a high R2 value and was a useful tool for to evaluate the risk of extreme climatic changes and to mitigate their detrimental effects. We conclude that the global climatic change (CCG) will have a negative effect on these agroecosystems functions, mainly in soil and water conservation, carbon sequestration, and productivity. Natural recovery of soil physical properties from treading damage of pastoral soils will be possible in the future with the implementation of soil management strategies, mainly through re-vegetation and recuperation of the BSC. Key word: Soil structure; aggregate stability; soil sealing index; hydraulic conductivity of surface sealing.

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...

Exploring soils and ecohydrological structure in small watersheds using electromagnetic induction

USDA-ARS?s Scientific Manuscript database

Soil moisture sensors generally strive to use the real permittivity as the basis for estimating soil water content from measured electrical properties of soil. It has been shown that a reasonably good general calibration can be developed for mineral soils on this basis. However, at the low measureme...

Calibrating Nonlinear Soil Material Properties for Seismic Analysis Using Soil Material Properties Intended for Linear Analysis

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

Spears, Robert Edward; Coleman, Justin Leigh

2015-08-01

Seismic analysis of nuclear structures is routinely performed using guidance provided in “Seismic Analysis of Safety-Related Nuclear Structures and Commentary (ASCE 4, 1998).” This document, which is currently under revision, provides detailed guidance on linear seismic soil-structure-interaction (SSI) analysis of nuclear structures. To accommodate the linear analysis, soil material properties are typically developed as shear modulus and damping ratio versus cyclic shear strain amplitude. A new Appendix in ASCE 4-2014 (draft) is being added to provide guidance for nonlinear time domain SSI analysis. To accommodate the nonlinear analysis, a more appropriate form of the soil material properties includes shear stressmore » and energy absorbed per cycle versus shear strain. Ideally, nonlinear soil model material properties would be established with soil testing appropriate for the nonlinear constitutive model being used. However, much of the soil testing done for SSI analysis is performed for use with linear analysis techniques. Consequently, a method is described in this paper that uses soil test data intended for linear analysis to develop nonlinear soil material properties. To produce nonlinear material properties that are equivalent to the linear material properties, the linear and nonlinear model hysteresis loops are considered. For equivalent material properties, the shear stress at peak shear strain and energy absorbed per cycle should match when comparing the linear and nonlinear model hysteresis loops. Consequently, nonlinear material properties are selected based on these criteria.« less

Slumping in the rain - winter soil structure across Scotland and its physical degradation from extreme weather

NASA Astrophysics Data System (ADS)

Hall, Rebecca; Hallett, Paul; Raffan, Annette; Lilly, Allan; Baggaley, Nikki; Rowan, John; Crookes, Bill; Ball, Bruce

2017-04-01

Scotland is blessed with fertile and resilient soils that produce great cereal yields and whisky. However, there is worrying anecdotal evidence, confirmed by a small body of science, that some farming practices are causing widespread physical degradation of these soils. Studies from other UK regions have identified soil physical degradation by compaction, unstable seedbeds and erosion as a moderate to serious problem, depending on farming practice, soil properties and climate. In 2015/2016 we sampled 120 fields from 4 catchments in Scotland to describe the state of soil structure in the winter. To obtain a rapid assessment, we used the increasingly popular and easily interpretable Visual Evaluations of Soil Structure (VESS) and Subsoil Structure (SubVESS). We found severe soil structural degradation in 18% of topsoils and 9% of subsoils for 120 fields in 4 catchments. The severe 2015/2016 winter precipitation, the worst ever recorded, caused a 30% increase in occurrence of severely degraded topsoils, as determined from sampling some of the same fields before and after this unprecedented weather event. Run-off, erosion and nutrient losses were about 10X from degraded parts of fields such as tramlines than either within the field or at less trafficked boundaries. There was some agreement between areas identified as structurally degraded and those ranked as being susceptible to topsoil compaction using a simple model. Broad scale surveys that incorporate temporal sampling, such as the study reported here, are essential to provide regional assessments of soil degradation and to inform follow-on, targeted studies, where more in-depth analysis would be feasible.

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

PubMed

Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

2015-10-01

Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

Soil microbial community profiles and functional diversity in limestone cedar glades

USGS Publications Warehouse

Cartwright, Jennifer M.; Dzantor, E. Kudjo; Momen, Bahram

2016-01-01

Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (< 25 cm), soil-moisture conditions fluctuate seasonally between xeric and saturated, and summer soil temperatures commonly exceed 48 °C. The effects of these stressors on soil microbial communities (SMC) remain largely unstudied, despite the importance of SMC-plant interactions in regulating the structure and function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles.

Influence of biochar on the physical, chemical and retention properties of an amended sandy soil

NASA Astrophysics Data System (ADS)

Baiamonte, Giorgio; De Pasquale, Claudio; Parrino, Francesco; Crescimanno, Giuseppina

2017-04-01

Soil porosity plays an important role in soil-water retention and water availability to crops, potentially affecting both agricultural practices and environmental sustainability. The pore structure controls fluid flow and transport through the soil, as well as the relationship between the properties of individual minerals and plants. Moreover, the anthropogenic pressure on soil properties has produced numerous sites with extensive desertification process close to residential areas. Biochar (biologically derived charcoal) is produced by pyrolysis of biomasses under low oxygen conditions, and it can be applied for recycling organic waste in soils and increase soil fertility, improving soil structure and enhancing soil water storage and soil water movement. Soil application of biochar might have agricultural, environmental and sustainability advantages over the use of organic manures or compost, as it is a porous material with a high inner surface area. The main objectives of the present study were to investigate the possible application of biochar from forest residues, derived from mechanically chipped trunks and large branches of Abies alba M., Larix decidua Mill., Picea excelsa L., Pinus nigra A. and Pinus sylvestris L. pyrolysed at 450 °C for 48h, to improve soil structural and hydraulic properties (achieving a stabilization of soil). Different amount of biochar were added to a desertic sandy soil, and the effect on soil porosity water retention and water available to crops were investigated. The High Energy Moisture Characteristic (HEMC) technique was applied to investigate soil-water retention at high-pressure head levels. The adsorption and desorption isotherms of N2 on external surfaces were also determined in order to investigate micro and macro porosity ratio. Both the described model of studies on adsorption-desorption experiments with the applied isotherms model explain the increasing substrate porosity with a particular attention to the macro and micro porosity, respectively.

Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

NASA Astrophysics Data System (ADS)

Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

2014-05-01

Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community development which was soil horizon specific and its effects on soil microbial activity may impact on nutrient cycling.

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

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

The engineering significance of shrinkage and swelling soils in blast damage investigations

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

Vitton, S.J.; Harris, W.W.

1996-12-01

In the US each year it has been estimated that expansive soils cause approximately $9.0 billion in damage to buildings, roads, airports, and other facilities. This figure alone exceeds the damage estimate for earthquakes, floods, tornadoes, and hurricanes combined. Unfortunately, some cases of expansive soil damage (swelling) are blamed on rock blasting operations if the blasting operations are located within the immediate area. While simple tests, such as the Atterberg limits test, can characterize a soil as expansive, it does not necessarily answer the question whether the foundation soils are causing distresses to a structure. In particular, it appears thatmore » once a soil has been labeled as nonexpansive it is no longer considered as a problem soil, in which case blast vibrations become the prime suspect. It should be emphasized, however, that even non-plastic soils, those soils with low to nonexistent plastic indexes, can exhibit significant shrinkage characteristics that can result in significant damage to structures. While expansive soil is a function of the mineralogy of the soil particles, i.e., swelling clay minerals, shrinkage is caused by the loss of moisture from soil as capillary pressures exceed the cohesion or tensile strength and is therefore a function of the soils particle size and its pore size distribution. This is a significant problem for all fine grained soils regardless of the soil`s mineralogy. It`s particularly important for regions of the US that typically have a positive water balance but experience significant drought periods when soil moisture is lost.« less

Preliminary Guidelines and Standard Operating Procedure for Drainage and Erosion Control at McMurdo Station

DTIC Science & Technology

2014-12-01

along the impermeable frozen soil layer. Soil freeze–thaw action disrupts soil structures, displaces soils particles , and creates voids both in...discharging along the bank face). This was caused by excess pore water pressure. Soil piping removes soil particles from their in-situ position, leaving...soil particles ERDC/CRREL SR-14-3 30 c. Maintain original side and bed slopes during the clearing efforts. d. Shape the channels to minimize

Spatial characterization of soil properties and influence in soil formation in oak-grassland of Sierra Morena, S Spain

NASA Astrophysics Data System (ADS)

Román-Sánchez, Andrea; Cáceres, Francisco; Pédèches, Remi; Giráldez Cervera, Juan Vicente; Vanwalleghem, Tom

2016-04-01

The Mediterranean oak-grassland ecosystem is very important for the rural economy and for the biodiversity of south-western European countries like Spain and Portugal. Nevertheless these ecosystems are not well characterized especially their soils. In this report soil carbon has been evaluated and related to other properties. The principal factors controlling the structure, productivity and evolution of forest ecosystems are bedrock, climate, relief, vegetation and time. Soil carbon has an important influence in the soil and ecosystem structures. The purpose of this study is to determine the relationship between relief, soil properties, spatial distribution of soil carbon and their influence in soil formation and geomorphology. This work is part of another study which aims to elucidate the processes involved in the soil formation and to examine their behaviour on long-term with a modelling. In our study area, located in oak-grassland of Sierra Morena, in Cordoba, S Spain, have been studied 67 points at 6 depths in 262 hectares in order to determine carbon content varying between 0-6%, soil properties such as soil depth between 0-4 m, horizon depth and the rocks amount in surface. The relationship between the soil carbon, soil properties and the relief characteristic like slope, aspect, curvature can shed light the processes that affect the mechanisms of bedrock weathering and their interrelationship with geomorphological processes.

Land-use changes influence soil bacterial communities in a meadow grassland in Northeast China

NASA Astrophysics Data System (ADS)

Cao, Chengyou; Zhang, Ying; Qian, Wei; Liang, Caiping; Wang, Congmin; Tao, Shuang

2017-10-01

The conversion of natural grassland into agricultural fields is an intensive anthropogenic perturbation commonly occurring in semiarid regions, and this perturbation strongly affects soil microbiota. In this study, the influences of land-use conversion on the soil properties and bacterial communities in the Horqin Grasslands in Northeast China were assessed. This study aimed to investigate (1) how the abundances of soil bacteria changed across land-use types, (2) how the structure of the soil bacterial community was altered in each land-use type, and (3) how these variations were correlated with soil physical and chemical properties. Variations in the diversities and compositions of bacterial communities and the relative abundances of dominant taxa were detected in four distinct land-use systems, namely, natural meadow grassland, paddy field, upland field, and poplar plantation, through the high-throughput Illumina MiSeq sequencing technique. The results indicated that land-use changes primarily affected the soil physical and chemical properties and bacterial community structure. Soil properties, namely, organic matter, pH, total N, total P, available N and P, and microbial biomass C, N, and P, influenced the bacterial community structure. The dominant phyla and genera were almost the same among the land-use types, but their relative abundances were significantly different. The effects of land-use changes on the structure of soil bacterial communities were more quantitative than qualitative.

Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soil.

PubMed

Priha; Grayston; Pennanen; Smolander

1999-10-01

The aim of this study was to determine whether Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) Karst.) and silver birch (Betula pendula Roth) seedlings have a selective influence on the soil microbial community structure and activity and whether this varies in different soils. Seedlings of pine, spruce and birch were planted into pots of two soil types: an organic soil and a mineral soil. Pots without seedlings were also included. After one growing season, microbial biomass C (C(mic)) and N (N(mic)), C mineralization, net ammonification, net nitrification, denitrification potential, phospholipid fatty acid (PLFA) patterns and community level physiological profiles (CLPPs) were measured in the rhizosphere soil of the seedlings. In the organic soil, C(mic) and N(mic) were higher in the birch rhizosphere than in pine and spruce rhizosphere. The C mineralization rate was not affected by tree species. Unplanted soil contained the highest amount of mineral N and birch rhizosphere the lowest, but rates of net N mineralization and net nitrification did not differ between treatments. The microbial community structure, measured by PLFAs, had changed in the rhizospheres of all tree species compared to the unplanted soil. Birch rhizosphere was most clearly separated from the others. There was more of the fungal specific fatty acid 18:2omega6,9 and more branched fatty acids, common in Gram-positive bacteria, in this soil. CLPPs, done with Biolog GN plates and 30 additional substrates, separated only birch rhizosphere from the others. In the mineral soil, roots of all tree species stimulated C mineralization in soil and prevented nitrification, but did not affect C(mic) and N(mic), PLFA patterns or CLPPs. The effects of different tree species did not vary in the mineral soil. Thus, in the mineral soil, the strongest effect on soil microbes was the presence of a plant, regardless of the tree species, but in the organic soil, different tree species varied in their influence on soil microbes.

Pore-Scale Effects of Soil Structure And Microbial EPS Production On Soil Water Retention

NASA Astrophysics Data System (ADS)

Orner, E.; Anderson, E.; Rubinstein, R. L.; Chau, J. F.; Shor, L. M.; Gage, D. J.

2013-12-01

Climate-induced changes to the hydrological cycle will increase the frequency of extreme weather events including powerful storms and prolonged droughts. Moving forward, one of the major factors limiting primary productivity in terrestrial ecosystems will be sub-optimal soil moisture. We focus here on the ability of soils to retain moisture under drying conditions. A soil's ability to retain moisture is influenced by many factors including its texture, its structure, and the activities of soil microbes. In soil microcosms, the addition of small amounts of microbially-produced extracellular polymeric substances (EPS) can dramatically shift moisture retention curves. The objective of this research is to better understand how soil structure and EPS may act together to retain moisture in unsaturated soils. Replicate micromodels with exactly-conserved 2-D physical geometry were initially filled with aqueous suspensions of one of two types of bacteria: one mutant was ultra- muccoid and the other was non-muccoid. Replicate micromodels were held at a fixed, external, relative humidity, and the position of the air-water interface was imaged over time as water evaporates. There was no forced convection of air or water inside the micromodels: drying was achieved by water evaporation and diffusion alone. We used a fully automated, inverted microscope to image replicate drying lanes each with dimensions of 1 mm x 10 mm. A complete set of images was collected every 30 minutes for 30 hours. The results show devices loaded with the highly muccoid strain remained >40% hydrated for 13 h, while devices loaded with the non-muccoid remained >40% hydrated for only 6 h, and were completely dry by 13 h. Current work is comparing interfacial water fluxes in structured and unstructured settings, and is attempting to model the synergistic effects of soil structure and EPS content on moisture retention in real soils. This research may allow more accurate description of naturally-occurring feedbacks between the soil carbon and water cycles, and may enable agriculture biotechnology that enhances natural soil processes for improved resiliency of terrestrial ecosystems.

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.

Directional reflectance factors for monitoring spatial changes in soil surface structure and soil organic matter erosion in agricultural systems

NASA Astrophysics Data System (ADS)

Croft, H.; Anderson, K.

2012-04-01

Soils can experience rapid structural degradation in response to land cover changes, resulting in reduced soil productivity, increased erodibility and a loss of soil organic matter (SOM). The breakdown of soil aggregates through slaking and raindrop impact is linked to organic matter turnover, with subsequently eroded material often displaying proportionally more SOM. A reduction in aggregate stability is reflected in a decline in soil surface roughness (SSR), indicating that a soil structural change can be used to highlight soil vulnerability to SOM loss through mineralisation or erosion. Accurate, spatially-continuous measurements of SSR are therefore needed at a variety of spatial and temporal scales to understand the spatial nature of SOM erosion and deposition. Remotely-sensed data can provide a cost-effective means of monitoring changes in soil surface condition over broad spatial extents. Previous work has demonstrated the ability of directional reflectance factors to monitor soil crusting within a controlled laboratory experiment, due to changes in the levels of self-shadowing effects by soil aggregates. However, further research is needed to test this approach in situ, where other soil variables may affect measured reflectance factors and to investigate the use of directional reflectance factors for monitoring soil erosion processes. This experiment assesses the potential of using directional reflectance factors to monitor changes in SSR, aggregate stability and soil organic carbon (SOC) content for two agricultural conditions. Five soil plots representing tilled and seedbed soils were subjected to different durations of natural rainfall, producing a range of different levels of SSR. Directional reflectance factors were measured concomitantly with sampling for soil structural and biochemical tests at each soil plot. Soil samples were taken to measure aggregate stability (wet sieving), SOC (loss on ignition) and soil moisture (gravimetric method). SSM values varied from 8.70 to 20.05% and SOC from 1.33 to 1.05%, across all soil plots. Each plot was characterised using a close-range laser scanning device with a 2 mm sampling interval. The point laser data were geostatistically analysed to provide a spatially-distributed measure of SSR, giving sill variance values from 3.15 to 22.99. Reflectance factors from the soil states were measured using a ground-based hyperspectral spectroradiometer (400-2500 nm) attached to an A-frame device. This method allowed measurement at a range of viewing zenith angles from extreme forwardscatter (-60°) to extreme backscatter (+60°) at a 10° sampling resolution in the solar principal plane. Reflectance measurements were compared to geostatistically-derived indicators of SSR from the laser profile data. Forward-scattered reflectance factors exhibited a very strong relationship to SSR (R2 = 0.84 at -60°; p< 0.05), demonstrating the operational potential of directional reflectance for providing SSR measurements, despite conflicting variation in SSM. SSM also presented an interesting directional signal (R2 = 0.99 at +20°; p< 0.01). Furthermore, the results showed an important link between SRR decline as measured using directional reflectance, with a decline in aggregate stability and SOC content. These findings provide an empirical and theoretical basis for the future retrieval of spatially-continuous assessments of soil surface structure and carbon turnover within a landscape context.

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.

Permafrost soils and carbon cycling

DOE PAGES

Ping, C. L.; Jastrow, J. D.; Jorgenson, M. T.; ...

2014-10-30

Knowledge of soils in the permafrost region has advanced immensely in recent decades, despite the remoteness and inaccessibility of most of the region and the sampling limitations posed by the severe environment. These efforts significantly increased estimates of the amount of organic carbon (OC) stored in permafrost-region soils and improved understanding of how pedogenic processes unique to permafrost environments built enormous OC stocks during the Quaternary. This knowledge has also called attention to the importance of permafrost-affected soils to the global C cycle and the potential vulnerability of the region's soil OC stocks to changing climatic conditions. In this review,more » we briefly introduce the permafrost characteristics, ice structures, and cryopedogenic processes that shape the development of permafrost-affected soils and discuss their effects on soil structures and on organic matter distributions within the soil profile. We then examine the quantity of OC stored in permafrost-region soils, as well as the characteristics, intrinsic decomposability, and potential vulnerability of this OC to permafrost thaw under a warming climate.« less

Changes in soil microbial community structure influenced by agricultural management practices in a mediterranean agro-ecosystem.

PubMed

García-Orenes, Fuensanta; Morugán-Coronado, Alicia; Zornoza, Raul; Cerdà, Artemi; Scow, Kate

2013-01-01

Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage.

Bacterial density and community structure associated with aggregate size fractions of soil-feeding termite mounds.

PubMed

Fall, S; Nazaret, S; Chotte, J L; Brauman, A

2004-08-01

The building and foraging activities of termites are known to modify soil characteristics such as the heterogeneity. In tropical savannas the impact of the activity of soil-feeding termites ( Cubitermes niokoloensis) has been shown to affect the properties of the soil at the aggregate level by creating new soil microenvironments (aggregate size fractions) [13]. These changes were investigated in greater depth by looking at the microbial density (AODC) and the genetic structure (automated rRNA intergenic spacer analysis: ARISA) of the communities in the different aggregate size fractions (i.e., coarse sand, fine sand, coarse silt, fine silt, and dispersible clays) separated from compartments (internal and external wall) of three Cubitermes niokoloensis mounds. The bacterial density of the mounds was significantly higher (1.5 to 3 times) than that of the surrounding soil. Within the aggregate size fractions, the termite building activity resulted in a significant increase in bacterial density within the coarser fractions (>20 mum). Multivariate analysis of the ARISA profiles revealed that the bacterial genetic structures of unfractionated soil and soil aggregate size fractions of the three mounds was noticeably different from the savanna soil used as a reference. Moreover, the microbial community associated with the different microenvironments in the three termite mounds revealed three distinct clusters formed by the aggregate size fractions of each mound. Except for the 2-20 mum fraction, these results suggest that the mound microbial genetic structure is more dependent upon microbial pool affiliation (the termite mound) than on the soil location (aggregate size fraction). The causes of the specificity of the microbial community structure of termite mound aggregate size fractions are discussed.

Nitrogen-mediated effects of elevated CO2 on intra-aggregate soil pore structure

USDA-ARS?s Scientific Manuscript database

While previous elevated atmospheric CO2 research has addressed changes in belowground processes, its effects on soil structure remain virtually undescribed. This study examined the long-term effects of elevated CO2 and N fertilization on soil structural changes in a bahiagrass pasture grown on a san...

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...

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage

USDA-ARS?s Scientific Manuscript database

Soil microorganisms play essential roles in soil organic matter dynamics and nutrient cycling in agroecosystems and have been used as soil quality indicators. The response of soil microbial communities to land management is complex and the long-term impacts of cropping systems on soil microbes is l...

Transformation of soil microbial community structure in response to anaerobic soil disinfestation for soil-borne disease control in strawberry

USDA-ARS?s Scientific Manuscript database

Anaerobic soil disinfestation (ASD) has been used to control soil-borne pathogens and nematodes in various plant production systems including strawberries. Disease control is commonly attributed to the depletion of oxygen and the generation of toxic compounds, including organic acids and volatiles....

Changes in the structure and function of soil ecosystems in soils contaminated with heavy metals

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

Kuperman, R.; Parmelee, R.; Carreiro, M.

1995-09-01

The structure and function of soil communities in an area with a wide range of concentrations of heavy metals was studied in portions of the U.S. Army`s Aberdeen Proving Ground, Maryland. The study included survey of soil macro- and microinvertebrate communities, soil microorganisms, enzyme activities and the rates of nutrient dynamics in soil. Soil macroinvertebrate communities showed significant reductions in the adundance of several taxonomic and functional groups in contaminated areas. The total numbers of nematodes and numbers of fungivore, bacterivore and omnivore-predator nematodes were lower in the more contaminated areas. The numbers of active bacteria and fungi were lowermore » in areas of soil contamination. Significant reduction in the activities of all enzymes closely paralleled the increase in heavy metal concentrations. Ten-to-fifty fold reductions in enzyme activities were observed as heavy metal concentrations increased. These results suggest that soil contamination with heavy metals may have detrimental effects on soil biota and the rates of organic matter degradation and subsequent release of nutrients to aboveground communities in the area.« less

Changes in the structure and function of soil ecosystems in soils contaminated with heavy metals

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

Kuperman, R.; Parmelee, R.; Carreiro, M.

1995-06-01

The structure and function of soil communities in an area with a wide range of concentrations of heavy metals was studied in portions of the U.S. Army`s Aberdeen Proving Ground, Maryland. The study included survey of soil macro- and microinvertebrate communities, soil microorganisms, enzyme activities and the rates of nutrient dynamics in soil. Soil macroinvertebrate communities showed significant reductions in the abundance of several taxonomic and functional groups in contaminated areas. The total numbers of nematodes and numbers of fungivore, bacterivore and omnivore-predator nematodes were lower in the more contaminated areas. The numbers of active bacteria and fungi were lowermore » in areas of soil contamination. Significant reduction in the activities of all enzymes closely paralleled the increase in heavy metal concentrations. Ten-to-fifty fold reductions in enzyme activities were observed as heavy metal concentrations increased. These results suggest that soil contamination with heavy metals may have detrimental effects on soil biota and the rates of organic matter degradation and subsequent release of nutrients to aboveground communities in the area.« less

Effects of spent mushroom compost application on the physicochemical properties of a degraded soil

NASA Astrophysics Data System (ADS)

Gümüş, İlknur; Şeker, Cevdet

2017-11-01

Under field and laboratory conditions, the application of organic amendments has generally shown an improvement in soil physicochemical properties. Here, spent mushroom compost (SMC) is proposed as a suitable organic amendment for soil structure restoration. Our study assessed the impact of SMC on the physicochemical properties of a weak-structured and physically degraded soil. The approach involved the establishment of a pot experiment with SMC applications into soil (control, 0.5, 1, 2, 4 and 8 %). Soils were incubated at field capacity (-33 kPa) for 21, 42, and 62 days under laboratory conditions. SMC applications into the soil significantly increased the aggregate stability (AS) and decreased the modulus of rupture. The application of SMC at rates of 1, 2, 4, and 8 % significantly increased the total nitrogen and soil organic carbon contents of the degraded soil at all incubation periods (p < 0.05). The results obtained in this study indicate that the application of SMC can improve soil physicochemical properties, which may benefit farmers, land managers, and mushroom growers.

Experimental evidence and modelling of drought induced alternative stable soil moisture states

NASA Astrophysics Data System (ADS)

Robinson, David; Jones, Scott; Lebron, Inma; Reinsch, Sabine; Dominguez, Maria; Smith, Andrew; Marshal, Miles; Emmett, Bridget

2017-04-01

The theory of alternative stable states in ecosystems is well established in ecology; however, evidence from manipulation experiments supporting the theory is limited. Developing the evidence base is important because it has profound implications for ecosystem management. Here we show evidence of the existence of alternative stable soil moisture states induced by drought in an upland wet heath. We used a long-term (15 yrs) climate change manipulation experiment with moderate sustained drought, which reduced the ability of the soil to retain soil moisture by degrading the soil structure, reducing moisture retention. Moreover, natural intense droughts superimposed themselves on the experiment, causing an unexpected additional alternative soil moisture state to develop, both for the drought manipulation and control plots; this impaired the soil from rewetting in winter. Our results show the coexistence of three stable states. Using modelling with the Hydrus 1D software package we are able to show the circumstances under which shifts in soil moisture states are likely to occur. Given the new understanding it presents a challenge of how to incorporate feedbacks, particularly related to soil structure, into soil flow and transport models?

Transport of four pharmaceuticals in different horizons of three soil types

NASA Astrophysics Data System (ADS)

Kodesova, Radka; Svatkova, Paula; Klement, Ales; Jaksik, Ondrej; Golovko, Oksana; Fer, Miroslav; Kocarek, Martin; Nikodem, Antonin; Grabic, Roman

2015-04-01

Soil structure, which varies in different soil types and the horizons of these soil types, has a significant impact on water flow and contaminant transport in soils. Transport of many contaminants is in addition strongly influenced by their sorption on soil particles. Transport of four pharmaceuticals (sulfamethoxazole, trimethoprim, atenolol and carbamazepine) was studied in soil columns (a diameter of 10.5 cm and a height of 13 cm) taken from all diagnostic horizons of three different soil types (Haplic Luvisol, Greyic Phaeozem and Haplic Cambisol). The irrigation by water contaminated by a mixture of all four compounds followed by ponding infiltration of distilled water was simulated and water outflow and solute concentrations from the bottom of the soil sample was monitored in time. The highest infiltration rates were observed for soil samples from the Bt horizons of the Greyic Phaeozem that exhibited prismatic structure, followed by rates observed in the Ap horizons of the Haplic Luvisol, Greyic Phaeozem and Haplic Cambisol (due to their granular soil structure and presence of root channels). The lowest infiltration rate was measured for the Bw horizon of the Haplic Cambisol, which had a poorly developed soil structure and a low fraction of macropores. Compound discharge was however also highly affected by their sorption on solids. The highest mobility was observed for sulfamethoxazole followed by carbamazepine atenolol and trimethoprim, which corresponds to measured sorption isotherms. Mobility of ionizable compounds in different soil samples was influenced by pH (i.e. degree and form of their ionization) and sites available for absorption. Mobility of sulfamethoxazole decreased with decreasing pH (i.e. the largest sorption measured in horizons of the Haplic Cambisol). While mobility of atenolol and trimethoprim decreased with increasing base cation saturation, and with increasing organic matter content for carbamazepine. As result of both affects (i.e. soil structure and compounds' sorption) the highest discharge of all compounds was observed from the Ap horizon of the Greyic Phaeozem followed by compound discharge from the C horizons of the Greyic Phaeozem and the C and Bt2 horizons of the Haplic Luvisol. Acknowledgement: The authors acknowledge the financial support of the Czech Science Foundation (Project No. 13-12477S, Transport of pharmaceuticals in soils). References: Kodesova, R., Grabic, R., Kocarek, M., Klement, A., Golovko, O., Fer, M., Nikodem, A., Jaksik, O., Pharmaceuticals' sorptions relative to properties of thirteen different soils. Science of the Total Environment 511 (2015) 435-443.

Minute tubular forms in soil

NASA Technical Reports Server (NTRS)

Casida, L. E., Jr.; Liu, K.-C.

1979-01-01

Large numbers of long, straight, flattened structures were observed during an electron-microscope study of bacteriophage in aqueous extracts. These structures were called tubules and ranged in width from 10 to 50 nm. Materials and methods were discussed relative to extraction of tubules from soil, electron microscopy, quantitation of tubules in filtrate suspension, tests performed on tubules, plaque formation, and nutrient amendments. It is found that all of the tubules recovered from soil are broken at one or both ends. They are present in surface soils but not in a subsurface sample. Their numbers decrease during bacterial multiplication in soil or broth-containing soil. The tubules appear to be composed of protein that could be disintegrated to liberate nonprotein fibers. A possible clue to the nature of the tubules is their apparent relation to soil bacteria.

Study on soil-pile-structure-TMD interaction system by shaking table model test

NASA Astrophysics Data System (ADS)

Lou, Menglin; Wang, Wenjian

2004-06-01

The success of the tuned mass damper (TMD) in reducing wind-induced structural vibrations has been well established. However, from most of the recent numerical studies, it appears that for a structure situated on very soft soil, soil-structure interaction (SSI) could render a damper on the structure totally ineffective. In order to experimentally verify the SSI effect on the seismic performance of TMD, a series of shaking table model tests have been conducted and the results are presented in this paper. It has been shown that the TMD is not as effective in controlling the seismic responses of structures built on soft soil sites due to the SSI effect. Some test results also show that a TMD device might have a negative impact if the SSI effect is neglected and the structure is built on a soft soil site. For structures constructed on a soil foundation, this research verifies that the SSI effect must be carefully understood before a TMD control system is designed to determine if the control is necessary and if the SSI effect must be considered when choosing the optimal parameters of the TMD device.

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.

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation.

PubMed

Koebernick, Nicolai; Daly, Keith R; Keyes, Samuel D; George, Timothy S; Brown, Lawrie K; Raffan, Annette; Cooper, Laura J; Naveed, Muhammad; Bengough, Anthony G; Sinclair, Ian; Hallett, Paul D; Roose, Tiina

2017-10-01

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm -3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Leuther, Frederic; Vogler, Steffen; Vogel, Hans-Jörg

2016-04-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of <-100kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent to any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

X-ray microtomography analysis of soil structure deformation caused by centrifugation

NASA Astrophysics Data System (ADS)

Schlüter, S.; Leuther, F.; Vogler, S.; Vogel, H.-J.

2016-01-01

Centrifugation provides a fast method to measure soil water retention curves over a wide moisture range. However, deformation of soil structure may occur at high angular velocities in the centrifuge. The objective of this study was to capture these changes in soil structure with X-ray microtomography and to measure local deformations via digital volume correlation. Two samples were investigated that differ in texture and rock content. A detailed analysis of the pore space reveals an interplay between shrinkage due to drying and soil compaction due to compression. Macroporosity increases at moderate angular velocity because of crack formation due to moisture release. At higher angular velocities, corresponding to capillary pressure of ψ < -100 kPa, macroporosity decreases again because of structure deformation due to compression. While volume changes due to swelling clay minerals are immanent in any drying process, the compaction of soil is a specific drawback of the centrifugation method. A new protocol for digital volume correlation was developed to analyze the spatial heterogeneity of deformation. In both samples the displacement of soil constituents is highest in the top part of the sample and exhibits high lateral variability explained by the spatial distribution of macropores in the sample. Centrifugation should therefore only be applied after the completion of all other hydraulic or thermal experiments, or any other analysis that depends on the integrity of soil structure.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

PubMed

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2015-03-20

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

Effects of Cd and Pb on soil microbial community structure and activities.

PubMed

Khan, Sardar; Hesham, Abd El-Latif; Qiao, Min; Rehman, Shafiqur; He, Ji-Zheng

2010-02-01

Soil contamination with heavy metals occurs as a result of both anthropogenic and natural activities. Heavy metals could have long-term hazardous impacts on the health of soil ecosystems and adverse influences on soil biological processes. Soil enzymatic activities are recognized as sensors towards any natural and anthropogenic disturbance occurring in the soil ecosystem. Similarly, microbial biomass carbon (MBC) is also considered as one of the important soil biological activities frequently influenced by heavy metal contamination. The polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) has recently been used to investigate changes in soil microbial community composition in response to environmental stresses. Soil microbial community structure and activities are difficult to elucidate using single monitoring approach; therefore, for a better insight and complete depiction of the soil microbial situation, different approaches need to be used. This study was conducted in a greenhouse for a period of 12 weeks to evaluate the changes in indigenous microbial community structure and activities in the soil amended with different application rates of Cd, Pb, and Cd/Pb mix. In a field environment, soil is contaminated with single or mixed heavy metals; so that, in this research, we used the selected metals in both single and mixed forms at different application rates and investigated their toxic effects on microbial community structure and activities, using soil enzyme assays, plate counting, and advanced molecular DGGE technique. Soil microbial activities, including acid phosphatase (ACP), urease (URE), and MBC, and microbial community structure were studied. A soil sample (0-20 cm) with an unknown history of heavy metal contamination was collected and amended with Cd, Pb, and Cd/Pb mix using the CdSO(4) and Pb(NO(3))(2) solutions at different application rates. The amended soils were incubated in the greenhouse at 25 +/- 4 degrees C and 60% water-holding capacity for 12 weeks. During the incubation period, samples were collected from each pot at 0, 2, 9, and 12 weeks for enzyme assays, MBC, numeration of microbes, and DNA extraction. Fumigation-extraction method was used to measure the MBC, while plate counting techniques were used to numerate viable heterotrophic bacteria, fungi, and actinomycetes. Soil DNAs were extracted from the samples and used for DGGE analysis. ACP, URE, and MBC activities of microbial community were significantly lower (p < 0.05) in the metal-amended samples than those in the control. The enzyme inhibition extent was obvious between different incubation periods and varied as the incubation proceeded, and the highest rate was detected in the samples after 2 weeks. However, the lowest values of ACP and URE activities (35.6% and 36.6% of the control, respectively) were found in the Cd(3)/Pb(3)-treated sample after 2 weeks. Similarly, MBC was strongly decreased in both Cd/Pb-amended samples and highest reduction (52.4%) was detected for Cd(3)/Pb(3) treatment. The number of bacteria and actinomycetes were significantly decreased in the heavy metal-amended samples compared to the control, while fungal cells were not significantly different (from 2.3% to 23.87%). In this study, the DGGE profile indicated that the high dose of metal amendment caused a greater change in the number of bands. DGGE banding patterns confirmed that the addition of metals had a significant impact on microbial community structure. In soil ecosystem, heavy metals exhibit toxicological effects on soil microbes which may lead to the decrease of their numbers and activities. This study demonstrated that toxicological effects of heavy metals on soil microbial community structure and activities depend largely on the type and concentration of metal and incubation time. The inhibition extent varied widely among different incubation periods for these enzymes. Furthermore, the rapid inhibition in microbial activities such as ACP, URE, and MBC were observed in the 2 weeks, which should be related to the fact that the microbes were suddenly exposed to heavy metals. The increased inhibition of soil microbial activities is likely to be related to tolerance and adaptation of the microbial community, concentration of pollutants, and mechanisms of heavy metals. The DGGE profile has shown that the structure of the bacterial community changed in amended heavy metal samples. In this research, the microbial community structure was highly affected, consistent with the lower microbial activities in different levels of heavy metals. Furthermore, a great community change in this study, particularly at a high level of contamination, was probably a result of metal toxicity and also unavailability of nutrients because no nutrients were supplied during the whole incubation period. The added concentrations of heavy metals have changed the soil microbial community structure and activities. The highest inhibitory effects on soil microbial activities were observed at 2 weeks of incubation. The bacteria were more sensitive than actinomycetes and fungi. The DGGE profile indicated that bacterial community structure was changed in the Cd/Pb-amended samples, particularly at high concentrations. The investigation of soil microbial community structure and activities together could give more reliable and accurate information about the toxic effects of heavy metals on soil health.

Radon entry into basements: Approach, experimental structures, and instrumentation of the small structures research project

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

Fisk, W.J.; Modera, M.P.; Sextro, R.G.

1992-02-01

We describe the experimental approach, structures, and instrumentation of a research project on radon generation and transport in soil and entry into basements. The overall approach is to construct small precisely-fabricated basements in areas of different geology and climate, to control the pressures and ventilation rates in the structures, and to monitor radon concentrations and other relevant parameters over a period of one year or more. Two nearly air-tight structures have been constructed at the first site. The floor of each structure contains adjustable-width slots that serve as the only significant pathway for advective entry of radon. A layer ofmore » gravel underlays the floor of one structure; otherwise they are identical. The structures are instrumented for continuous or periodic monitoring of soil, structural, and meteorological parameters that affect radon entry. The pressure difference that drives advective radon entry can be maintained constant or varied over time. Soil gas and radon entry rates and associated parameters, such as soil gas pressures and radon concentrations, have been monitored for a range of steady-state and time-varying pressure differences between the interior of the structure and the soil. Examples of the experimentally-measured pressure and permeability fields in the soil around a structure are presented and discussed.« less

Organic layer serves as a hotspot of microbial activity and abundance in Arctic tundra soils.

PubMed

Lee, Seung-Hoon; Jang, Inyoung; Chae, Namyi; Choi, Taejin; Kang, Hojeong

2013-02-01

Tundra ecosystem is of importance for its high accumulation of organic carbon and vulnerability to future climate change. Microorganisms play a key role in carbon dynamics of the tundra ecosystem by mineralizing organic carbon. We assessed both ecosystem process rates and community structure of Bacteria, Archaea, and Fungi in different soil layers (surface organic layer and subsurface mineral soil) in an Arctic soil ecosystem located at Spitsbergen, Svalbard during the summer of 2008 by using biochemical and molecular analyses, such as enzymatic assay, terminal restriction fragment length polymorphism (T-RFLP), quantitative polymerase chain reaction (qPCR), and pyrosequencing. Activity of hydrolytic enzymes showed difference according to soil type. For all three microbial communities, the average gene copy number did not significantly differ between soil types. However, archaeal diversities appeared to differ according to soil type, whereas bacterial and fungal diversity indices did not show any variation. Correlation analysis between biogeochemical and microbial parameters exhibited a discriminating pattern according to microbial or soil types. Analysis of the microbial community structure showed that bacterial and archaeal communities have different profiles with unique phylotypes in terms of soil types. Water content and hydrolytic enzymes were found to be related with the structure of bacterial and archaeal communities, whereas soil organic matter (SOM) and total organic carbon (TOC) were related with bacterial communities. The overall results of this study indicate that microbial enzyme activity were generally higher in the organic layer than in mineral soils and that bacterial and archaeal communities differed between the organic layer and mineral soils in the Arctic region. Compared to mineral soil, peat-covered organic layer may represent a hotspot for secondary productivity and nutrient cycling in this ecosystem.

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships.

PubMed

Zhao, Jun; Zhou, Xing; Jiang, Anqi; Fan, Juanzi; Lan, Tao; Zhang, Jinbo; Cai, Zucong

2018-06-21

Soil disinfestation is an important agricultural practice to conquer soil-borne diseases and thereby ensure crop productivity. Reductive soil disinfestation (RSD) had been developed as an environmentally friendly alternative to chemical soil disinfestation (CSD). However, the differences between CSD and RSD on soil-borne pathogen suppression and fungal community structure remain poorly understood. In this work, five treatments, i.e., untreated soil (CK), CSD with 0.5 t ha -1 dazomet (DZ), RSD with 10 t ha -1 ethanol (ET), 15 t ha -1 sugarcane bagasse (SB), and 15 t ha -1 bean dregs (BD), were performed to investigate their influences on disinfestation efficiency, fungal abundance, diversity, and community structure via quantitative PCR and high-throughput sequencing. RSD-related treatments, especially the BD treatment, effectively alleviated soil acidification and salinization. The fungal abundance and microbial activity considerably increased in the BD treatment and significantly declined in the DZ treatment as compared to the CK treatment. Moreover, both CSD and RSD-related treatments significantly inhibited the population of Fusarium oxysporum and the relative abundance of genus Fusarium. Fungal community structure was notably altered by CSD and RSD practices. Furthermore, both CSD and RSD harbored a distinct unique microbiome, with the DZ treatment dominated by the genus Mortierella and BD treatment predominated by the genera Zopfiella, Chaetomium, and Penicillium. Taken together, these results indicate that the BD treatment could considerably alleviate the soil deterioration, improve soil microbial activity, and reassemble a non-pathogen unique microbiome that have more disease-suppressive agents and thus might be a promising disinfestation practice to control soil-borne disease in monoculture system.

Contrasting elevational diversity patterns for soil bacteria between two ecosystems divided by the treeline.

PubMed

Li, Guixiang; Xu, Guorui; Shen, Congcong; Tang, Yong; Zhang, Yuxin; Ma, Keming

2016-11-01

Above- and below-ground organisms are closely linked, but how elevational distribution pattern of soil microbes shifting across the treeline still remains unknown. Sampling of 140 plots with transect, we herein investigated soil bacterial distribution pattern from a temperate forest up to a subalpine meadow along an elevational gradient using Illumina sequencing. Our results revealed distinct elevational patterns of bacterial diversity above and below the treeline in responding to changes in soil conditions: a hollow elevational pattern in the forest (correlated with soil temperature, pH, and C:N ratio) and a significantly decreasing pattern in the meadow (correlated with soil pH, and available phosphorus). The bacterial community structure was also distinct between the forest and meadow, relating to soil pH in the forest and soil temperature in the meadow. Soil bacteria did not follow the distribution pattern of herb diversity, but bacterial community structure could be predicted by herb community composition. These results suggest that plant communities have an important influence on soil characteristics, and thus change the elevational distribution of soil bacteria. Our findings are useful for future assessments of climate change impacts on microbial community.

Fungal community composition in soils subjected to long-term chemical fertilization is most influenced by the type of organic matter.

PubMed

Sun, Ruibo; Dsouza, Melissa; Gilbert, Jack A; Guo, Xisheng; Wang, Daozhong; Guo, Zhibin; Ni, Yingying; Chu, Haiyan

2016-12-01

Organic matter application is a widely used practice to increase soil carbon content and maintain soil fertility. However, little is known about the effect of different types of organic matter, or the input of exogenous species from these materials, on soil fungal communities. In this study, fungal community composition was characterized from soils amended with three types of organic matter over a 30-year fertilization experiment. Chemical fertilization significantly changed soil fungal community composition and structure, which was exacerbated by the addition of organic matter, with the direction of change influenced by the type of organic matter used. The addition of organic matter significantly increased soil fungal richness, with the greatest richness achieved in soils amended with pig manure. Importantly, following addition of cow and pig manure, fungal taxa associated with these materials could be found in the soil, suggesting that these exogenous species can augment soil fungal composition. Moreover, the addition of organic matter decreased the relative abundance of potential pathogenic fungi. Overall, these results indicate that organic matter addition influences the composition and structure of soil fungal communities in predictable ways. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Rheological properties of soil: a review

NASA Astrophysics Data System (ADS)

Zhu, Guangli; Zhu, Long; Yu, Chao

2017-05-01

Recently rheological methods have been applied to investigate the mechanical properties of soil micro-structure. Rheological techniques have a number of quantitative physically based measurements and offer a better understanding of how soil micro-structure behaves when subject to stress. Rheological material is refers to deformation properties similar to the solid and flow properties similar to the liquid of bound water and colloidal substances under stress. Soil rheology is divided into fluid rheology and plasticity rheology. Fluid rheology is produced by rheological material. Plasticity rheology mainly refers to the sliding and peristaltic between soil solid particles under shear stress. It is generally believed that the soft soil rheology mainly belongs to fluid rheology, while the rheology of sand and other coarse grained soil mainly belongs to plasticity rheology. Thus, rheology mechanisms of soft soil and sand are different. This paper introduces the methods of the research progress on the rheology of soil, in the soil rheological mechanism, rheological model and rheological numerical aspects of the research at home and abroad were summarized and analysed, discussed the problems existed in related research, and puts forward some suggestions for the future study on the rheology of soil.

Differences between bacterial communities in the gut of a soil-feeding termite (Cubitermes niokoloensis) and its mounds.

PubMed

Fall, Saliou; Hamelin, Jérôme; Ndiaye, Farma; Assigbetse, Komi; Aragno, Michel; Chotte, Jean Luc; Brauman, Alain

2007-08-01

In tropical ecosystems, termite mound soils constitute an important soil compartment covering around 10% of African soils. Previous studies have shown (S. Fall, S. Nazaret, J. L. Chotte, and A. Brauman, Microb. Ecol. 28:191-199, 2004) that the bacterial genetic structure of the mounds of soil-feeding termites (Cubitermes niokoloensis) is different from that of their surrounding soil. The aim of this study was to characterize the specificity of bacterial communities within mounds with respect to the digestive and soil origins of the mound. We have compared the bacterial community structures of a termite mound, termite gut sections, and surrounding soil using PCR-denaturing gradient gel electrophoresis (DGGE) analysis and cloning and sequencing of PCR-amplified 16S rRNA gene fragments. DGGE analysis revealed a drastic difference between the genetic structures of the bacterial communities of the termite gut and the mound. Analysis of 266 clones, including 54 from excised bands, revealed a high level of diversity in each biota investigated. The soil-feeding termite mound was dominated by the Actinobacteria phylum, whereas the Firmicutes and Proteobacteria phyla dominate the gut sections of termites and the surrounding soil, respectively. Phylogenetic analyses revealed a distinct clustering of Actinobacteria phylotypes between the mound and the surrounding soil. The Actinobacteria clones of the termite mound were diverse, distributed among 10 distinct families, and like those in the termite gut environment lightly dominated by the Nocardioidaceae family. Our findings confirmed that the soil-feeding termite mound (C. niokoloensis) represents a specific bacterial habitat in the tropics.

Properties of Soil Pore Space Regulate Pathways of Plant Residue Decomposition and Community Structure of Associated Bacteria

PubMed Central

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; Marsh, Terence L.; Hildebrandt, Britton; Rivers, Mark L.

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes. PMID:25909444

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

DOE PAGES

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.; ...

2015-07-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Fractal Feature of Particle-Size Distribution in the Rhizospheres and Bulk Soils during Natural Recovery on the Loess Plateau, China

PubMed Central

Song, Zilin; Zhang, Chao; Liu, Guobin; Qu, Dong; Xue, Sha

2015-01-01

The application of fractal geometry to describe soil structure is an increasingly useful tool for better understanding the performance of soil systems. Only a few studies, however, have focused on the structure of rhizospheric zones, where energy flow and nutrient recycling most frequently occur. We used fractal dimensions to investigate the characteristics of particle-size distribution (PSD) in the rhizospheres and bulk soils of six croplands abandoned for 1, 5, 10, 15, 20, and 30 years on the Loess Plateau of China and evaluated the changes over successional time. The PSDs of the rhizospheres and the fractal dimensions between rhizosphere soil and bulk soils during the natural succession differed significantly due to the influence of plant roots. The rhizospheres had higher sand (0.05–1.00 mm) contents, lower silt (<0.002 mm) contents, and lower fractal dimensions than the bulk soils during the early and intermediate successional stages (1–15 years). The fractal dimensions of the rhizosphere soil and bulk soil ranged from 2.102 to 2.441 and from 2.214 to 2.459, respectively, during the 30-year restoration. Rhizospheric clay and silt contents and fractal dimension tended to be higher and sand content tended to be lower as abandonment age increased, but the bulk soils had the opposite trend. Linear regression analysis indicated that the fractal dimensions of both the rhizospheres and bulk soils were significantly linearly correlated with clay, sand, organic-carbon, and total-nitrogen contents, with R 2 ranging from 0.526 to 0.752 (P<0.001). In conclusion, PSD differed significantly between the rhizosphere soil and bulk soil. The fractal dimension was a sensitive and useful index for quantifying changes in the properties of the different soil zones. This study will greatly aid the application of the fractal method for describing soil structure and nutrient status and the understanding of the performance of rhizospheric zones during ecological restoration. PMID:26368339

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria.

PubMed

Negassa, Wakene C; Guber, Andrey K; Kravchenko, Alexandra N; Marsh, Terence L; Hildebrandt, Britton; Rivers, Mark L

2015-01-01

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S-18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75-80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g(-1) soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g(-1) soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.

Properties of soil pore space regulate pathways of plant residue decomposition and community structure of associated bacteria

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

Negassa, Wakene C.; Guber, Andrey K.; Kravchenko, Alexandra N.

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO₂ emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis ofmore » amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO₂ emission constituted 1,200 µm C g⁻¹ soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO₂ emission constituted 2,000 µm C g⁻¹ soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO₂ emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes.« less

Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.

PubMed

Song, He; Che, Zhao; Cao, Wenchao; Huang, Ting; Wang, Jingguo; Dong, Zhaorong

2016-06-01

Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.

Chitin amendment increases soil suppressiveness toward plant pathogens and modulates the actinobacterial and oxalobacteraceal communities in an experimental agricultural field.

PubMed

Cretoiu, Mariana Silvia; Korthals, Gerard W; Visser, Johnny H M; van Elsas, Jan Dirk

2013-09-01

A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment.

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.

Chitin Amendment Increases Soil Suppressiveness toward Plant Pathogens and Modulates the Actinobacterial and Oxalobacteraceal Communities in an Experimental Agricultural Field

PubMed Central

Cretoiu, Mariana Silvia; Korthals, Gerard W.; Visser, Johnny H. M.

2013-01-01

A long-term experiment on the effect of chitin addition to soil on the suppression of soilborne pathogens was set up and monitored for 8 years in an experimental field, Vredepeel, The Netherlands. Chitinous matter obtained from shrimps was added to soil top layers on two different occasions, and the suppressiveness of soil toward Verticillium dahliae, as well as plant-pathogenic nematodes, was assessed, in addition to analyses of the abundances and community structures of members of the soil microbiota. The data revealed that chitin amendment had raised the suppressiveness of soil, in particular toward Verticillium dahliae, 9 months after the (second) treatment, extending to 2 years following treatment. Moreover, major effects of the added chitin on the soil microbial communities were detected. First, shifts in both the abundances and structures of the chitin-treated soil microbial communities, both of total soil bacteria and fungi, were found. In addition, the abundances and structures of soil actinobacteria and the Oxalobacteraceae were affected by chitin. At the functional gene level, the abundance of specific (family-18 glycoside hydrolase) chitinase genes carried by the soil bacteria also revealed upshifts as a result of the added chitin. The effects of chitin noted for the Oxalobacteraceae were specifically related to significant upshifts in the abundances of the species Duganella violaceinigra and Massilia plicata. These effects of chitin persisted over the time of the experiment. PMID:23811512

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community.

PubMed

Wang, Yi; Li, Chunyue; Tu, Cong; Hoyt, Greg D; DeForest, Jared L; Hu, Shuijin

2017-12-31

Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. Copyright © 2017 Elsevier B.V. All rights reserved.

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

PubMed

Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

2015-01-01

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions. © 2014 John Wiley & Sons Ltd.

The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem.

PubMed

Lee, Seung-Hoon; Kang, Hojeong

2016-02-01

The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain niche role according to biogeochemical factors, the study of the microbial community even in surface soil should be performed in detail by considering the soil depth.

Accuracy of quantitative visual soil assessment

NASA Astrophysics Data System (ADS)

van Leeuwen, Maricke; Heuvelink, Gerard; Stoorvogel, Jetse; Wallinga, Jakob; de Boer, Imke; van Dam, Jos; van Essen, Everhard; Moolenaar, Simon; Verhoeven, Frank; Stoof, Cathelijne

2016-04-01

Visual soil assessment (VSA) is a method to assess soil quality visually, when standing in the field. VSA is increasingly used by farmers, farm organisations and companies, because it is rapid and cost-effective, and because looking at soil provides understanding about soil functioning. Often VSA is regarded as subjective, so there is a need to verify VSA. Also, many VSAs have not been fine-tuned for contrasting soil types. This could lead to wrong interpretation of soil quality and soil functioning when contrasting sites are compared to each other. We wanted to assess accuracy of VSA, while taking into account soil type. The first objective was to test whether quantitative visual field observations, which form the basis in many VSAs, could be validated with standardized field or laboratory measurements. The second objective was to assess whether quantitative visual field observations are reproducible, when used by observers with contrasting backgrounds. For the validation study, we made quantitative visual observations at 26 cattle farms. Farms were located at sand, clay and peat soils in the North Friesian Woodlands, the Netherlands. Quantitative visual observations evaluated were grass cover, number of biopores, number of roots, soil colour, soil structure, number of earthworms, number of gley mottles and soil compaction. Linear regression analysis showed that four out of eight quantitative visual observations could be well validated with standardized field or laboratory measurements. The following quantitative visual observations correlated well with standardized field or laboratory measurements: grass cover with classified images of surface cover; number of roots with root dry weight; amount of large structure elements with mean weight diameter; and soil colour with soil organic matter content. Correlation coefficients were greater than 0.3, from which half of the correlations were significant. For the reproducibility study, a group of 9 soil scientists and 7 farmers carried out quantitative visual observations all independently from each other. All observers assessed five sites, having a sand, peat or clay soil. For almost all quantitative visual observations the spread of observed values was low (coefficient of variation < 1.0), except for the number of biopores and gley mottles. Furthermore, farmers' observed mean values were significantly higher than soil scientists' mean values, for soil structure, amount of gley mottles and compaction. This study showed that VSA could be a valuable tool to assess soil quality. Subjectivity, due to the background of the observer, might influence the outcome of visual assessment of some soil properties. In countries where soil analyses can easily be carried out, VSA might be a good replenishment to available soil chemical analyses, and in countries where it is not feasible to carry out soil analyses, VSA might be a good start to assess soil quality.

Simulating root-induced rhizosphere deformation and its effect on water flow

NASA Astrophysics Data System (ADS)

Aravena, J. E.; Ruiz, S.; Mandava, A.; Regentova, E. E.; Ghezzehei, T.; Berli, M.; Tyler, S. W.

2011-12-01

Soil structure in the rhizosphere is influenced by root activities, such as mucilage production, microbial activity and root growth. Root growth alters soil structure by moving and deforming soil aggregates, affecting water and nutrient flow from the bulk soil to the root surface. In this study, we utilized synchrotron X-ray micro-tomography (XMT) and finite element analysis to quantify the effect of root-induced compaction on water flow through the rhizosphere to the root surface. In a first step, finite element meshes of structured soil around the root were created by processing rhizosphere XMT images. Then, soil deformation by root expansion was simulated using COMSOL Multiphysics° (Version 4.2) considering the soil an elasto-plastic porous material. Finally, fluid flow simulations were carried out on the deformed mesh to quantify the effect of root-induced compaction on water flow to the root surface. We found a 31% increase in water flow from the bulk soil to the root due to a 56% increase in root diameter. Simulations also show that the increase of root-soil contact area was the dominating factor with respect to the calculated increase in water flow. Increase of inter-aggregate contacts in size and number were observed within a couple of root diameters away from the root surface. But their influence on water flow was, in this case, rather limited compared to the immediate soil-root contact.

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

PubMed

van Wyk, Deidré A B; Adeleke, Rasheed; Rhode, Owen H J; Bezuidenhout, Carlos C; Mienie, Charlotte

2017-09-01

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nonlinear Time Domain Seismic Soil-Structure Interaction (SSI) Deep Soil Site Methodology Development

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

Spears, Robert Edward; Coleman, Justin Leigh

Currently the Department of Energy (DOE) and the nuclear industry perform seismic soil-structure interaction (SSI) analysis using equivalent linear numerical analysis tools. For lower levels of ground motion, these tools should produce reasonable in-structure response values for evaluation of existing and new facilities. For larger levels of ground motion these tools likely overestimate the in-structure response (and therefore structural demand) since they do not consider geometric nonlinearities (such as gaping and sliding between the soil and structure) and are limited in the ability to model nonlinear soil behavior. The current equivalent linear SSI (SASSI) analysis approach either joins the soilmore » and structure together in both tension and compression or releases the soil from the structure for both tension and compression. It also makes linear approximations for material nonlinearities and generalizes energy absorption with viscous damping. This produces the potential for inaccurately establishing where the structural concerns exist and/or inaccurately establishing the amplitude of the in-structure responses. Seismic hazard curves at nuclear facilities have continued to increase over the years as more information has been developed on seismic sources (i.e. faults), additional information gathered on seismic events, and additional research performed to determine local site effects. Seismic hazard curves are used to develop design basis earthquakes (DBE) that are used to evaluate nuclear facility response. As the seismic hazard curves increase, the input ground motions (DBE’s) used to numerically evaluation nuclear facility response increase causing larger in-structure response. As ground motions increase so does the importance of including nonlinear effects in numerical SSI models. To include material nonlinearity in the soil and geometric nonlinearity using contact (gaping and sliding) it is necessary to develop a nonlinear time domain methodology. This methodology will be known as, NonLinear Soil-Structure Interaction (NLSSI). In general NLSSI analysis should provide a more accurate representation of the seismic demands on nuclear facilities their systems and components. INL, in collaboration with a Nuclear Power Plant Vender (NPP-V), will develop a generic Nuclear Power Plant (NPP) structural design to be used in development of the methodology and for comparison with SASSI. This generic NPP design has been evaluated for the INL soil site because of the ease of access and quality of the site specific data. It is now being evaluated for a second site at Vogtle which is located approximately 15 miles East-Northeast of Waynesboro, Georgia and adjacent to Savanna River. The Vogtle site consists of many soil layers spanning down to a depth of 1058 feet. The reason that two soil sites are chosen is to demonstrate the methodology across multiple soil sites. The project will drive the models (soil and structure) using successively increasing acceleration time histories with amplitudes. The models will be run in time domain codes such as ABAQUS, LS-DYNA, and/or ESSI and compared with the same models run in SASSI. The project is focused on developing and documenting a method for performing time domain, non-linear seismic soil structure interaction (SSI) analysis. Development of this method will provide the Department of Energy (DOE) and industry with another tool to perform seismic SSI analysis.« less

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses

PubMed Central

Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures. PMID:28346463

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses.

PubMed

Li, Tianzhu; Liu, Tongtong; Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving the problems of greenhouse eggplant monocultures.

Land use and hydromechanical heterogeneities in marshland soils.

NASA Astrophysics Data System (ADS)

Tojo Radimy, Raymond; Dupont, Jean-Paul; Dudoignon, Patrick

2017-04-01

In the interpretation of soil moisture profiles, mechanical properties were most often considered homogeneous. The structural heterogeneities of the soil are knows to be at the origin of the distribution and the availability of water in the vadose zone. The soils study is located in the French Atlantic coastal marshlands, characterized by the succession polderization/desiccation/consolidation and maturation. The work is carried out within the framework of the farming of old salt marshes with two concerns in the farmers: the salinity of the soil and the distribution of the available water capacity of the soils according to the crop growth. The present work shows the knowledge of the soil storage transfers during seasonal cycles on drained corn field and undrained grassland. We analyze the vertical water profiles observed to reveal the hydromechanical heterogeneities in the soils depending the porosity and gravity water parameter. This approach is based on mechanical tests between the compaction pathways carried out in the laboratory using materials taken in situ. Comparing to grasslands profiles, we highlight the influence of agricultural practices and the establishment of drainage in the marshland. However, the vertical homogenization of hydromechanical structures, desalination has been taken into account for the estimation of water in crop. The concept of a homogeneous structure is not adapted to real vertical profile. Finally, the authors conclude by discussing the notion of the mechanical availability of water in terms of porosity and gravity water. These parameters are good tools to the sustainable management of marshland soils. Keywords: hydromechanics, vadose zone, soil structure, land use, available water capacity

Environmental Factors Shaping the Community Structure of Ammonia-Oxidizing Bacteria and Archaea in Sugarcane Field Soil

PubMed Central

Tago, Kanako; Okubo, Takashi; Shimomura, Yumi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Nagayama, Atsushi; Hayatsu, Masahito

2015-01-01

The effects of environmental factors such as pH and nutrient content on the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in soil has been extensively studied using experimental fields. However, how these environmental factors intricately influence the community structure of AOB and AOA in soil from farmers’ fields is unclear. In the present study, the abundance and diversity of AOB and AOA in soils collected from farmers’ sugarcane fields were investigated using quantitative PCR and barcoded pyrosequencing targeting the ammonia monooxygenase alpha subunit (amoA) gene. The abundances of AOB and AOA amoA genes were estimated to be in the range of 1.8 × 105–9.2 × 106 and 1.7 × 106–5.3 × 107 gene copies g dry soil−1, respectively. The abundance of both AOB and AOA positively correlated with the potential nitrification rate. The dominant sequence reads of AOB and AOA were placed in Nitrosospira-related and Nitrososphaera-related clusters in all soils, respectively, which varied at the level of their sub-clusters in each soil. The relationship between these ammonia-oxidizing community structures and soil pH was shown to be significant by the Mantel test. The relative abundances of the OTU1 of Nitrosospira cluster 3 and Nitrososphaera subcluster 7.1 negatively correlated with soil pH. These results indicated that soil pH was the most important factor shaping the AOB and AOA community structures, and that certain subclusters of AOB and AOA adapted to and dominated the acidic soil of agricultural sugarcane fields. PMID:25736866

Divergent taxonomic and functional responses of microbial communities to field simulation of aeolian soil erosion and deposition.

PubMed

Ma, Xingyu; Zhao, Cancan; Gao, Ying; Liu, Bin; Wang, Tengxu; Yuan, Tong; Hale, Lauren; Nostrand, Joy D Van; Wan, Shiqiang; Zhou, Jizhong; Yang, Yunfeng

2017-08-01

Aeolian soil erosion and deposition have worldwide impacts on agriculture, air quality and public health. However, ecosystem responses to soil erosion and deposition remain largely unclear in regard to microorganisms, which are the crucial drivers of biogeochemical cycles. Using integrated metagenomics technologies, we analysed microbial communities subjected to simulated soil erosion and deposition in a semiarid grassland of Inner Mongolia, China. As expected, soil total organic carbon and plant coverage were decreased by soil erosion, and soil dissolved organic carbon (DOC) was increased by soil deposition, demonstrating that field simulation was reliable. Soil microbial communities were altered (p < .039) by both soil erosion and deposition, with dramatic increase in Cyanobacteria related to increased stability in soil aggregates. amyA genes encoding α-amylases were specifically increased (p = .01) by soil deposition and positively correlated (p = .02) to DOC, which likely explained changes in DOC. Surprisingly, most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or unaltered by both erosion and deposition, probably arising from acceleration of organic matter mineralization. These divergent responses support the necessity to include microbial components in evaluating ecological consequences. Furthermore, Mantel tests showed strong, significant correlations between soil nutrients and functional structure but not taxonomic structure, demonstrating close relevance of microbial function traits to nutrient cycling. © 2017 John Wiley & Sons Ltd.

Combining Sequential Extractions and X-ray Absorption Spectroscopy for Quantitative and Qualitative Zinc Speciation in Soil

NASA Astrophysics Data System (ADS)

Bauer, Tatiana; Minkina, Tatiana; Batukaev, Abdulmalik; Nevidomskaya, Dina; Burachevskaya, Marina; Tsitsuashvili, Viktoriya; Urazgildieva, Kamilya

2017-04-01

The combined use of X-ray absorption spectrometry and extractive fractionation is an effective approach for studying the interaction of metal ions with soil compounds and identifying the phases-carriers of metals in soil and their stable fixation. These studies were carried out using the technique of X-ray absorption spectroscopy and chemical extractive fractionation. In a model experiment the samples taken in Calcic Chernozem were artificially contaminated with higher portion of Zn(NO3)2 (2000 mg/kg). The metal were incubated in soil samples for 2 year. The samples of soil mineral and organic phases (calcite, kaolinite, bentonite, humic acids) were saturated with Zn2+ from a solution of nitrate salts of metal. The total content of Zn in soil and soil various phases was determined using the X-ray fluorescence method. Extended X-ray absorption fine structure (EXAFS) Zn was measured at the Structural Materials Science beamline of the Kurchatov Center for Synchrotron Radiation. Sequential fractionation of Zn in soil conducted by Tessier method (Tessier et al., 1979) which determining 5 fractions of metals in soil: exchangeable, bound to Fe-Mn oxide, bound to carbonate, bound to the organic matter, and bound to silicate (residual). This methodology has so far more than 4000 citations (Web of Science), which demonstrates the popularity of this approach. Much Zn compounds are contained in uncontaminated soils in stable primary and secondary silicates inherited from the parental rocks (67% of the total concentrations in all fractions), which is a regional trait of soils in the fore-Caucasian plain. Extracted fractionation of metal compounds in soil samples, artificially contaminated with Zn salts, indicates the priority holding of Zn2+ ions by silicates, carbonates and Fe-Mn oxides. The Zn content significantly increases in the exchangeable fraction. Atomic structure study of the soil various phases saturated with Zn2+ ion by using (XANES) X-ray absorption spectroscopy allowed the determination of mechanism of metal ions interaction with soil phases and the resulting types of chemical bonds. Interaction with soil components modifies the electron structure of the metal ions themselves. The soil contamination with Zn is accompanied by decreasing the stable connection between metal and soil components. Interacting with humic acids in chernozem, the Zn2+ ion is coordinated by functional groups and ligands and forms unstable outer-sphere complexes. Zinc included into octahedral structures of layered minerals and hydro(oxides) can be inner-and outer-sphere adsorbed. The Zn2+ ions enable to replace Ca2+ ions in octahedral positions being coordinated with carbonate ions as ligands, thus forming absorbed complexes at the surface of mineral calcite. This work was supported by grant of the Russian Scientific Foundation № 16-14-10217.

Soil structural stability assessment with the fluidized bed, aggregate stability, and rainfall simulation on long-term tillage and crop rotation systems

USDA-ARS?s Scientific Manuscript database

The formation of stable soil aggregates is an important indicator of soil susceptibility to erosion and a factor defining soil health. On cropland, tillage practices and crop rotations have shown to control soil biophysical properties with potential consequences on erosion susceptibility. Thus, the ...

The importance of humin in soil characterisation: A study on Amazonian soils using different fluorescence techniques.

PubMed

Tadini, Amanda Maria; Nicolodelli, Gustavo; Mounier, Stephane; Montes, Célia Regina; Milori, Débora Marcondes Bastos Pereira

2015-12-15

Soil organic matter (SOM) is a complex mixture of molecules with different physicochemical properties, with humic substances (HS) being the main component as it represents around 20-50% of SOM structure. Soil of the Amazon region is considered one of the larger carbon pools of the world; thus, studies of the humic fractions are important for understanding the dynamics of organic matter (OM) in these soils. The aim of this study was to use laser-induced fluorescence spectroscopy (LIFS) and a combination of excitation-emission matrix (EEM) fluorescence with Parallel Factor Analysis (CP/PARAFAC) to assess the characteristics of humin (HU) extracted from Amazonian soils. The results obtained using LIFS showed that there was an increasing gradient of humification degree with depth, the deeper horizon presenting a higher amount of aromatic groups in the structure of HU. From the EEM, the contribution of two fluorophores with similar behaviour in the structures of HU and whole soil was assessed. Additionally, the results showed that the HU fraction might represent a larger fraction of SOM than previously thought: about 80-93% of some Amazon soils. Therefore, HU is an important humic fraction, thus indicating its role in environmental analysis, mainly in soil analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Visualizing Rhizosphere Soil Structure Around Living Roots

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2008-12-01

The rhizosphere, a thin layer of soil (0 to 2 mm) surrounding a living root, is an important interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 ìm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

Seismic behavior of breakwaters on complex ground by numerical tests: Liquefaction and post liquefaction ground settlements

NASA Astrophysics Data System (ADS)

Gu, Linlin; Zhang, Feng; Bao, Xiaohua; Shi, Zhenming; Ye, Guanlin; Ling, Xianzhang

2018-04-01

A large number of breakwaters have been constructed along coasts to protect humans and infrastructures from tsunamis. There is a risk that foundation soils of these structures may liquefy, or partially liquefy during the earthquake preceding a tsunami, which would greatly reduce the structures' capacity to resist the tsunami. It is necessary to consider not only the soil's liquefaction behavior due to earthquake motions but also its post-liquefaction behavior because this behavior will affect the breakwater's capacity to resist an incoming tsunami. In this study, numerical tests based on a sophisticated constitutive model and a soil-water coupled finite element method are used to predict the mechanical behavior of breakwaters and the surrounding soils. Two real breakwaters subjected to two different seismic excitations are examined through numerical simulation. The simulation results show that, earthquakes affect not only the immediate behavior of breakwaters and the surrounding soils but also their long-term settlements due to post-earthquake consolidation. A soil profile with thick clayey layers beneath liquefied soil is more vulnerable to tsunami than a soil profile with only sandy layers. Therefore, quantitatively evaluating the seismic behavior of breakwaters and surrounding soils is important for the design of breakwater structures to resist tsunamis.

Rhizospheric effects on the microbial community of e-waste-contaminated soils using phospholipid fatty acid and isoprenoid glycerol dialkyl glycerol tetraether analyses.

PubMed

Song, Mengke; Cheng, Zhineng; Luo, Chunling; Jiang, Longfei; Zhang, Dayi; Yin, Hua; Zhang, Gan

2018-04-01

We performed the study of rhizospheric effects on soil microbial community structure, including bacteria, fungi, actinomycete, and archaea, at an electronic waste (e-waste) recycling site by analyzing the phospholipid fatty acid (PLFA) and isoprenoid glycerol dialkyl glycerol tetraether (GDGT) contents. By comparing PLFA and isoprenoid GDGT profiles of rhizospheric and surrounding bulk soils of 11 crop species, we observed distinct microbial community structures. The total PLFA concentration was significantly higher in rhizospheric soils than in non-rhizospheric soils, whereas no obvious difference was found in the total isoprenoid GDGT concentrations. The microbial community structure was also different, with higher ratios of fungal-to-bacterial PLFAs (F/B) and lower relative abundance of Gram-positive bacteria in rhizospheric soils. The extent of rhizospheric effects varied among plant species, and Colocasia esculenta L. had the greatest positive effects on the total microbial biomass. Dissolved organic carbon and pH were the main environmental factors affecting the microbial community represented by PLFAs, while the archaeal community was influenced by copper and zinc in all soils. These results offer a comprehensive view of rhizospheric effects on microbes in heavy metal and persistent organic pollutant co-contaminated soil, and provide fundamental knowledge regarding microbial ecology in e-waste-contaminated soils.

Demonstrations in Solute Transport Using Dyes: Part I. Procedures and Results.

ERIC Educational Resources Information Center

Butters, Greg; Bandaranayake, Wije

1993-01-01

Presents the general theory to explain chemical movement in soil. Describes classroom demonstrations with visually stimulating results that show the effects of soil structure, soil texture, soil pH, and soluble organic matter on that movement. (MDH)

Factors Affecting Soil Microbial Community Structure in Tomato Cropping Systems

USDA-ARS?s Scientific Manuscript database

Soil and rhizosphere microbial communities in agroecosystems may be affected by soil, climate, plant species, and management. We identified some of the most important factors controlling microbial biomass and community structure in an agroecosystem utilizing tomato plants with the following nine tre...

The Effect of Vegetation on Soil Water Infiltration and Retention Capacity by Improving Soil Physiochemical Property in Semi-arid Grassland

NASA Astrophysics Data System (ADS)

A, Y.; Wang, G.

2017-12-01

Water shortage is the main limiting factor for semi-arid grassland development. However, the grassland are gradually degraded represented by species conversion, biomass decrease and ecosystem structure simplification under the influence of human activity. Soil water characteristics such as moisture, infiltration and conductivity are critical variables affecting the interactions between soil parameters and vegetation. In this study, Cover, Height, Shannon-Wiener diversity index, Pielou evenness index and Richness index are served as indexes of vegetation productivity and community structure. And saturated hydraulic conductivity (Ks) and soil moisture content are served as indexes of soil water characters. The interaction between vegetation and soil water is investigated through other soil parameters, such as soil organic matter content at different vertical depths and in different degradation area (e.g., initial, transition and degraded plots). The results show that Ks significantly controlled by soil texture other than soil organic matter content. So the influence of vegetation on Ks through increasing soil organic content (SOM) might be slight. However, soil moisture content (SMC) appeared significantly positive relationship with SOM and silt content and negative relationship with sand content at all depth, significantly. This indicated that capacity of soil water storage was influenced both by soil texture and organic matter. In addition, the highest correlation coefficient of SMC was with SOM at the sub-surficial soil layer (20 40 cm). At the depth of 20 40 cm, the soil water content was relatively steady which slightly influenced by precipitation and evaporation. But it significantly influenced by soil organic matter content which related to vegetation. The correlation coefficient between SOM and SMC at topsoil layer (0 20 cm) was lowest (R2=0.36, p<0.01), which indicated the influence of vegetation on soil water content not only by soil organic matter content but also the other influential factors, such as the root water uptake, precipitation and evaporation.

Vibration control of a cluster of buildings through the Vibrating Barrier

NASA Astrophysics Data System (ADS)

Tombari, A.; Garcia Espinosa, M.; Alexander, N. A.; Cacciola, P.

2018-02-01

A novel device, called Vibrating Barrier (ViBa), that aims to reduce the vibrations of adjacent structures subjected to ground motion waves has been recently proposed. The ViBa is a structure buried in the soil and detached from surrounding buildings that is able to absorb a significant portion of the dynamic energy arising from the ground motion. The working principle exploits the dynamic interaction among vibrating structures due to the propagation of waves through the soil, namely the structure-soil-structure interaction. In this paper the efficiency of the ViBa is investigated to control the vibrations of a cluster of buildings. To this aim, a discrete model of structures-site interaction involving multiple buildings and the ViBa is developed where the effects of the soil on the structures, i.e. the soil-structure interaction (SSI), the structure-soil-structure interaction (SSSI) as well as the ViBa-soil-structures interaction are taken into account by means of linear elastic springs. Closed-form solutions are derived to design the ViBa in the case of harmonic excitation from the analysis of the discrete model. Advanced finite element numerical simulations are performed in order to assess the efficiency of the ViBa for protecting more than a single building. Parametric studies are also conducted to identify beneficial/adverse effects in the use of the proposed vibration control strategy to protect cluster of buildings. Finally, experimental shake table tests are performed to a prototype of a cluster of two buildings protected by the ViBa device for validating the proposed numerical models.

Relationship between gaseous N dynamics and the hydraulic state of hierarchically structured soils

NASA Astrophysics Data System (ADS)

Schlüter, Steffen; Dörsch, Peter; Vogel, Hans-Jörg

2017-04-01

The inherent spatial heterogeneity of soil generates spatially distributed micro-sites with different local N gas (NO, N2O, N2) production and release rates. Moreover, local micro-site conditions and the pathways between them depend on soil moisture which itself is highly dynamic close to the soil surface. These relationships need to be taken into account for a quantitative understanding of soil denitrification and associated N gas dynamics. Soil structure has been recognized as a key factor to understand the high spatial variability of N gas emissions. In particular gaseous N release from soils depends on: i) the total denitrification rate, which is related to the spatial extent and distribution of anaerobic sites and ii) the probability of N2O to escape from the soil without being further reduced to N2. This impact of soil structure is typically ignored in studies with soil slurries or repacked soil. In this project we run well-defined mesocosm experiments on N gas dynamics with hierarchically structured, artificial soils in which the spatial distribution of substrate and denitrifiers is known exactly. Sintered, porous glass pellets are inoculated with strains of Paracoccus denitrificans and/or Agrobacterium tumefaciens and amended with nutrient solution. These pellets are embedded in coarse-grained sand within gas-tight columns under O2/He atmosphere. The pellets are either places in layers or randomly to create different patterns of N gas production sites and diffusion pathways. Denitrification occurs in the anaerobic centers of the porous pellets, while the partially saturated sand matrix controls the diffusive transport of N gases towards the headspace, where all relevant gas concentrations are monitored with gas chromatography. Water saturations are adjusted such that the diffusive pathways are either fully continuous or partially discontinuous. Preliminary results indicate that the water content exert a major control on the magnitude of denitrification, whereas the onset and dynamics are mainly controlled by the position of the substrate and the denitrifiers.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

Soil Tillage Conservation and its Effect on Soil Properties Bioremediation and Sustained Production of Crops

NASA Astrophysics Data System (ADS)

Rusu, Teodor; Ioana Moraru, Paula; Muresan, Liliana; Andriuca, Valentina; Cojocaru, Olesea

2017-04-01

Soil Tillage Conservation (STC) is considered major components of agricultural technology for soil conservation strategies and part of Sustainable Agriculture (SA). Human action upon soil by tillage determines important morphological, physical-chemical and biological changes, with different intensities and evaluative directions. Nowadays, internationally is unanimous accepted the fact that global climatic changes are the results of human intervention in the bio-geo-chemical water and material cycle, and the sequestration of carbon in soil is considered an important intervention to limit these changes. STC involves reducing the number of tillage's (minimum tillage) to direct sowing (no-tillage) and plant debris remains at the soil surface in the ratio of at least 30%. Plant debris left on the soil surface or superficial incorporated contributes to increased biological activity and is an important source of carbon sequestration. STC restore soil structure and improve overall soil drainage, allowing more rapid infiltration of water into soil. The result is a soil bioremediation, more productive, better protected against wind and water erosion and requires less fuel for preparing the germinative bed. Carbon sequestration in soil is net advantageous, improving the productivity and sustainability. We present the influence of conventional plough tillage system on soil, water and organic matter conservation in comparison with an alternative minimum tillage (paraplow, chisel plow and rotary harrow) and no-tillage system. The application of STC increased the organic matter content 0.8 to 22.1% and water stabile aggregate content from 1.3 to 13.6%, in the 0-30 cm depth, as compared to the conventional system. For the organic matter content and the wet aggregate stability, the statistical analysis of the data showed, increasing positive significance of STC. While the soil fertility and the wet aggregate stability were initially low, the effect of conservation practices on the soil features resulted in a positive impact on the water permeability of the soil. Availability of soil moisture during the crop growth resulted in better plant water status. Subsequent release of conserved soil water regulated proper plant water status, soil structure, and lowered soil penetrometer resistance. Productions obtained at STC did not have significant differences for the wheat and maize crop but were higher for soybean. The advantages of minimum soil tillage systems for Romanian pedo-climatic conditions can be used to improve methods in low producing soils with reduced structural stability on sloped fields, as well as measures of water and soil conservation on the whole agroecosystem. Presently, it is necessary to make a change concerning the concept of conservation practices and to consider a new approach regarding the good agricultural practice. We need to focus on an upper level concerning conservation by focusing on soil quality. Carbon management is necessary for a complexity of matters including soil, water management, field productivity, biological fuel and climatic change. In conclusion a Sustainable Agriculture includes a range of complementary agricultural practices: (i) minimum soil tillage (through a system of reduced tillage or no-tillage) to preserve the structure, fauna and soil organic matter; (ii) permanent soil cover (cover crops, residues and mulches) to protect the soil and help to remove and control weeds; (iii) various combinations and rotations of the crops which stimulate the micro-organisms in the soil and controls pests, weeds and plant diseases. Acknowledgements: This paper was performed under the frame of the Partnership in priority domains - PNII, developed with the support of MEN-UEFISCDI, project no. PN-II-PT-PCCA-2013-4-0015: Expert System for Risk Monitoring in Agriculture and Adaptation of Conservative Agricultural Technologies to Climate Change, and International Cooperation Program - Sub-3.1. Bilateral AGROCEO c. no. 21BM/2016, PN-III-P3-3.1-PM-RO-MD-2016-0034: The comparative evaluation of conventional and conservative tillage systems regarding carbon sequestration and foundation of sustainable agroecosystems.

[Effect of ground mulch managements on soil bacterial community structure and diversity in the non-irrigated apple orchard in Weibei Loess Plateau].

PubMed

Chen, Yuexing; Wen, Xiaoxia; Sun, Yulin; Zhang, Junli; Lin, Xiaoli; Liao, Yuncheng

2015-07-04

We studied the changes in soil bacterial communities induced by ground mulch managements at different apple growth periods. We adopted the denaturing gradient gel electrophoresis (DGGE) with PCR-amplified 16S rRNA fragments to determine soil bacterial community structure and diversity. Soil bacterial community structure with different ground mulch managements were significantly different. Both the mulch management strategies and apple growth periods affected the predominant groups and their abundance in soil bacterial communities. Grass mulch and cornstalk mulch treatments had higher bacterial diversity and richness than the control at young fruit period and fruit expanding period, whereas film mulch treatment had no significant difference compared with the control. During mature period, bacterial diversity in the control reached its maximum, which may be ascribed to the rapid growth and reproduction of the r-selection bacteria. The clustering and detrended correspondence analysis revealed that differences in soil bacterial communities were closely correlated to apple growth periods and ground mulch managements. Soil samples from the grass mulch and cornstalk mulch treatments clustered together while those mulched with plastic film treatment were similar to the control. The most abundant phylum in soil bacterial community was Proteobacteria followed by Bacteroidetes. Some other phyla were also detected, such as Acidobacteria, Firmicutes, Actinobacteria and Chloroflexi. Mulching with plant (Grass/Cornstalk) had great effects on soil bacterial community structure and enhanced the diversity while film mulch management had no significant effects.

Effects of soil structure destruction on methane production and carbon partitioning between methanogenic pathways in tropical rain forest soils

NASA Astrophysics Data System (ADS)

Teh, Yit Arn; Silver, Whendee L.

2006-03-01

Controls on methanogenesis are often determined from laboratory incubations of soils converted to slurries. Destruction of soil structure during slurry conversion may disrupt syntrophic associations, kill methanogens, and/or alter the microsite distribution of methanogenic activity, suppressing CH4 production. The effects of slurry conversion on methanogenesis were investigated to determine if disruption of aggregate structure impacted methanogenesis, substrate utilization, and C partitioning between methanogenic pathways. Soils were collected from the tropical rain forest life zone of the Luquillo Experimental Forest, Puerto Rico, and exposed to different physical disturbances, including flooding and physical homogenization. Slurry conversion negatively impacted methanogenesis. Rates of CH4 production declined by a factor of 17 after well-aggregated soils were converted to slurries. Significantly more 13C-acetate was recovered in CO2 compared to CH4 after slurry conversion, suggesting that methanogens consumed less acetate after slurry conversion and may have competed less effectively with other anaerobes for acetate. Isotopic data indicate that the relative partitioning of C between aceticlastic and hydrogenotrophic pathways was unchanged after slurry conversion. These data suggest that experiments which destroy soil structure may significantly underestimate methanogenesis and overestimate the potential for other microorganisms to compete with methanogens for organic substrates. Current knowledge of the factors that regulate methanogenesis in soil may be biased by the findings of slurry-based experiments, that do not accurately represent the complex, spatially heterogeneous conditions found in well-aggregated soils.

Modelling and interpreting biologically crusted dryland soil sub-surface structure using automated micropenetrometry

NASA Astrophysics Data System (ADS)

Hoon, Stephen R.; Felde, Vincent J. M. N. L.; Drahorad, Sylvie L.; Felix-Henningsen, Peter

2015-04-01

Soil penetrometers are used routinely to determine the shear strength of soils and deformable sediments both at the surface and throughout a depth profile in disciplines as diverse as soil science, agriculture, geoengineering and alpine avalanche-safety (e.g. Grunwald et al. 2001, Van Herwijnen et al. 2009). Generically, penetrometers comprise two principal components: An advancing probe, and a transducer; the latter to measure the pressure or force required to cause the probe to penetrate or advance through the soil or sediment. The force transducer employed to determine the pressure can range, for example, from a simple mechanical spring gauge to an automatically data-logged electronic transducer. Automated computer control of the penetrometer step size and probe advance rate enables precise measurements to be made down to a resolution of 10's of microns, (e.g. the automated electronic micropenetrometer (EMP) described by Drahorad 2012). Here we discuss the determination, modelling and interpretation of biologically crusted dryland soil sub-surface structures using automated micropenetrometry. We outline a model enabling the interpretation of depth dependent penetration resistance (PR) profiles and their spatial differentials using the model equations, σ {}(z) ={}σ c0{}+Σ 1n[σ n{}(z){}+anz + bnz2] and dσ /dz = Σ 1n[dσ n(z) /dz{} {}+{}Frn(z)] where σ c0 and σ n are the plastic deformation stresses for the surface and nth soil structure (e.g. soil crust, layer, horizon or void) respectively, and Frn(z)dz is the frictional work done per unit volume by sliding the penetrometer rod an incremental distance, dz, through the nth layer. Both σ n(z) and Frn(z) are related to soil structure. They determine the form of σ {}(z){} measured by the EMP transducer. The model enables pores (regions of zero deformation stress) to be distinguished from changes in layer structure or probe friction. We have applied this method to both artificial calibration soils in the laboratory, and in-situ field studies. In particular, we discuss the nature and detection of surface and buried (fossil) subsurface Biological Soil Crusts (BSCs), voids, macroscopic particles and compositional layers. The strength of surface BSCs and the occurrence of buried BSCs and layers has been detected at sub millimetre scales to depths of 40mm. Our measurements and field observations of PR show the importance of morphological layering to overall BSC functions (Felde et al. 2015). We also discuss the effect of penetrometer shaft and probe-tip profiles upon the theoretical and experimental curves, EMP resolution and reproducibility, demonstrating how the model enables voids, buried biological soil crusts, exotic particles, soil horizons and layers to be distinguished one from another. This represents a potentially important contribution to advancing understanding of the relationship between BSCs and dryland soil structure. References: Drahorad SL, Felix-Henningsen P. (2012) An electronic micropenetrometer (EMP) for field measurements of biological soil crust stability, J. Plant Nutr. Soil Sci., 175, 519-520 Felde V.J.M.N.L., Drahorad S.L., Felix-Henningsen P., Hoon S.R. (2015) Ongoing oversanding induces biological soil crust layering - a new approach for BSC structure elucidation determined from high resolution penetration resistance data (submitted) Grunwald, S., Rooney D.J., McSweeney K., Lowery B. (2001) Development of pedotransfer functions for a profile cone penetrometer, Geoderma, 100, 25-47 Van Herwijnen A., Bellaire S., Schweizer J. (2009) Comparison of micro-structural snowpack parameters derived from penetration resistance measurements with fracture character observations from compression tests, Cold Regions Sci. {& Technol.}, 59, 193-201

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

DOE PAGES

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe; ...

2014-06-16

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Understanding Cultivar-Specificity and Soil Determinants of the Cannabis Microbiome

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

Winston, Max E.; Hampton-Marcell, Jarrad; Zarraonaindia, Iratxe

Understanding microbial partnerships with the medicinally and economically important crop Cannabis has the potential to affect agricultural practice by improving plant fitness and production yield. Furthermore, Cannabis presents an interesting model to explore plant-microbiome interactions as it produces numerous secondary metabolic compounds. Here we present the first description of the endorhiza-, rhizosphere-, and bulk soil-associated microbiome of five distinct Cannabis cultivars. Bacterial communities of the endorhiza showed significant cultivar-specificity. When controlling cultivar and soil type the microbial community structure was significantly different between plant cultivars, soil types, and between the endorhiza, rhizosphere and soil. In conclusion, the influence of soilmore » type, plant cultivar and sample type differentiation on the microbial community structure provides support for a previously published two-tier selection model, whereby community composition across sample types is determined mainly by soil type, while community structure within endorhiza samples is determined mainly by host cultivar.« less

Basin-wide variations in Amazon forest structure and function are mediated by both soils and climate

NASA Astrophysics Data System (ADS)

Quesada, C. A.; Phillips, O. L.; Schwarz, M.; Czimczik, C. I.; Baker, T. R.; Patiño, S.; Fyllas, N. M.; Hodnett, M. G.; Herrera, R.; Almeida, S.; Alvarez Dávila, E.; Arneth, A.; Arroyo, L.; Chao, K. J.; Dezzeo, N.; Erwin, T.; di Fiore, A.; Higuchi, N.; Honorio Coronado, E.; Jimenez, E. M.; Killeen, T.; Lezama, A. T.; Lloyd, G.; López-González, G.; Luizão, F. J.; Malhi, Y.; Monteagudo, A.; Neill, D. A.; Núñez Vargas, P.; Paiva, R.; Peacock, J.; Peñuela, M. C.; Peña Cruz, A.; Pitman, N.; Priante Filho, N.; Prieto, A.; Ramírez, H.; Rudas, A.; Salomão, R.; Santos, A. J. B.; Schmerler, J.; Silva, N.; Silveira, M.; Vásquez, R.; Vieira, I.; Terborgh, J.; Lloyd, J.

2012-06-01

Forest structure and dynamics vary across the Amazon Basin in an east-west gradient coincident with variations in soil fertility and geology. This has resulted in the hypothesis that soil fertility may play an important role in explaining Basin-wide variations in forest biomass, growth and stem turnover rates. Soil samples were collected in a total of 59 different forest plots across the Amazon Basin and analysed for exchangeable cations, carbon, nitrogen and pH, with several phosphorus fractions of likely different plant availability also quantified. Physical properties were additionally examined and an index of soil physical quality developed. Bivariate relationships of soil and climatic properties with above-ground wood productivity, stand-level tree turnover rates, above-ground wood biomass and wood density were first examined with multivariate regression models then applied. Both forms of analysis were undertaken with and without considerations regarding the underlying spatial structure of the dataset. Despite the presence of autocorrelated spatial structures complicating many analyses, forest structure and dynamics were found to be strongly and quantitatively related to edaphic as well as climatic conditions. Basin-wide differences in stand-level turnover rates are mostly influenced by soil physical properties with variations in rates of coarse wood production mostly related to soil phosphorus status. Total soil P was a better predictor of wood production rates than any of the fractionated organic- or inorganic-P pools. This suggests that it is not only the immediately available P forms, but probably the entire soil phosphorus pool that is interacting with forest growth on longer timescales. A role for soil potassium in modulating Amazon forest dynamics through its effects on stand-level wood density was also detected. Taking this into account, otherwise enigmatic variations in stand-level biomass across the Basin were then accounted for through the interacting effects of soil physical and chemical properties with climate. A hypothesis of self-maintaining forest dynamic feedback mechanisms initiated by edaphic conditions is proposed. It is further suggested that this is a major factor determining endogenous disturbance levels, species composition, and forest productivity across the Amazon Basin.

Changes in the Metagenome of Prokaryotic Community as an Indicator of Fertility of Arable Soddy-Podzolic Soils upon Fertilizer Application

NASA Astrophysics Data System (ADS)

Naliukhin, A. N.; Khamitova, S. M.; Glinushkin, A. P.; Avdeev, Yu. M.; Snetilova, V. S.; Laktionov, Yu. V.; Surov, V. V.; Siluyanova, O. V.; Belozerov, D. A.

2018-03-01

The influence of different systems of fertilization and liming on the changes in the taxonomic structure of prokaryotic community in arable soddy-podzolic soil (Albic Retisol (Loamic, Aric, Cutanic, Differentic, Ochric)) was studied in a stationary field experiment of Vologda State Dairy Farming Academy with the use of high-performance sequencing method of gene 16S rRNA. The 25-year-old fallow plot, in which the intensity of microbiological processes was close to that in the virgin soddy-podzolic soils, was used as a control. At the first stage, dominant phyla were identified: Proteobacteria (45.3-56.2%), Actinobacteria (13.6-20.4%), Bacteroidetes (7.2-19.3%), Acidobacteria (7.1-11.5%), and Verrucomicrobia (4.3-10.3%). Several groups of microorganisms-indicators, whose portion changes in the arable soil under the influence of liming, fertilizer application, and soil treatment in comparison with the control, were determined. The applied approach made it possible to relate the taxonomic structure of the soil microbial cenosis with external factors for assessing changes in the structure of soil microbial complex under the impact of different uses of the arable soil.

A soil-landscape framework for understanding spatial and temporal variability in biogeochemical processes in catchments

NASA Astrophysics Data System (ADS)

McGuire, K. J.; Bailey, S. W.; Ross, D. S.

2017-12-01

Heterogeneity in biophysical properties within catchments challenges how we quantify and characterize biogeochemical processes and interpret catchment outputs. Interactions between the spatiotemporal variability of hydrological states and fluxes and soil development can spatially structure catchments, leading to a framework for understanding patterns in biogeochemical processes. In an upland, glaciated landscape at the Hubbard Brook Experimental Forest (HBEF) in New Hampshire, USA, we are embracing the structure and organization of soils to understand the spatial relations between runoff production zones, distinct soil-biogeochemical environments, and solute retention and release. This presentation will use observations from the HBEF to demonstrate that a soil-landscape framework is essential in understanding the spatial and temporal variability of biogeochemical processes in this catchment. Specific examples will include how laterally developed soils reveal the location of active runoff production zones and lead to gradients in primary mineral dissolution and the distribution of weathering products along hillslopes. Soil development patterns also highlight potential carbon and nitrogen cycling hotspots, differentiate acidic conditions, and affect the regulation of surface water quality. Overall, this work demonstrates the importance of understanding the landscape-level structural organization of soils in characterizing the variation and extent of biogeochemical processes that occur in catchments.

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

[Community structure of soil fauna in Eucalyptus grandis plantations at different slope locations].

PubMed

Zhao, Yu; Zhong, Yu; Zhang, Jian; Yang, Wan-qin

2010-09-01

To understand the effects of slope location on the community structure of soil fauna in Eucalyptus grandis plantation, an investigation was made on the soil fauna in 3 E. grandis plantations at different slope locations in the hilly area of Sichuan Province from January to October 2009. A total of 39,2762 individuals were observed, belonging to 146 groups, 7 phyla, 16 classes, and 31 orders. The community composition, trophic group, diversity, and seasonal dynamics of soil fauna in the plantations all varied with slope. The abundance of macro-fauna, xeric meso- and micro-fauna, saprophagous macro-fauna, and omnivorous xeric meso- and micro-fauna increased with the decrease of slope, indicating that soil fauna had sensitive responses to the soil environmental factors affected by slope. Significant differences in the diversity of soil saprophagous macro-fauna and hygrophilous meso- and micro-fauna were observed at different slope locations, suggesting that these two faunal groups could be used as the indicators of the habitat heterogeneity of E. grandis plantations at different slope. Overall, slope location had definite effects on the community structure and distribution of soil fauna in the E. grandis plantations, but the effects were not statistically significant.

Coal mining activities change plant community structure due to air pollution and soil degradation.

PubMed

Pandey, Bhanu; Agrawal, Madhoolika; Singh, Siddharth

2014-10-01

The aim of this study was to investigate the effects of coal mining activities on the community structures of woody and herbaceous plants. The response of individual plants of community to defilement caused by coal mining was also assessed. Air monitoring, soil physico-chemical and phytosociological analyses were carried around Jharia coalfield (JCF) and Raniganj coalfield. The importance value index of sensitive species minified and those of tolerant species enhanced with increasing pollution load and altered soil quality around coal mining areas. Although the species richness of woody and herbaceous plants decreased with higher pollution load, a large number of species acclimatized to the stress caused by the coal mining activities. Woody plant community at JCF was more affected by coal mining than herbaceous community. Canonical correspondence analysis revealed that structure of herbaceous community was mainly driven by soil total organic carbon, soil nitrogen, whereas woody layer community was influenced by sulphur dioxide in ambient air, soil sulphate and soil phosphorus. The changes in species diversity observed at mining areas indicated an increase in the proportion of resistant herbs and grasses showing a tendency towards a definite selection strategy of ecosystem in response to air pollution and altered soil characteristics.

Resource seeking strategies of zoosporic true fungi in heterogeneous soil habitats at the microscale level

PubMed Central

Gleason, Frank H.; Crawford, John W.; Neuhauser, Sigrid; Henderson, Linda E.; Lilje, Osu

2012-01-01

Zoosporic true fungi have frequently been identified in samples from soil and freshwater ecosystems using baiting and molecular techniques. In fact some species can be components of the dominant groups of microorganisms in particular soil habitats. Yet these microorganisms have not yet been directly observed growing in soil ecosystems. Significant physical characteristics and features of the three-dimensional structures of soils which impact microorganisms at the microscale level are discussed. A thorough knowledge of soil structures is important for studying the distribution of assemblages of these fungi and understanding their ecological roles along spatial and temporal gradients. A number of specific adaptations and resource seeking strategies possibly give these fungi advantages over other groups of microorganisms in soil ecosystems. These include chemotactic zoospores, mechanisms for adhesion to substrates, rhizoids which can penetrate substrates in small spaces, structures which are resistant to environmental extremes, rapid growth rates and simple nutritional requirements. These adaptations are discussed in the context of the characteristics of soils ecosystems. Recent advances in instrumentation have led to the development of new and more precise methods for studying microorganisms in three-dimensional space. New molecular techniques have made identification of microbes possible in environmental samples. PMID:22308003

Water regime history drives responses of soil Namib Desert microbial communities to wetting events

NASA Astrophysics Data System (ADS)

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

2015-07-01

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

PubMed

Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A

2015-07-21

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

Environmental and management influences on temporal variability of near saturated soil hydraulic properties.

PubMed

Bodner, G; Scholl, P; Loiskandl, W; Kaul, H-P

2013-08-01

Structural porosity is a decisive property for soil productivity and soil environmental functions. Hydraulic properties in the structural range vary over time in response to management and environmental influences. Although this is widely recognized, there are few field studies that determine dominant driving forces underlying hydraulic property dynamics. During a three year field experiment we measured temporal variability of soil hydraulic properties by tension infiltrometry. Soil properties were characterized by hydraulic conductivity, effective macroporosity and Kosugi's lognormal pore size distribution model. Management related influences comprised three soil cover treatment (mustard and rye vs. fallow) and an initial mechanical soil disturbance with a rotary harrow. Environmental driving forces were derived from meteorological and soil moisture data. Soil hydraulic parameters varied over time by around one order of magnitude. The coefficient of variation of soil hydraulic conductivity K(h) decreased from 69.5% at saturation to 42.1% in the more unsaturated range (- 10 cm pressure head). A slight increase in the Kosugi parameter showing pore heterogeneity was observed under the rye cover crop, reflecting an enhanced structural porosity. The other hydraulic parameters were not significantly influenced by the soil cover treatments. Seedbed preparation with a rotary harrow resulted in a fourfold increase in macroporosity and hydraulic conductivity next to saturation, and homogenized the pore radius distribution. Re-consolidation after mechanical loosening lasted over 18 months until the soil returned to its initial state. The post-tillage trend of soil settlement could be approximated by an exponential decay function. Among environmental factors, wetting-drying cycles were identified as dominant driving force explaining short term hydraulic property changes within the season (r 2  = 0.43 to 0.59). Our results suggested that beside considering average management induced changes in soil properties (e.g. cover crop introduction), a dynamic approach to hydrological modeling is required to capture over-seasonal (tillage driven) and short term (environmental driven) variability in hydraulic parameters.

The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

NASA Astrophysics Data System (ADS)

Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

2011-12-01

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial communities, while the quality of available organic matter may have played a significant role in supporting high performing microbial communities.

Environmental and management influences on temporal variability of near saturated soil hydraulic properties☆

PubMed Central

Bodner, G.; Scholl, P.; Loiskandl, W.; Kaul, H.-P.

2013-01-01

Structural porosity is a decisive property for soil productivity and soil environmental functions. Hydraulic properties in the structural range vary over time in response to management and environmental influences. Although this is widely recognized, there are few field studies that determine dominant driving forces underlying hydraulic property dynamics. During a three year field experiment we measured temporal variability of soil hydraulic properties by tension infiltrometry. Soil properties were characterized by hydraulic conductivity, effective macroporosity and Kosugi's lognormal pore size distribution model. Management related influences comprised three soil cover treatment (mustard and rye vs. fallow) and an initial mechanical soil disturbance with a rotary harrow. Environmental driving forces were derived from meteorological and soil moisture data. Soil hydraulic parameters varied over time by around one order of magnitude. The coefficient of variation of soil hydraulic conductivity K(h) decreased from 69.5% at saturation to 42.1% in the more unsaturated range (− 10 cm pressure head). A slight increase in the Kosugi parameter showing pore heterogeneity was observed under the rye cover crop, reflecting an enhanced structural porosity. The other hydraulic parameters were not significantly influenced by the soil cover treatments. Seedbed preparation with a rotary harrow resulted in a fourfold increase in macroporosity and hydraulic conductivity next to saturation, and homogenized the pore radius distribution. Re-consolidation after mechanical loosening lasted over 18 months until the soil returned to its initial state. The post-tillage trend of soil settlement could be approximated by an exponential decay function. Among environmental factors, wetting-drying cycles were identified as dominant driving force explaining short term hydraulic property changes within the season (r2 = 0.43 to 0.59). Our results suggested that beside considering average management induced changes in soil properties (e.g. cover crop introduction), a dynamic approach to hydrological modeling is required to capture over-seasonal (tillage driven) and short term (environmental driven) variability in hydraulic parameters. PMID:24748683

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.

78 FR 13097 - Electric Power Research Institute; Seismic Evaluation Guidance

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-26

... outcrop motion for which the soil layers above the foundation elevation have been removed. Updating the... performing soil-structure interaction analyses. Consistent with guidance described in DC/COL-ISG-017, ``Ensuring Hazard-Consistent Seismic Input for Site Response and Soil Structure Interaction Analyses,'' the...

Carbendazim induces a temporary change in soil bacterial community structure.

PubMed

Wang, Xiuguo; Song, Min; Gao, Chunming; Dong, Bin; Zhang, Qun; Fang, Hua; Yu, Yunlong

2009-01-01

The effect of carbendazim applications on the diversity and structure of a soil bacterial community was studied under field conditions using temperature gradient gel electrophoresis (TGGE) and partial sequence analysis of PCR-amplified 16S rRNA gene. After four successive introductions of carbendazim at a level of 0.94 kg active ingredient (a.i.)/ha, the genetic diversity (expressed as Shannon index, H') decreased from 1.43 in the control to 1.29 in treated soil. This harmful effect seems to increase with the concentration of carbendazim. The value of H' in the soil treated with carbendazim at 4.70 kg a.i./ha was reduced to 1.05 (P < or = 0.05). The structure of soil bacterial community was also affected after four repeated applications of carbendazim at levels of 0.94, 1.88 and 4.70 kg a.i./ha, as seen in the relative intensities of the individual band. However, the bacterial community in carbendazim-treated soil recovered to that in the control 360 d after the first treatment. The results indicated that repeated applications of carbendazim could reduce soil microbial diversity and alter the bacterial community structure temporarily.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation.

PubMed

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-07-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant 'seed bank'.

Clay minerals and metal oxides strongly influence the structure of alkane-degrading microbial communities during soil maturation

PubMed Central

Steinbach, Annelie; Schulz, Stefanie; Giebler, Julia; Schulz, Stephan; Pronk, Geertje J; Kögel-Knabner, Ingrid; Harms, Hauke; Wick, Lukas Y; Schloter, Michael

2015-01-01

Clay minerals, charcoal and metal oxides are essential parts of the soil matrix and strongly influence the formation of biogeochemical interfaces in soil. We investigated the role of these parental materials for the development of functional microbial guilds using the example of alkane-degrading bacteria harbouring the alkane monooxygenase gene (alkB) in artificial mixtures composed of different minerals and charcoal, sterile manure and a microbial inoculum extracted from an agricultural soil. We followed changes in abundance and community structure of alkane-degrading microbial communities after 3 and 12 months of soil maturation and in response to a subsequent 2-week plant litter addition. During maturation we observed an overall increasing divergence in community composition. The impact of metal oxides on alkane-degrading community structure increased during soil maturation, whereas the charcoal impact decreased from 3 to 12 months. Among the clay minerals illite influenced the community structure of alkB-harbouring bacteria significantly, but not montmorillonite. The litter application induced strong community shifts in soils, maturated for 12 months, towards functional guilds typical for younger maturation stages pointing to a resilience of the alkane-degradation function potentially fostered by an extant ‘seed bank'. PMID:25535940

Activity, abundance and structure of ammonia-oxidizing microorganisms in plateau soils.

PubMed

Dai, Yu; Wu, Zhen; Zhou, Qiheng; Zhao, Qun; Li, Ningning; Xie, Shuguang; Liu, Yong

2015-10-01

Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) can be involved in biotransformation of ammonia to nitrite in soil ecosystems. However, the distribution of AOA and AOB in plateau soils and influential factors remain largely unclear. In the present study, the activity, abundance and structure of ammonia oxidizers in different soils on the Yunnan Plateau were assessed using potential nitrification rates (PNRs), quantitative PCR assay and clone library analysis, respectively. Wide variation was found in both AOA and AOB communities in plateau soils. PNRs showed a significant positive correlation with AOB abundance. Both were determined by the ratio of organic carbon to nitrogen (C/N) and total phosphorous (TP). AOB could play a more important role in ammonia oxidation. AOB community diversity was likely affected by soil total nitrogen (TN) and total organic carbon (TOC) and was usually higher than AOA community diversity. Moreover, Nitrososphaera- and Nitrosospira-like organisms, respectively, were the dominant AOA and AOB in plateau soils. AOA community structure was likely shaped by TP and C/N, while AOB community structure was determined by pH. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

[Diversity and community structure of soil ammonia-oxidizing bacteria in Hulunbeier Grassland, Inner Mongolia].

PubMed

Wendu, Ri-le; Li, Gang; Yang, Dian-lin; Zhang, Jing-ni; Yi, Jin

2011-04-01

By the methods of polymerase chain reaction-denaturing gradient gel electrophoresis and sequence analysis, a comparative study was conducted on the diversity and community structure of soil ammonia-oxidizing bacteria in the Filifolium sibiricum steppe, Stipa baicalensis steppe, Leymus chinensis steppe, Stipa grandis steppe, and Stipa kryrowi steppe in Hulunbeier Grassland, Inner Mongolia. A significant difference was observed in the community structure of soil ammonia-oxidizing bacteria among the five steppes, with the similarity lower than 50%. The diversity of soil ammonia-oxidizing bacteria was the highest in F. sibiricum steppe, followed by in S. baicalensis steppe, L. chinensis steppe, S. kryrowi steppe, and S. grandis steppe. In the five steppes, Nitrosospira cluster 3 was the dominant group, and the Nitrosospira cluster 1, 2, and 4 as well as Nitrosomonas were also found. The community structure of soil ammonia oxidizing bacteria in F. sibiricum steppe was most complex, while that in L. chinensis steppe and S. grandis steppe was relatively simple. Correlation analysis indicated that there existed significant positive correlations between the diversity of soil ammonia-oxidizing bacteria and the soil moisture, total nitrogen, total organic carbon, and C/N ratio (P<0.05).

A simple procedure for estimating soil porosity

NASA Astrophysics Data System (ADS)

Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Holden, Nick

2016-04-01

Soil degradation from mismanagement is of international concern. Simple, accessible tools for rapidly assessing impacts of soil management are required. Soil structure is a key component of soil quality and porosity is a useful indicator of structure. We outline a version of a procedure described by Piwowarczyk et al. (2011) used to estimate porosity of samples taken during a soil quality survey of 38 sites across Ireland as part of the Government funded SQUARE (Soil Quality Assessment Research) project. This required intact core (r = 2.5 cm, H = 5cm) samples taken at 5-10 cm and 10-20 cm depth, to be covered with muslin cloth at one end and secured with a jubilee clip. Samples were saturated in sealable water tanks for ≈ 64 hours, then allowed to drain by gravity for 24 hours, at which point Field Capacity (F.C.) was assumed to have been reached, followed by oven drying with weight determined at each stage. This allowed the calculation of bulk density and the estimation of water content at saturation and following gravitational drainage, thus total and functional porosity. The assumption that F.C. was reached following 24 hours of gravitational drainage was based on the Soil Moisture Deficit model used in Ireland to predict when soils are potentially vulnerable to structural damage and used nationally as a management tool. Preliminary results indicate moderately strong, negative correlations between estimated total porosity at 5-10 cm and 10-20 cm depth (rs = -0.7, P < 0.01 in both cases) and soil quality scores of the Visual Evaluation of Soil Structure (VESS) method which was conducted at each survey site. Estimated functional porosity at 5-10 cm depth was found to moderately, negatively correlate with VESS scores (rs = - 0.5, P < 0.05). This simple procedure requires inexpensive equipment and appears useful in indicating porosity of a large quantity of samples taken at numerous sites or if done periodically, temporal changes in porosity at a field scale, indicating the impacts of soil management. Reference Piwowarczyk, A., Giuliani, G. & Holden, N.M. 2011. Can soil moisture deficit be used to forecast when soils are at high risk of damage owing to grazing animals? Soil Use and Management, 27, 255-263.

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

On the Need to Establish an International Soil Modeling Consortium

NASA Astrophysics Data System (ADS)

Vereecken, H.; Vanderborght, J.; Schnepf, A.

2014-12-01

Soil is one of the most critical life-supporting compartments of the Biosphere. Soil provides numerous ecosystem services such as a habitat for biodiversity, water and nutrients, as well as producing food, feed, fiber and energy. To feed the rapidly growing world population in 2050, agricultural food production must be doubled using the same land resources footprint. At the same time, soil resources are threatened due to improper management and climate change. Despite the many important functions of soil, many fundamental knowledge gaps remain, regarding the role of soil biota and biodiversity on ecosystem services, the structure and dynamics of soil communities, the interplay between hydrologic and biotic processes, the quantification of soil biogeochemical processes and soil structural processes, the resilience and recovery of soils from stress, as well as the prediction of soil development and the evolution of soils in the landscape, to name a few. Soil models have long played an important role in quantifying and predicting soil processes and related ecosystem services. However, a new generation of soil models based on a whole systems approach comprising all physical, mechanical, chemical and biological processes is now required to address these critical knowledge gaps and thus contribute to the preservation of ecosystem services, improve our understanding of climate-change-feedback processes, bridge basic soil science research and management, and facilitate the communication between science and society. To meet these challenges an international community effort is required, similar to initiatives in systems biology, hydrology, and climate and crop research. Our consortium will bring together modelers and experimental soil scientists at the forefront of new technologies and approaches to characterize soils. By addressing these aims, the consortium will contribute to improve the role of soil modeling as a knowledge dissemination instrument in addressing key global issues and stimulate the development of translational research activities. This presentation will provide a compelling case for this much-needed effort, with a focus on tangible benefits to the scientific and food security communities.

Soil properties and not inputs control carbon, nitrogen, phosphorus ratios in cropped soils in the long-term

NASA Astrophysics Data System (ADS)

Frossard, E.; Buchmann, N.; Bünemann, E. K.; Kiba, D. I.; Lompo, F.; Oberson, A.; Tamburini, F.; Traoré, O. Y. A.

2015-09-01

Stoichiometric approaches have been applied to understand the relationship between soil organic matter dynamics and biological nutrient transformations. However, very few studies explicitly considered the effects of agricultural management practices on soil C : N : P ratio. The aim of this study was to assess how different input types and rates would affect the C : N : P molar ratios of bulk soil, organic matter and microbial biomass in cropped soils in the long-term. Thus, we analysed the C, N and P inputs and budgets as well as soil properties in three long-term experiments established on different soil types: the Saria soil fertility trial (Burkina Faso), the Wagga Wagga rotation/stubble management/soil preparation trial (Australia), and the DOK cropping system trial (Switzerland). In each of these trials, there was a large range of C, N and P inputs which had a strong impact on element concentrations in soils. However, although C : N : P ratios of the inputs were highly variable, they had only weak effects on soil C : N : P ratios. At Saria, a positive correlation was found between the N : P ratio of inputs and microbial biomass, while no relation was observed between the nutrient ratios of inputs and soil organic matter. At Wagga Wagga, the C : P ratio of inputs was significantly correlated to total soil C : P, N : P and C : N ratios, but had no impact on the elemental composition of microbial biomass. In the DOK trial, a positive correlation was found between the C budget and the C to organic P ratio in soils, while the nutrient ratios of inputs were not related to those in the microbial biomass. We argue that these responses are due to differences in soil properties among sites. At Saria, the soil is dominated by quartz and some kaolinite, has a coarse texture, a fragile structure and a low nutrient content. Thus, microorganisms feed on inputs (plant residues, manure). In contrast, the soil at Wagga Wagga contains illite and haematite, is richer in clay and nutrients and has a stable structure. Thus, organic matter is protected from mineralization and can therefore accumulate, allowing microorganisms to feed on soil nutrients and to keep a constant C : N : P ratio. The DOK soil represents an intermediate situation, with high nutrient concentrations, but a rather fragile soil structure, where organic matter does not accumulate. We conclude that the study of C, N, and P ratios is important to understand the functioning of cropped soils in the long-term, but that it must be coupled with a precise assessment of element inputs and budgets in the system and a good understanding of the ability of soils to stabilize C, N and P compounds.

The influence of nitrogen fertilization on the magnitude of rhizosphere effects

NASA Astrophysics Data System (ADS)

Zhu, B.; Panke-Buisse, K.; Kao-Kniffin, J.

2012-12-01

The labile carbon released from roots to the rhizosphere enhances soil microbial activity and nutrient availability, but factors that regulate such "rhizosphere effects" are poorly understood. Nitrogen fertilization may suppress rhizosphere effects by reducing plant carbon allocation belowground. Here we investigated the impact of nitrogen fertilization (+100 mg NH4NO3-N kg soil-1) on the magnitude of rhizosphere effects of two grass species (Bermuda grass Cynodon dactylon and smooth crabgrass Digitaria ischaemum) grown in a nutrient-poor soil for 80-100 days inside a growth chamber. Rhizosphere effects were estimated by the percentage difference between the planted soil (rhizosphere soil) and the unplanted soil (bulk soil) for several assays. We found that the rhizosphere soil of both plants had higher pH (+ 0.5~0.7 units), similar microbial biomass carbon, but lower microbial biomass nitrogen (- 27~37%) compared to the bulk soil. The rate of net N mineralization and the activity of three soil enzymes that degrade chitin (NAG), protein (LAP) and lignin (peroxidase) and produce mineral nitrogen were generally enhanced by the rhizosphere effects (up to 80%). Although nitrogen fertilization significantly increased plant biomass, it generally affected microbial biomass, activity and net N mineralization rate to a similar extent between rhizosphere soil and bulk soil, and thus did not significantly impact the magnitude of rhizosphere effects. Moreover, the community structure of soil bacteria (indicated by T-RFLP) showed remarkable divergence between the planted and unplanted soils, but not between the control and fertilized soils. Collectively, these results suggest that grass roots affects soil microbial activity and community structure, but short-term nitrogen fertilization may not significantly influence these rhizosphere effects.

An ecosystem approach to assess soil quality in organically and conventionally managed farms in Iceland and Austria

NASA Astrophysics Data System (ADS)

van Leeuwen, J. P.; Lehtinen, T.; Lair, G. J.; Bloem, J.; Hemerik, L.; Ragnarsdóttir, K. V.; Gísladóttir, G.; Newton, J. S.; de Ruiter, P. C.

2015-01-01

Intensive agricultural production can be an important driver for the loss of long-term soil quality. For this reason, the European Critical Zone Observatory (CZO) network adopted four pairs of agricultural CZO sites that differ in their management: conventional or organic. The CZO sites include two pairs of grassland farms in Iceland and two pairs of arable farms in Austria. Conventional fields differed from the organic fields in the use of artificial fertilisers and pesticides. Soils of these eight farms were analysed in terms of their physical, chemical, and biological properties, including soil aggregate size distribution, soil organic matter contents, abundance of soil microbes and soil fauna, and taxonomic diversity of soil microarthropods. In Icelandic grasslands, organically farmed soils had larger mean weight diameters of soil aggregates than the conventional farms, while there were no differences on the Austrian farms. Organic farming did not systematically influence organic matter contents or composition, nor soil carbon and nitrogen contents. Also, soil food web structures, in terms of presence of trophic groups of soil organisms, were highly similar among all farms, indicating a low sensitivity of trophic structure to land use or climate. However, soil organism biomass, especially of bacteria and nematodes, was consistently higher on organic farms than on conventional farms. Within the microarthropods, taxonomic diversity was systematically higher in the organic farms compared to the conventional farms. This difference was found across countries and farm, crop, and soil types. The results do not show systematic differences in physical and chemical properties between organic and conventional farms, but confirm that organic farming can enhance soil biomass and that microarthropod diversity is a sensitive and consistent indicator for land management.

A soil alteration index based on phospholipid fatty acids.

PubMed

Puglisi, Edoardo; Nicelli, Marco; Capri, Ettore; Trevisan, Marco; Del Re, Attilio A M

2005-12-01

Phospholipid fatty acid (PLFA) analysis has gained great importance in the study of soil microbial community structure. This structure can give indication of the soil status. Purpose of the present paper is to analyse PLFA patterns in altered agricultural soils in order to develop a soil status alteration index. Soils subjected either to intensive agricultural exploitation, or to overflow by municipal and industrial wastes, or to irrigation with saline waters were analysed for PLFA content and compared to adjacent untreated soils by means of different statistical techniques. Principal component analysis separated PLFAs in three groups: unsaturated PLFAs (first axis, 48% of total variance), monounsaturated and cyclopropane PLFAs (second axis, 28% of total variance) and polyunsaturated PLFAs (third axis, 24% of total variance). By means of canonical discriminant analysis, a soil alteration index (SAI) was produced from 15 PLFAs using two data sets. A third data set was used to test the SAI general validity together with other data sets reported in literature. The index validity was confirmed in most cases: SAI gave higher scores for control soils and was generally able to classify soils according to their reported degree of alteration.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem

PubMed Central

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D.; Zhou, Jizhong

2015-01-01

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems. PMID:25791904

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

Uncertainty in Ecohydrological Modeling in an Arid Region Determined with Bayesian Methods

PubMed Central

Yang, Junjun; He, Zhibin; Du, Jun; Chen, Longfei; Zhu, Xi

2016-01-01

In arid regions, water resources are a key forcing factor in ecosystem circulation, and soil moisture is the critical link that constrains plant and animal life on the soil surface and underground. Simulation of soil moisture in arid ecosystems is inherently difficult due to high variability. We assessed the applicability of the process-oriented CoupModel for forecasting of soil water relations in arid regions. We used vertical soil moisture profiling for model calibration. We determined that model-structural uncertainty constituted the largest error; the model did not capture the extremes of low soil moisture in the desert-oasis ecotone (DOE), particularly below 40 cm soil depth. Our results showed that total uncertainty in soil moisture prediction was improved when input and output data, parameter value array, and structure errors were characterized explicitly. Bayesian analysis was applied with prior information to reduce uncertainty. The need to provide independent descriptions of uncertainty analysis (UA) in the input and output data was demonstrated. Application of soil moisture simulation in arid regions will be useful for dune-stabilization and revegetation efforts in the DOE. PMID:26963523

Community structure and elevational diversity patterns of soil Acidobacteria.

PubMed

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Qu, Yuanyuan; Su, Xiujiang; Zhou, Jizhong; Li, Diqiang

2014-08-01

Acidobacteria is one of the most dominant and abundant phyla in soil, and was believed to have a wide range of metabolic and genetic functions. Relatively little is known about its community structure and elevational diversity patterns. We selected four elevation gradients from 1000 to 2800 m with typical vegetation types of the northern slope of Shennongjia Mountain in central China. The vegetation types were evergreen broadleaved forest, deciduous broadleaved forest, coniferous forest and sub-alpine shrubs. We analyzed the soil acidobacterial community composition, elevational patterns and the relationship between Acidobacteria subdivisions and soil enzyme activities by using the 16S rRNA meta-sequencing technique and multivariate statistical analysis. The result found that 19 known subdivisions as well as an unclassified phylotype were presented in these forest sites, and Subdivision 6 has the highest number of detectable operational taxonomic units (OTUs). A significant single peak distribution pattern (P<0.05) between the OTU number and the elevation was observed. The Jaccard and Bray-Curtis index analysis showed that the soil Acidobacteria compositional similarity significantly decreased (P<0.01) with the increase in elevation distance. Mantel test analysis showed the most of the soil Acidobacteria subdivisions had the significant relationship (P<0.01) with different soil enzymes. Therefore, soil Acidobacteria may be involved in different ecosystem functions in global elemental cycles. Partial Mantel tests and CCA analysis showed that soil pH, soil temperature and plant diversity may be the key factors in shaping the soil Acidobacterial community structure. Copyright © 2014. Published by Elsevier B.V.

CO2 efflux from soil under influence of cadmium and glucose

NASA Astrophysics Data System (ADS)

Gilmullina, Aliia; Galitskaya, Polina; Selivanovskaya, Svetlana

2017-04-01

Soil is the largest pool of organic carbon. Any anthropogenic activity may change the soil organic carbon stock resulting in the atmospheric carbon concentration increase. Organic wastes and sewage sludge are often used for soil fertilization. These amendments often contain not only organic compounds stimulating soil microflora but also toxic compounds e.g. metals inhibiting them. The question about the influence of such amendments on soil carbon stock still remains open. The aim of this study was to evaluate individual glucose and cadmium (Cd) additions and their combined effects on carbon mineralization and microbial community structure in forest soil sampled from different depths (0-20 cm, 20-40 cm and 40-60 cm). We incubated soil samples for 14 days after the addition of: glucose (10000 mg kg-1), Cd (300 mg kg-1) and their mixture. CO2 efflux was measured by CO2 trapping in NaOH, at the 3rd, 7th and 14th days of incubation DNA was extracted from soil samples for assessment of microbial community structure via real-time PCR and Illumina sequencing. Glucose addition induced the increase of soil respiration and fungal-bacterial ratio. However, bacterial alpha-biodiversity decreased as glucose addition caused the dominance of Proteobacteria (0-20 cm, 20-40 cm and 40-60 cm), Actinobacteria (20-40 cm) and Acidobacteria (40-60 cm) phyla. Single Cd addition did not have any effect on parameters studied. In case of simultaneous addition of glucose and Cd, soil respiration and microbial community structure mainly depended more on glucose amendment as compared with metal.

Soil Organic Matter in Its Native State: Unravelling the Most Complex Biomaterial on Earth.

PubMed

Masoom, Hussain; Courtier-Murias, Denis; Farooq, Hashim; Soong, Ronald; Kelleher, Brian P; Zhang, Chao; Maas, Werner E; Fey, Michael; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Simpson, Myrna J; Simpson, André J

2016-02-16

Since the isolation of soil organic matter in 1786, tens of thousands of publications have searched for its structure. Nuclear magnetic resonance (NMR) spectroscopy has played a critical role in defining soil organic matter but traditional approaches remove key information such as the distribution of components at the soil-water interface and conformational information. Here a novel form of NMR with capabilities to study all physical phases termed Comprehensive Multiphase NMR, is applied to analyze soil in its natural swollen-state. The key structural components in soil organic matter are identified to be largely composed of macromolecular inputs from degrading biomass. Polar lipid heads and carbohydrates dominate the soil-water interface while lignin and microbes are arranged in a more hydrophobic interior. Lignin domains cannot be penetrated by aqueous solvents even at extreme pH indicating they are the most hydrophobic environment in soil and are ideal for sequestering hydrophobic contaminants. Here, for the first time, a complete range of physical states of a whole soil can be studied. This provides a more detailed understanding of soil organic matter at the molecular level itself key to develop the most efficient soil remediation and agricultural techniques, and better predict carbon sequestration and climate change.

Effect of Activated Carbon Amendment on Bacterial Community Structure and Functions in a PAH Impacted Urban Soil

PubMed Central

2012-01-01

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. PMID:22455603

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.

Complex Forms of Soil Organic Phosphorus-A Major Component of Soil Phosphorus.

PubMed

McLaren, Timothy I; Smernik, Ronald J; McLaughlin, Mike J; McBeath, Therese M; Kirby, Jason K; Simpson, Richard J; Guppy, Christopher N; Doolette, Ashlea L; Richardson, Alan E

2015-11-17

Phosphorus (P) is an essential element for life, an innate constituent of soil organic matter, and a major anthropogenic input to terrestrial ecosystems. The supply of P to living organisms is strongly dependent on the dynamics of soil organic P. However, fluxes of P through soil organic matter remain unclear because only a minority (typically <30%) of soil organic P has been identified as recognizable biomolecules of low molecular weight (e.g., inositol hexakisphosphates). Here, we use (31)P nuclear magnetic resonance spectroscopy to determine the speciation of organic P in soil extracts fractionated into two molecular weight ranges. Speciation of organic P in the high molecular weight fraction (>10 kDa) was markedly different to that of the low molecular weight fraction (<10 kDa). The former was dominated by a broad peak, which is consistent with P bound by phosphomonoester linkages of supra-/macro-molecular structures, whereas the latter contained all of the sharp peaks that were present in unfractionated extracts, along with some broad signal. Overall, phosphomonoesters in supra-/macro-molecular structures were found to account for the majority (61% to 73%) of soil organic P across the five diverse soils. These soil phosphomonoesters will need to be integrated within current models of the inorganic-organic P cycle of soil-plant terrestrial ecosystems.

Effect of activated carbon amendment on bacterial community structure and functions in a PAH impacted urban soil.

PubMed

Meynet, Paola; Hale, Sarah E; Davenport, Russell J; Cornelissen, Gerard; Breedveld, Gijs D; Werner, David

2012-05-01

We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2% powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GAC-amended soil. PAH availability assessments in batch tests showed the greatest difference of 75% with and without biocide addition for unamended soil, while the lowest PAH availability overall was measured in PAC-amended, live soil. We conclude that AC had no detrimental effects on soil microbiology, AC-amended soils retained the potential to biodegrade PAHs, but the removal of available pollutants by biodegradation was most notable in unamended soil. © 2012 American Chemical Society

Peculiarities of changes in the soil cover of landscapes adjacent to a megalopolis

NASA Astrophysics Data System (ADS)

Lazareva, Margarita; Aparin, Boris; Sukhacheva, Elena

2017-04-01

The progressive growth of cities has a significant impact on the soil cover of territories adjacent to the same. Megalopolises are centers of anthropogenic impact on the soils. Generally, forms and intensity of the urban impact on the soil cover weaken with increasing distance from the city's boundaries. In this respect, ample opportunities for the analysis of urban impact on the adjacent territories are provided by the study of the soil cover in the Leningrad Region (the LR). Saint Petersburg is a major European megalopolis, which is the administrative center of the LR. The time period of Saint Petersburg's impact on the environment does not exceed 300 years, which allows us to identify very clearly the character and areas of its impact on the soil cover. Over the past decades, there have been significant changes in the soils and the soil cover of the LR. In a large territory, there appeared new anthropogenic soils and soil cover organization forms, having no natural analogues, with a dramatic increase in the surface area of degraded soils. To access the current state of soil cover, to identify the role of anthropogenic factors of changes in this state; to carry out land reclamation, remediation and rehabilitation measures; to perform land cadastral valuation etc., we need an information resource containing data on the current state of soils and soil cover in the LR, the key element of which should be a map. We carried out mapping and created a 1:200 000 digital soil map (DSM) for the LR's territories. Diagnostics of soil contours were performed using traditionally drawn-up (paper) maps of soils and soil-formation factors; satellite images (Google, Yandex); data of remote sensing (Spot 5, Landsat 7,8); digital maps of main soil-formation factors (topographical ones, etc.). The digital soil map of the LR has been created in the geographic information system - QGIS. The map clarifies the contours of natural soils and soil combinations, and shows, for the first time, the contours of: - non-soil formations; - soils of the initial soil formation; - soils of agricultural lands within their existing boundaries; - soils and soil combinations that are specific for human settlements and horticultural land plots; - fallow lands; - anthropogenically disturbed soils. During the analysis of the created digital medium-scale soil map, we identified some changes in the soil cover of the territories adjacent to Saint Petersburg. Virtually in all the landscapes, we found a large number of soil cover structures, the components of which, along with natural soils, are anthropogenically disturbed soils, anthropogenic soils and non-soil formations. We revealed that the human impact on the soil cover is manifested within the range that varies from insignificant changes in soil parameters to radical transformations of the soil profile, complete destruction of soil and "creation" of new soil forms and soil cover organization forms. We have developed a typology of anthropogenically changed and anthropogenically created soil cover structures, taking into consideration the types of the economic impact on and the quality of environmental functions performed by the soils.

Factors Affecting Performance of Soil Termiticides

USDA-ARS?s Scientific Manuscript database

Applying liquid insecticide to soil under and around structures is one of the most widely used methods of subterranean termite prevention and control. Failure of soil termiticide treatments is often related to factors other than the active ingredient. Efficacy and longevity of soil treatments vary g...

The Vertical Structure of Urban Soils - Portland

EPA Science Inventory

We compared observed to reference pedons for two cities (Detroit MI; Cleveland OH), where it was clearly illustrated that urban soils had fewer soil horizons than their non-urban references. The ordering of observed urban soil horizons was distinct from both the theoretical (A-B-...

Effect of soil properties, heavy metals and emerging contaminants in the soil nematodes diversity.

PubMed

Gutiérrez, Carmen; Fernández, Carlos; Escuer, Miguel; Campos-Herrera, Raquel; Beltrán Rodríguez, Mª Eulalia; Carbonell, Gregoria; Rodríguez Martín, Jose Antonio

2016-06-01

Among soil organisms, nematodes are seen as the most promising candidates for bioindications of soil health. We hypothesized that the soil nematode community structure would differ in three land use areas (agricultural, forest and industrial soils), be modulated by soil parameters (N, P, K, pH, SOM, CaCO3, granulometric fraction, etc.), and strongly affected by high levels of heavy metals (Cd, Pb, Zn, Cr, Ni, Cu, and Hg) and emerging contaminants (pharmaceuticals and personal care products, PPCPs). Although these pollutants did not significantly affect the total number of free-living nematodes, diversity and structure community indices vastly altered. Our data showed that whereas nematodes with r-strategy were tolerant, genera with k-strategy were negatively affected by the selected pollutants. These effects diminished in soils with high levels of heavy metals given their adaptation to the historical pollution in this area, but not to emerging pollutants like PPCPs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Effects of the inoculant strain Sphingomonas paucimobilis 20006FA on soil bacterial community and biodegradation in phenanthrene-contaminated soil.

PubMed

Coppotelli, B M; Ibarrolaza, A; Del Panno, M T; Morelli, I S

2008-02-01

The effects of the inoculant strain Sphingomonas paucimobilis 20006FA (isolated from a phenanthrene-contaminated soil) on the dynamics and structure of microbial communities and phenanthrene elimination rate were studied in soil microcosms artificially contaminated with phenanthrene. The inoculant managed to be established from the first inoculation as it was evidenced by denaturing gradient gel electrophoresis analysis, increasing the number of cultivable heterotrophic and PAH-degrading cells and enhancing phenanthrene degradation. These effects were observed only during the inoculation period. Nevertheless, the soil biological activity (dehydrogenase activity and CO(2) production) showed a late increase. Whereas gradual and successive changes in bacterial community structures were caused by phenanthrene contamination, the inoculation provoked immediate, significant, and stable changes on soil bacterial community. In spite of the long-term establishment of the inoculated strain, at the end of the experiment, the bioaugmentation did not produce significant changes in the residual soil phenanthrene concentration and did not improve the residual effects on the microbial soil community.

Profile analysis of microbiomes in soils of solonetz complex in the Caspian Lowland

NASA Astrophysics Data System (ADS)

Chernov, T. I.; Lebedeva, M. P.; Tkhakakhova, A. K.; Kutovaya, O. V.

2017-01-01

The taxonomic structure of the microbiota in two associated soils—solonetz on a microhigh and meadow-chestnut soil in a microlow—was studied in the semidesert of the Caspian Lowland. A highthroughput sequencing of the 16S rRNA gene was used for the soil samples from genetic horizons. A considerable reduction in the bacterial diversity was found in the lower horizons of the solonetz and compact solonetzic horizon with a high content of exchangeable sodium. In the meadow-chestnut soil, the microbial diversity little decreased with the depth. In both soils, a portion of archaea from the Thaumarchaeota group also decreased in the deeper horizons. In the soil horizons with the lower total bacterial diversity, a share of proteobacteria of the Enterobacteriaceae, Pseudomonadaceae, and Sphingomonadaceae families became higher. The difference between the structure of the microbial population in the solonetz and meadow- chestnut soil can be first explained by the different water regimes and soil consistence.

Spatial effects of aboveground biomass on soil ecological parameters and trace gas fluxes in a savannah ecosystem of Mount Kilimanjaro

NASA Astrophysics Data System (ADS)

Becker, Joscha; Gütlein, Adrian; Sierra Cornejo, Natalia; Kiese, Ralf; Hertel, Dietrich; Kuzyakov, Yakov

2015-04-01

The savannah biome is a hotspot for biodiversity and wildlife conservation in Africa and recently got in the focus of research on carbon sequestration. Savannah ecosystems are under strong pressure from climate and land-use change, especially around populous areas like the Mt. Kilimanjaro region. Savannah vegetation in this area consists of grassland with isolated trees and is therefore characterized by high spatial variation of canopy cover, aboveground biomass and root structure. Canopy structure is known to affect microclimate, throughfall and evapotranspiration and thereby controls soil moisture conditions. Consequently, the canopy structure is a major regulator for soil ecological parameters and soil-atmospheric trace gas exchange (CO2, N2O, CH4) in water limited environments. The spatial distribution of these parameters and the connection between above and belowground processes are important to understand and predict ecosystem changes and estimate its vulnerability. Our objective was to determine trends and changes of soil parameters and relate their spatial variability to the vegetation structure. We chose three trees from each of the two most dominant species (Acacia nilotica and Balanites aegyptiaca) in our research area. For each tree, we selected transects with nine sampling points of the same relative distances to the stem. Distances were calculated in relation to the crown radius. At these each sampling point a soil core was taken and separated in 0-10 cm and 10-30 cm depth. We measured soil carbon (C) and nitrogen (N) storage, microbial biomass carbon C and N, soil respiration as well as root biomass and -density, soil temperature and soil water content. Each tree was characterized by crown spread, leaf area index and basal area. Preliminary results show that C and N stocks decreased about 50% with depth independently of distance to the tree. Soil water content under the tree crown increased with depth while it decreased under grass cover. Microbial Biomass C and N in the upper 10 cm decreased with distance (C: r²=0.22, p<0.001; N: r²=0.3, p<0.001) as well as total soil respiration. This decrease was affected by tree size but independent from tree species. We conclude that savannah ecosystems exhibit a large spatial variability of soil parameters within the upper horizons which is strongly depend on the structure of aboveground biomass.

Wettability, soil organic matter and structure-properties of typical chernozems under the forest and under the arable land

NASA Astrophysics Data System (ADS)

Bykova, Galina; Umarova, Aminat; Tyugai, Zemfira; Milanovskiy, Evgeny; Shein, Evgeny

2017-04-01

Intensive tillage affects the properties of soil: decrease in content of soil organic matter and in hydrophobicity of the soil's solid phase, the reduction of amount of water stable aggregates - all this leads to deterioration of the structure of the soil and affects the process of movement of moisture in the soil profile. One of the hypotheses of soil's structure formation ascribes the formation of water stable aggregates with the presence of hydrophobic organic substances on the surface of the soil's solid phase. The aim of this work is to study the effect of tillage on properties of typical chernozems (pachic Voronic Chernozems, Haplic Chernozems) (Russia, Kursk region), located under the forest and under the arable land. The determination of soil-water contact angle was performed by a Drop Shape Analyzer DSA100 (Krüss GmbH, Germany) by the static sessile drop method. For all samples the content of total and organic carbon by dry combustion in oxygen flow and the particle size distribution by the laser diffraction method on the device Analysette 22 comfort, FRITCH, Germany were determined. The estimation of aggregate composition was performed by dry sieving (AS 200, Retsch, Germany), the content of water stable aggregates was estimated by the Savvinov method. There was a positive correlation between the content of organic matter and soil's wettability in studied soils, a growth of contact angle with the increasing the content of organic matter. Under the forest the content of soil organic matter was changed from 6,41% on the surface up to 1,9% at the depth of 100 cm. In the Chernozem under the arable land the organic carbon content in arable horizon is almost two times less. The maximum of hydrophobicity (78.1o) was observed at the depth of 5 cm under the forest. In the profile under the arable land the contact angle value at the same depth was 50o. The results of the structure analysis has shown a decrease in the content of agronomically valuable and water stable aggregates in the profile under arable land. These data indicate the correlation between the wettability of soils with the content of organic matter and their influence on the formation of water stable structure, as well as the negative impact of tillage on the analyzed characteristics.

Effect of iron oxide reductive dissolution on the transformation and immobilization of arsenic in soils: New insights from X-ray photoelectron and X-ray absorption spectroscopy.

PubMed

Fan, Jian-Xin; Wang, Yu-Jun; Liu, Cun; Wang, Li-Hua; Yang, Ke; Zhou, Dong-Mei; Li, Wei; Sparks, Donald L

2014-08-30

The geochemical behavior and speciation of arsenic (As) in paddy soils is strongly controlled by soil redox conditions and the sequestration by soil iron oxyhydroxides. Hence, the effects of iron oxide reductive dissolution on the adsorption, transformation and precipitation of As(III) and As(V) in soils were investigated using batch experiments and synchrotron based techniques to gain a deeper understanding at both macroscopic and microscopic scales. The results of batch sorption experiments revealed that the sorption capacity of As(V) on anoxic soil was much higher than that on control soil. Synchrotron based X-ray fluorescence (μ-XRF) mapping studies indicated that As was heterogeneously distributed and was mainly associated with iron in the soil. X-ray absorption near edge structure (XANES), micro-X-ray absorption near edge structure (μ-XANES) and X-ray photoelectron spectroscopy (XPS) analyses revealed that the primary speciation of As in the soil is As(V). These results further suggested that, when As(V) was introduced into the anoxic soil, the rapid coprecipitation of As(V) with ferric/ferrous ion prevented its reduction to As(III), and was the main mechanism controlling the immobilization of As. This research could improve the current understanding of soil As chemistry in paddy and wetland soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China

PubMed Central

Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

2016-01-01

The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community. PMID:27241173

Soil Texture Often Exerts a Stronger Influence Than Precipitation on Mesoscale Soil Moisture Patterns

NASA Astrophysics Data System (ADS)

Dong, Jingnuo; Ochsner, Tyson E.

2018-03-01

Soil moisture patterns are commonly thought to be dominated by land surface characteristics, such as soil texture, at small scales and by atmospheric processes, such as precipitation, at larger scales. However, a growing body of evidence challenges this conceptual model. We investigated the structural similarity and spatial correlations between mesoscale (˜1-100 km) soil moisture patterns and land surface and atmospheric factors along a 150 km transect using 4 km multisensor precipitation data and a cosmic-ray neutron rover, with a 400 m diameter footprint. The rover was used to measure soil moisture along the transect 18 times over 13 months. Spatial structures of soil moisture, soil texture (sand content), and antecedent precipitation index (API) were characterized using autocorrelation functions and fitted with exponential models. Relative importance of land surface characteristics and atmospheric processes were compared using correlation coefficients (r) between soil moisture and sand content or API. The correlation lengths of soil moisture, sand content, and API ranged from 12-32 km, 13-20 km, and 14-45 km, respectively. Soil moisture was more strongly correlated with sand content (r = -0.536 to -0.704) than with API for all but one date. Thus, land surface characteristics exhibit coherent spatial patterns at scales up to 20 km, and those patterns often exert a stronger influence than do precipitation patterns on mesoscale spatial patterns of soil moisture.

Permafrost soils and carbon cycling

DOE PAGES

Ping, C. L.; Jastrow, J. D.; Jorgenson, M. T.; ...

2015-02-05

Knowledge of soils in the permafrost region has advanced immensely in recent decades, despite the remoteness and inaccessibility of most of the region and the sampling limitations posed by the severe environment. These efforts significantly increased estimates of the amount of organic carbon stored in permafrost-region soils and improved understanding of how pedogenic processes unique to permafrost environments built enormous organic carbon stocks during the Quaternary. This knowledge has also called attention to the importance of permafrost-affected soils to the global carbon cycle and the potential vulnerability of the region's soil organic carbon (SOC) stocks to changing climatic conditions. Inmore » this review, we briefly introduce the permafrost characteristics, ice structures, and cryopedogenic processes that shape the development of permafrost-affected soils, and discuss their effects on soil structures and on organic matter distributions within the soil profile. We then examine the quantity of organic carbon stored in permafrost-region soils, as well as the characteristics, intrinsic decomposability, and potential vulnerability of this organic carbon to permafrost thaw under a warming climate. Overall, frozen conditions and cryopedogenic processes, such as cryoturbation, have slowed decomposition and enhanced the sequestration of organic carbon in permafrost-affected soils over millennial timescales. Due to the low temperatures, the organic matter in permafrost soils is often less humified than in more temperate soils, making some portion of this stored organic carbon relatively vulnerable to mineralization upon thawing of permafrost.« less

HYDRAULIC REDISTRIBUTION OF SOIL WATER BY ROOTS IN FORESTS OF THE PACIFIC NORTHWEST

EPA Science Inventory

One aspect of structural complexity of forest canopies is the root system structure belowground, which influences patterns of soil water utilization by trees. Deeply rooted trees and other plants can hydraulically lift water via their roots from several m below the soil surface ...

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.

Structural changes of green roof growing substrate layer studied by X-ray CT

NASA Astrophysics Data System (ADS)

Jelinkova, Vladimira; Sacha, Jan; Dohnal, Michal; Snehota, Michal

2017-04-01

Increasing interest in green infrastructure linked with newly implemented legislation/rules/laws worldwide opens up research potential for field of soil hydrology. A better understanding of function of engineered soils involved in green infrastructure solutions such as green roofs or rain garden is needed. A soil layer is considered as a highly significant component of the aforesaid systems. In comparison with a natural soil, the engineered soil is assumed to be the more challenging case due to rapid structure changes early stages after its build-up. The green infrastructure efficiency depends on the physical and chemical properties of the soil, which are, in the case of engineered soils, a function of its initial composition and subsequent soil formation processes. The project presented in this paper is focused on fundamental processes in the relatively thick layer of engineered soil. The initial structure development, during which the pore geometry is altered by the growth of plant roots, water influx, solid particles translocation and other soil formation processes, is investigated with the help of noninvasive imaging technique  X-ray computed tomography. The soil development has been studied on undisturbed soil samples taken periodically from green roof test system during early stages of its life cycle. Two approaches and sample sizes were employed. In the first approach, undisturbed samples (volume of about 63 cm3) were taken each time from the test site and scanned by X-ray CT. In the second approach, samples (volume of about 630 cm3) were permanently installed at the test site and has been repeatedly removed to perform X-ray CT imaging. CT-derived macroporosity profiles reveal significant temporal changes of soil structure. Clogging of pores by fine particles and fissures development are two most significant changes that would affect the green roof system efficiency. This work has been supported by the Ministry of Education, Youth and Sports within National Sustainability Programme I, project number LO1605 and with financial support from the Czech Science Foundation under project number GAČR 17-21011S.

Impact of land management on soil structure and soil hydraulic properties

NASA Astrophysics Data System (ADS)

Kodesova, Radka; Jirku, Veronika; Nikodem, Antonin; Muhlhanselova, Marcela; Zigova, Anna

2010-05-01

Study is focused on a comparison of a soil structure and soil hydraulic properties within soil profiles of a same soil type under different land management. Study was performed in Haplic Luvisol in Hnevceves the Czech Republic. Two soil profiles, which were in close distance from each other, were chosen: 1. under the conventional tillage, 2. under the permanent (30 years) grass cover. Soil sampling and field experiments were carried out immediately after the harvest of winter barley in 2008. The micromorphological images were used to evaluate the soil structure of all Ap, Bt1, Bt2 and C diagnostic horizons. The hydraulic properties of the diagnostic horizons were studied in the laboratory using multistep outflow experiments performed on the undisturbed 100-cm3 soil samples. A tension disc infiltrometer (with a disc radius of 10 cm) and minidisc tension infiltrometers (with a disc radius of 2.2 cm) were used to measure cumulative water infiltration under unsaturated conditions created using a pressure head of -2 cm. Measurements were performed at a depths of 5, 45, 75 and 110 cm, which corresponded to the Ap, Bt1, Bt2 and C horizons of studied Haplic Luvisol at both locations. The Guelph permeameter was used to measure cumulative water flux under surface ponding conditions. The depth of the drilled well was 10, 50, 80 and 115 cm, the well radius was 3 cm, and the well ponding depth was 5 cm. Both tests were used to evaluate hydraulic conductivity (K for h=-2cm, and Ks) values. Results showed, that while properties in the Bt2 and C horizons of both soil profiles were relatively similar, properties in the Ap and Bt1 horizons were different. The fraction of gravitational pores (which may cause preferential flow) in the Ap and Bt1 horizons of the soil profile under the convectional tillage was large than those in the Ap and Bt1 horizons of the soil profile under the permanent grass. This influenced for instance the Ks values measured using the Guelph permeametr. The Ks values were higher and more variable in the soil profile under the convectional tillage than those in the soil profile under the permanent grass. On the other hand, due to the periodical tillage and consequent soil structure breakdown, the fraction of the large capillary pores were smaller in the Ap horizon of the soil profile under the convectional tillage than that in the Ap horizon of the soil profile under the permanent grass. As result the K (h=-2cm) values measured using the tension infiltrometer in the soil profile under the permanent grass was higher than those in the soil profile under the convectional tillage. However, the fraction of the large capillary pores and K (h=-2cm) values were similar in the Bt1 horizons of both soil profiles. Thus the land management impacted both macropores and matrix pores in the Ap horizon and macropores (prismatic structure and biopores) in the Bt1 horizon. Acknowledgement: Authors acknowledge the financial support of the Grant Agency of the Czech Republic (grant No. GA CR 526/08/0434) and the Ministry of Education, Youth and Sports of the Czech Republic (grant No. MSM 6046070901).

Role of model structure on the response of soil biogeochemistry to hydro-climatic fluctuations

NASA Astrophysics Data System (ADS)

Manzoni, S.; Porporato, A.

2005-05-01

Soil carbon and nutrient cycles are strongly affected by hydro-climatic variability, which interacts with the internal ecosystem structure. Here we test the implications of biogeochemical model structure on such dynamics by extending an existing model by the authors and coworkers. When forced by hydro-climatic fluctuations, the different model structures induce specific preferential nutrient paths among the soil pools, which in turn affect nutrient distribution and availability to microbes and plants. In particular, if it is assumed that microbes can directly assimilate organic nitrogen, plants tend to be inferior competitors for nutrients even in well-watered conditions, while if a certain amount of organic nitrogen is assumed to be mineralized without being first incorporated into microbial cells, vegetation can be advantaged over a wide range of soil moisture values. We also investigate the intensification of competition for nutrients (e.g., nitrogen) between plant and soil microbial communities under extreme hydrologic conditions, such as droughts and intense storms. Frequent rainfall events may determine ideal soil moisture conditions for plant uptake, enhancing nitrogen leaching while lowering oxygen concentration and inhibiting microbial activity. During droughts, the soil water potential often drops to the point of hampering the plant nutrient uptake while still remaining high enough for microbial decomposition and nitrogen immobilization. The interplay of microbe and vegetation water stress is investigated in depth as it controls the ability of one community (e.g., plants or soil microbes) to establish competitive advantage on the other. The long-term effects of these dynamics of competition and nutrient allocation are explored under steady-state and stochastic soil moisture conditions to analyze the feedbacks between soil organic matter and vegetation dynamics.

Soil microcosm for testing the effects of chemical pollutants on soil fauna communities and trophic structure

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

Parmelee, R.W.; Wentsel, R.S.; Phillips, C.T.

1993-08-01

A microcosm technique is presented that uses community and trophic-level analysis of soil nematodes and microarthropods to determine the effects of chemicals on soil systems. Forest soil was treated with either copper, p-nitrophenol, or trinitrotoluene. Nematodes were sorted into bacterivore, fungivore, herbivore, and omnivore-predator trophic groups, and a hatchling category. Microarthropods were sorted to the acarine suborders Prostigmata, Mesostigmata, and Oribatida; the insectan order Collembola; and a miscellaneous group. Omnivore-predator nematodes and meso-stigmatid and oribatid mites were the groups most sensitive to copper and were significantly reduced at levels as low as 100 [mu]g g[sup [minus]1] copper. Total nematode andmore » microarthropod numbers declined above 200 [mu]g g[sup [minus]1] copper. Trophic structure analysis suggested that high sensitivity of nematode predators to intermediate levels of copper reduced predation on herbivore nematodes and resulted in greater numbers of nematodes compared to controls. p-Nitrophenol was very toxic to the nematode community, and all trophic groups were significantly reduced above 20 [mu]g g[sup [minus]1]. However, there was no effect of p-nitrophenol on microarthropods. Trinitrotoluene had no significant negative effect on total abundance of either groups of soil fauna, but oribatids were significantly reduced at 200 [mu]g g[sup [minus]1]. The results demonstrated that soil nematodes and microarthropods were sensitive indicators of environmental contaminants and that trophic-structure and community analysis has the potential to detect more subtle indirect effects of chemicals on soil food-web structure. The authors conclude that microcosms with field communities of soil microfauna offer high resolution of the ecotoxicological effects of chemicals in complex soil systems.« less

The potential of cover crops for improving soil function

NASA Astrophysics Data System (ADS)

Stoate, Chris; Crotty, Felicity

2017-04-01

Cover crops can be grown over the autumn and winter ensuring green cover throughout the year. They have been described as improving soil structure, reducing soil erosion and potentially even a form of grass weed control. These crops retain nutrients within the plant, potentially making them available for future crops, as well as increasing soil organic matter. Over the last three years, we have investigated how different cover crop regimes affect soil quality. Three separate experiments over each autumn/winter period have investigated how different cover crops affect soil biology, physics and chemistry, with each experiment building on the previous one. There have been significant effects of cover crops on soil structure, as well as significantly lower weed biomass and increased yields in the following crop - in comparison to bare stubble. For example, the effect of drilling the cover crops on soil structure in comparison to a bare stubble control that had not been driven on by machinery was quantified, and over the winter period the soil structure of the cover crop treatments changed, with compaction reduced in the cover crop treatments, whilst the bare stubble control remained unchanged. Weeds were found in significantly lower biomass in the cover crop mixes in comparison to the bare stubble control, and significantly lower weed biomass continued to be found in the following spring oat crop where the cover crops had been, indicating a weed suppressive effect that has a continued legacy in the following crop. The following spring oats have shown similar results in the last two years, with higher yields in the previous cover crop areas compared to the bare stubble controls. Overall, these results are indicating that cover crops have the potential to provide improvements to soil quality, reduce weeds and improve yields. We discuss the economic implications.

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.

Ectomycorrhizal fungal associates of Pinus contorta in soils associated with a hot spring in Norris Geyser Basin, Yellowstone National Park, Wyoming

NASA Technical Reports Server (NTRS)

Cullings, K.; Makhija, S.

2001-01-01

Molecular methods and comparisons of fruiting patterns (i.e., presence or absence of fungal fruiting bodies in different soil types) were used to determine ectomycorrhizal (EM) associates of Pinus contorta in soils associated with a thermal soil classified as ultra-acidic to extremely acidic (pH 2 to 4). EM were sampled by obtaining 36 soil cores from six paired plots (three cores each) of both thermal soils and forest soils directly adjacent to the thermal area. Fruiting bodies (mushrooms) were collected for molecular identification and to compare fruiting body (above-ground) diversity to below-ground diversity. Our results indicate (i) that there were significant decreases in both the level of EM infection (130 +/- 22 EM root tips/core in forest soil; 68 +/- 22 EM root tips/core in thermal soil) and EM fungal species richness (4.0 +/- 0.5 species/core in forest soil; 1.2 +/- 0.2 species/core in thermal soil) in soils associated with the thermal feature; (ii) that the EM mycota of thermal soils was comprised of a small set of dominant species and included very few rare species, while the EM mycota of forest soils contained a few dominant species and several rare EM fungal species; (iii) that Dermocybe phoenecius and a species of Inocybe, which was rare in forest soils, were the dominant EM fungal species in thermal soils; (iv) that other than the single Inocybe species, there was no overlap in the EM fungal communities of the forest and thermal soils; and (v) that the fungal species forming the majority of the above-ground fruiting structures in thermal soils (Pisolithus tinctorius, which is commonly used in remediation of acid soils) was not detected on a single EM root tip in either type of soil. Thus, P. tinctorius may have a different role in these thermal soils. Our results suggest that this species may not perform well in remediation of all acid soils and that factors such as pH, soil temperature, and soil chemistry may interact to influence EM fungal community structure. In addition, we identified at least one new species with potential for use in remediation of hot acidic soil.

Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

NASA Astrophysics Data System (ADS)

Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

2002-12-01

The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

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.

Arbuscular Mycorrhizal Fungi Community Structure, Abundance and Species Richness Changes in Soil by Different Levels of Heavy Metal and Metalloid Concentration

PubMed Central

Krishnamoorthy, Ramasamy; Kim, Chang-Gi; Subramanian, Parthiban; Kim, Ki-Yoon; Selvakumar, Gopal; Sa, Tong-Min

2015-01-01

Arbuscular Mycorrhizal Fungi (AMF) play major roles in ecosystem functioning such as carbon sequestration, nutrient cycling, and plant growth promotion. It is important to know how this ecologically important soil microbial player is affected by soil abiotic factors particularly heavy metal and metalloid (HMM). The objective of this study was to understand the impact of soil HMM concentration on AMF abundance and community structure in the contaminated sites of South Korea. Soil samples were collected from the vicinity of an abandoned smelter and the samples were subjected to three complementary methods such as spore morphology, terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE) for diversity analysis. Spore density was found to be significantly higher in highly contaminated soil compared to less contaminated soil. Spore morphological study revealed that Glomeraceae family was more abundant followed by Acaulosporaceae and Gigasporaceae in the vicinity of the smelter. T-RFLP and DGGE analysis confirmed the dominance of Funneliformis mosseae and Rhizophagus intraradices in all the study sites. Claroideoglomus claroideum, Funneliformis caledonium, Rhizophagus clarus and Funneliformis constrictum were found to be sensitive to high concentration of soil HMM. Richness and diversity of Glomeraceae family increased with significant increase in soil arsenic, cadmium and zinc concentrations. Our results revealed that the soil HMM has a vital impact on AMF community structure, especially with Glomeraceae family abundance, richness and diversity. PMID:26035444

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing.

PubMed

Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

2015-01-01

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system.

The Effect of Long-Term Continuous Cropping of Black Pepper on Soil Bacterial Communities as Determined by 454 Pyrosequencing

PubMed Central

Xiong, Wu; Li, Zhigang; Liu, Hongjun; Xue, Chao; Zhang, Ruifu; Wu, Huasong; Li, Rong; Shen, Qirong

2015-01-01

In the present study, 3 replanted black pepper orchards with continuously cropping histories for 10, 21, and 55 years in tropical China, were selected for investigating the effect of monoculture on soil physiochemical properties, enzyme activities, bacterial abundance, and bacterial community structures. Results showed long-term continuous cropping led to a significant decline in soil pH, organic matter contents, enzymatic activities, and resulted in a decrease in soil bacterial abundance. 454 pyrosequencing analysis of 16S rRNA genes revealed that the Acidobacteria and Proteobacteria were the main phyla in the replanted black pepper orchard soils, comprising up to 73.82% of the total sequences; the relative abundances of Bacteroidetes and Firmicutes phyla decreased with long-term continuous cropping; and at genus level, the Pseudomonas abundance significantly depleted after 21 years continuous cropping. In addition, bacterial diversity significantly decreased after 55 years black pepper continuous cropping; obvious variations for community structures across the 3 time-scale replanted black pepper orchards were observed, suggesting monoculture duration was the major determinant for bacterial community structure. Overall, continuous cropping during black pepper cultivation led to a significant decline in soil pH, organic matter contents, enzymatic activities, resulted a decrease in soil bacterial abundance, and altered soil microbial community membership and structure, which in turn resulted in black pepper poor growth in the continuous cropping system. PMID:26317364

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Impact of soil structure heterogeneity on the degradation of organic pollutants at the centimeter scale : 3D Modeling using graph based method

NASA Astrophysics Data System (ADS)

Sinclair Yemini, Francis; Chenu, Claire; Monga, Olivier; Vieuble Gonond, Laure; Juarez, Sabrina; Pihneiro, Marc; otten, Wilfred; Garnier, Patricia

2014-05-01

Contaminant degradation by microorganisms is very variable in soils because of the very heterogeneous spatial relationship of contaminant/degraders. Repacked Soil columns were carried out to study the degradation of 2,4D pesticide labelled with C14 for different scenarios of microorganisms and pesticide initial location. Measurements of global C14-CO2 emission and C14 distribution in the soil column showed that the initial location play a crucial rule on the dissipation of the pollutant. Experiments were simulated using a 3D model able to model microbial degradation and substrate diffusion between aggregates by considering explicitly the 3D structure of soil from CT images. The initial version of the model (Monga et al., 2008) was improved in order to simulate diffusion in samples of large size. Partial differential equations were implemented using freefem++ solver. The model simulates properly the dynamics of 2,4D in the column for the different initial situations. CT images of the same soil but using undisturbed structure instead of repacked aggregates were also carried out. Significant differences of the simulated results were observed between the repacked and the undisturbed soil. The conclusion of our work is that the heterogeneity of the soil structure and location of pollutants and decomposers has a very strong influence on the dissipation of pollutants.

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.

Do shrubs reduce the adverse effects of grazing on soil properties?

USGS Publications Warehouse

Eldridge, David J.; Beecham, Genevieve; Grace, James B.

2015-01-01

Increases in the density of woody plants are a global phenomenon in drylands, and large aggregations of shrubs, in particular, are regarded as being indicative of dysfunctional ecosystems. There is increasing evidence that overgrazing by livestock reduces ecosystem functions in shrublands, but that shrubs may buffer the negative effects of increasing grazing. We examined changes in water infiltration and nutrient concentrations in soils under shrubs and in their interspaces in shrublands in eastern Australia that varied in the intensity of livestock grazing. We used structural equation modelling to test whether shrubs might reduce the negative effects of overgrazing on infiltration and soil carbon and nitrogen (henceforth ‘soil nutrients’). Soils under shrubs and subject to low levels of grazing were more stable and had greater levels of soil nutrients. Shrubs had a direct positive effect on soil nutrients; but, grazing negatively affected nutrients by increasing soil bulk density. Structural equation modelling showed that shrubs had a direct positive effect on water flow under ponded conditions but also enhanced water flow, indirectly, through increased litter cover. Any positive effects of shrubs on water flow under low levels of grazing waned at high levels of grazing. Our results indicate that shrubs may reduce the adverse effects of grazing on soil properties. Specifically, shrubs could restrict access to livestock and therefore protect soils and plants beneath their canopies. Low levels of grazing are likely to ensure the retention of soil water and soil carbon and nitrogen in shrubland soils.

[Characteristics of soil ammonia-oxidation microbial communities in different subtropical forests, China].

PubMed

Li, Yong-Chun; Liu, Bu-Rong; Guo, Shuai; Wu, Qi-Feng; Qin, Hua; Wu, Jia-Sen; Xu, Qiu-Fang

2014-01-01

To investigate the effects of different forest stands in subtropical China on the communities of soil ammonia-oxidizing microorganisms, we characterized the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), and the community structure of AOA in soils under stands of broad-leaved (BF) , Chinese fir (CF) , Pinus massoniana (PF) and moso bamboo (MB) forests using real-time quantitative PCR and denaturing gradient gel electrophoresis (DGGE). The results showed that the AOA gene copy numbers (1.62 x 10(6)-1.88 x 10(7) per gram of dry soil) were significantly higher than those of AOB genes (2.41 x 10(5)-4.36 x 10(5) per gram of dry soil). Significantly higher soil AOA abundance was detected in the MB than that in the CF (P < 0.05), and the latter was significantly higher than that in the BF and PF soils (P < 0.05). There were no significant differences in the soil AOB abundance among the four forest stands. As indicated by DGGE pattern, soil AOA species varied among the four forest stands. There was a difference in the soil AOA communities between the CF and MB stands. The AOA demonstrated a competitive advantage over the AOB in the soils under these major subtropical forests. Soil pH, concentrations of soil available potassium and organic carbon as well as the forest type were the main factors that influence the variation of AOA community structure and diversity.

Responses of soil ammonia oxidizers to a short-term severe mercury stress.

PubMed

Zhou, Zhi-Feng; Liu, Yu-Rong; Sun, Guo-Xin; Zheng, Yuan-Ming

2015-12-01

The responses of soil ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) to mercury (Hg) stress were investigated through a short-term incubation experiment. Treated with four different concentrations of Hg (CK, Hg25, Hg50, and Hg100, denoting 0, 25, 50, and 100mgHg/kg dry soil, respectively), samples were harvested after 3, 7, and 28day incubation. Results showed that the soil potential nitrification rate (PNR) was significantly inhibited by Hg stress during the incubation. However, lower abundances of AOA (the highest in CK: 9.20×10(7)copies/g dry soil; the lowest in Hg50: 2.68×10(7)copies/g dry soil) and AOB (the highest in CK: 2.68×10(7)copies/g dry soil; the lowest in Hg50: 7.49×10(6)copies/g dry soil) were observed only at day 28 of incubation (P<0.05). Moreover, only the community structure of soil AOB obviously shifted under Hg stress as seen through DGGE profiles, which revealed that 2-3 distinct AOB bands emerged in the Hg treatments at day 28. In summary, soil PNR might be a very useful parameter to assess acute Hg stress on soil ecosystems, and the community structure of soil AOB might be a realistic biological indicator for the assessment of heavy metal stress on soil ecosystems in the future. Copyright © 2015. Published by Elsevier B.V.

Visualization of soil structure and pore structure modifications by pioneering ground beetles (Cicindelidae) in surface sediments of an artificial catchment

NASA Astrophysics Data System (ADS)

Badorreck, Annika; Gerke, Horst H.; Weller, Ulrich; Vontobel, Peter

2010-05-01

An artificial catchment was constructed to study initial soil and ecosystem development. As a key process, the pore structure dynamics in the soil at the surface strongly influences erosion, infiltration, matter dynamics, and vegetation establishment. Little is known, however, about the first macropore formation in the very early stage. This presentation focuses on observations of soil pore geometry and its effect on water flow at the surface comparing samples from three sites in the catchment and in an adjacent "younger" site composed of comparable sediments. The surface soil was sampled in cylindrical plastic rings (10 cm³) down to 2 cm depth in three replicates each site and six where caves from pioneering ground-dwelling beetles Cicindelidae were found. The samples were scanned with micro-X-ray computed tomography (at UFZ-Halle, Germany) with a resolution of 0.084 mm. The infiltration dynamics were visualized with neutronradiography (at Paul-Scherer-Institute, Switzerland) on slab-type soil samples in 2D. The micro-tomographies exhibit formation of surface sealing whose thickness and intensity vary with silt and clay content. The CT images show several coarser- and finer-textured micro-layers at the sample surfaces that were formed as a consequence of repeated washing in of finer particles in underlying coarser sediment. In micro-depressions, the uppermost layers consist of sorted fine sand and silt due to wind erosion. Similar as for desert pavements, a vesicular pore structure developed in these sediments on top, but also scattered in fine sand- and silt-enriched micro-layers. The ground-dwelling activity of Cicindelidae beetles greatly modifies the soil structure through forming caves in the first centimetres of the soil. Older collapsed caves, which form isolated pores within mixed zones, were also found. The infiltration rates were severely affected both, by surface crusts and activity of ground-dwelling beetles. The observations demonstrate relatively high abiotic and biotic dynamics of soil pore structure in the soil surface even during the very early development stages. The structure formation has potentially great effects on changing runoff and infiltration by forming sealing layers or preferential flow paths.

Physical soil quality indicators for monitoring British soils

NASA Astrophysics Data System (ADS)

Corstanje, Ron; Mercer, Theresa G.; Rickson, Jane R.; Deeks, Lynda K.; Newell-Price, Paul; Holman, Ian; Kechavarsi, Cedric; Waine, Toby W.

2017-09-01

Soil condition or quality determines its ability to deliver a range of functions that support ecosystem services, human health and wellbeing. The increasing policy imperative to implement successful soil monitoring programmes has resulted in the demand for reliable soil quality indicators (SQIs) for physical, biological and chemical soil properties. The selection of these indicators needs to ensure that they are sensitive and responsive to pressure and change, e.g. they change across space and time in relation to natural perturbations and land management practices. Using a logical sieve approach based on key policy-related soil functions, this research assessed whether physical soil properties can be used to indicate the quality of British soils in terms of their capacity to deliver ecosystem goods and services. The resultant prioritised list of physical SQIs was tested for robustness, spatial and temporal variability, and expected rate of change using statistical analysis and modelling. Seven SQIs were prioritised: soil packing density, soil water retention characteristics, aggregate stability, rate of soil erosion, depth of soil, soil structure (assessed by visual soil evaluation) and soil sealing. These all have direct relevance to current and likely future soil and environmental policy and are appropriate for implementation in soil monitoring programmes.

[Community structure of soil meso- and micro-fauna in different habitats of urbanized region].

PubMed

Qin, Zhong; Zhang, Jia-en; Li, Qing-fang

2009-12-01

Investigations were made in May, June, and November 2007 and January 2008 to study the structural characteristics and their seasonal variations of soil meso- and micro-fauna communities in six habitats of three land use types (forest land, constructed grassland and farmland) in Tianhe District of Guangzhou City. The horizontal spatial distribution of soil fauna differed with habitat. During the investigation periods, the Botanical Garden of South China Agricultural University had the highest individual number (1286) of soil mesa- and micro-fauna, while the farmland, especially in the Fenghuang Street area, had the lowest number of individuals and groups. The seasonal variation of the individual number was in order of autumn (1815) > spring (1623) > winter (1365) > summer (1276). Hierarchical clustering and detrended correspondence analysis also showed that the community composition of soil meso- and micro-fauna in different habitats exhibited distinct seasonal variation. In the same seasons, the community structure and composition of soil meso- and micro-fauna in different habitats were correlated to the degrees of human interferences and the properties of soil environment.

Greatest soil microbial diversity found in micro-habitats

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

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils

PubMed Central

Chiri, Eleonora; Nauer, Philipp A.; Rainer, Edda-Marie; Zeyer, Josef

2017-01-01

ABSTRACT Glacier forefield soils can provide a substantial sink for atmospheric CH4, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH4 oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH4 flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH4 uptake rates ranging from −3.7 to −0.03 mg CH4 m−2 day−1. Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH4 emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH4 flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH4 sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH4 inventories. IMPORTANCE Oxidation of methane (CH4) in well-drained, “upland” soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH4 oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH4 oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH4 in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH4 oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH4 inventories. PMID:28687652

High temporal and spatial variability of atmospheric-methane oxidation in Alpine glacier-forefield soils.

PubMed

Chiri, Eleonora; Nauer, Philipp A; Rainer, Edda-Marie; Zeyer, Josef; Schroth, Martin H

2017-07-07

Glacier-forefield soils can provide a substantial sink for atmospheric CH 4 , facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, location in different forefield landforms, and temporal fluctuations in soil-physical parameters. We assessed spatial and temporal variability of atmospheric CH 4 oxidation in an Alpine glacier forefield during the snow-free season 2013. We quantified CH 4 flux in soils of increasing age and in different landforms (sandhill, terrace, floodplain) using soil-gas-profile and static flux-chamber methods. To determine MOB abundance and community structure, we employed pmoA -gene-based quantitative PCR and targeted-amplicon sequencing. Uptake of CH 4 increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH 4 uptake ranging from -0.03- -3.7 mg CH 4 m -2 d -1 Floodplain and terrace soils exhibited smaller uptake and even intermittent CH 4 emissions. Linear mixed-effect models indicated that soil age and landform were dominating factors shaping CH 4 flux, followed by cumulative rainfall (weighted sum ≤ 4 d prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with Upland Soil Clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical, but differed significantly from highly variable sandhill-soil communities. We conclude that soil age and landform modulate the soil CH 4 sink strength in glacier forefields, and recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH 4 inventories. Importance Oxidation of methane (CH 4 ) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric CH 4 oxidation in mature upland soils, little is known about this important function in young, developing soils such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat.In this field-based study we investigated spatial and temporal variability of atmospheric CH 4 oxidation and associated MOB communities in Alpine glacier-forefield soils, aiming at better understanding factors that shape the sink for atmospheric CH 4 in this young soil ecosystem. The study contributes to the knowledge on the dynamics of atmospheric CH 4 oxidation in developing upland soils, and represents a further step towards the inclusion of Alpine glacier-forefield soils in global CH 4 inventories. Copyright © 2017 American Society for Microbiology.

Visualization of soil particulate organic matter by means of X-ray CT?

NASA Astrophysics Data System (ADS)

Sleutel, Steven; Van Loo, Denis; Maenhout, Peter; Van Hoorebeke, Luc; Cnudde, Veerle; De Neve, Stefaan

2014-05-01

The role of soil structure in organic matter (OM) stabilization has been primarily investigated through physical fractionation studies operative at the scale of aggregates and smaller organo-mineral particles. By narrowing down soil structure to an arrangement of mineral and organic particles, the majority of studies did not explore the spatial organization of the soil pore network, the actual habitat of microorganisms. The pore structure of soil can have a significant impact on soil processes like OM decomposition by excluding OM from micro-organisms in small pores, by regulating the diffusion of substrates and metabolites and by regulating aeration and presence of moisture. Because of its ability to visualize the 3D architecture of soil non-destructively, X-ray Computed Tomography (CT) is becoming a widespread tool for studying soil pore network structure. However, phase determination of pore space, soil OM, soil mineral matter (MM) and water is often limited even with the latest technological and software advances, allowing high resolution and better quality imaging. Contrast agents commonly used in histology enable enhancement of X-ray attenuation of targeted structures or compounds. Here we report on the first systematic investigation of the use of such X-ray contrast agents for soil research. An evaluation procedure as well as a method to apply the agents to soil samples was developed and applied on reference soil samples. The effectiveness and selectivity of the contrast agents was evaluated for soil organic matter (SOM), MM and water. Several products were found to selectively increase the attenuation of water or SOM. The four agents with the best OM-staining capabilities (Phosphomolybdenic acid (PMA), silver nitrate, lead nitrate and lead acetate) were further tested on an OM-MM mixture. Observed differences in reactivity of the staining agents with MM components were apparent, suggesting that contrasting agents may have to be selected for the specific composition of the soil mineral matrix. Furthermore, techniques such as multiple-energy scanning and K-edge imaging, even in the future perhaps in combination with spectral resolving detectors or spectroscopic techniques can could further enhance the potential benefit from this study of X-ray CT staining agents. The high Z elements of the staining agents have unique and characteristic traits that can be detected or quantified with the abovementioned techniques and methods. We conclude that, given resolution limits and inherent presence of partial volume effects staining, X-ray CT-based localization of discrete SOM particles will be limited to a lower limit of 20-50 µm. Still, the improved 3D visualization of OM and soil pore space opens up possibilities for tailored lab experiments with measures of microbial activity, which could generate new insights in carbon cycling at small scales. In addition, we report on a lab incubation experiment in which CO2 respiration from soil cores was monitored (headspace GC analysis) and an X-ray CT approach yielded soil pore size distributions. We incubated a sandy loam soil (with application of ground grass or sawdust) in 18 small aluminium rings (Ø 1 cm, h 1 cm). Bulk density was adjusted to 1.1 or 1.3 Mg m-3 (compaction) and 6 rings were filled at a coarser Coarse Sand:Fine Sand:Silt+Clay ratio. While compaction induced a strong reduction in the cumulative C mineralization for both grass and sawdust substrates, artificial change to a coarser soil texture only reduced net C mineralization from the added sawdust. There thus appears to be a strong interaction effect between soil pore structure and substrate type on substrate decomposition. Correlation coefficients between the C mineralization rates and volumes of 7 pore size classes (from the X-ray CT data) also showed an increasing positive correlation with increasing pore size. Since any particulate organic matter initially present in the soil was removed prior to the experiment (sieving, ashing the >53µm fraction and recombining with the <53µm fraction), the added OM can be localized by means of X-ray CT. Through on-going image analysis the surrounding porosity of the added grass or sawdust particles is being quantified to further study the interaction between the soil pore structure and substrate decomposition.

Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils

PubMed Central

Prescott, Cindy E.; Renaut, Sébastien; Terrat, Yves; Grayston, Sue J.

2017-01-01

ABSTRACT The Athabasca oil sand deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess whether the soil prokaryotic alpha diversity (α-diversity) and β-diversity in oil sand soils reconstructed 20 to 30 years previously and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal forest soils subject to wildfire disturbance. Prokaryotic α-diversity and β-diversity were assessed using massively parallel sequencing of 16S rRNA genes. The β-diversity, but not the α-diversity, differed between reconstructed and natural soils. Bacteria associated with an oligotrophic lifestyle were more abundant in natural forest soils, whereas bacteria associated with a copiotrophic lifestyle were more abundant in reconstructed soils. Ammonia-oxidizing archaea were most abundant in reconstructed soils planted with grasses. Plant species were the main factor influencing α-diversity in natural and in reconstructed soils. Nitrogen deposition, pH, and plant species were the main factors influencing the β-diversity of the prokaryotic communities in natural and reconstructed soils. The results highlight the importance of nitrogen deposition and aboveground-belowground relationships in shaping soil microbial communities in natural and reconstructed soils. IMPORTANCE Covering over 800 km2, land disturbed by the exploitation of the oil sands in Canada has to be restored. Here, we take advantage of the proximity between these reconstructed ecosystems and the boreal forest surrounding the oil sand mining area to study soil microbial community structure and processes in both natural and nonnatural environments. By identifying key characteristics shaping the structure of soil microbial communities, this study improved our understanding of how vegetation, soil characteristics and microbial communities interact and drive soil functions. PMID:28213542

Radioisotope tracer approach for understanding the impacts of global change-induced pedoturbation on soil C dynamics

NASA Astrophysics Data System (ADS)

Gonzalez-Meler, M. A.; Sturchio, N. C.; Sanchez-de Leon, Y.; Blanc-Betes, E.; Taneva, L.; Poghosyan, A.; Norby, R. J.; Filley, T. R.; Guilderson, T. P.; Welker, J. M.

2010-12-01

Biogeochemical carbon-cycle feedbacks to climate are apparent but uncertain, primarily because of gaps in mechanistic understanding on the ecosystem processes that drive carbon cycling and storage in terrestrial ecosystems, particularly in soils. Recent findings are increasingly recognizing the interaction between soil biota and the soil physical environment. Soil carbon turnover is partly determined by burial of organic matter and its physical and chemical protection. These factors are potentially affected by changes in climate (freezing-thawing or wet-drying cycles) or ecosystem structure including biological invasions. A major impediment to understanding dynamics of soil C in terrestrial systems is our inability to measure soil physical processes such as soil mixing rates or turnover of soil structures, including aggregates. Here we present a multiple radioisotope tracer approach (naturally occurring and man-made) to measure soil mixing rates in response to global change. We will present evidence of soil mixing rate changes in a temperate forest exposed to increased levels of atmospheric CO2 and in a tundra ecosystem exposed to increased thermal insulation. In both cases, radioisotope tracers proved to be an effective way to measure effects of global change on pedoturbation. Results also provided insights into the specific mechanisms involved in the responses. Elevated CO2 resulted in deeper soil mixing cells (increased by about 5cm on average) when compared to control soils as a consequence of changes in biota (increased root growth, higher earthworm density). In the tundra, soil warming induced higher rates of cryoturbation, resulting in what appears to be a net uplift of organic matter to the surface thereby exposing deeper C to decomposers. In both cases, global change factors affected the vertical distribution of C and changed the amount of bulk soil actively involved in soil processes. As a consequence, comparisons of C budgets to a given soil depth in response to global change factors may be misleading if they do not account for the depth change in the soil mixing cells.

Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils.

PubMed

Masse, Jacynthe; Prescott, Cindy E; Renaut, Sébastien; Terrat, Yves; Grayston, Sue J

2017-05-01

The Athabasca oil sand deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess whether the soil prokaryotic alpha diversity (α-diversity) and β-diversity in oil sand soils reconstructed 20 to 30 years previously and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal forest soils subject to wildfire disturbance. Prokaryotic α-diversity and β-diversity were assessed using massively parallel sequencing of 16S rRNA genes. The β-diversity, but not the α-diversity, differed between reconstructed and natural soils. Bacteria associated with an oligotrophic lifestyle were more abundant in natural forest soils, whereas bacteria associated with a copiotrophic lifestyle were more abundant in reconstructed soils. Ammonia-oxidizing archaea were most abundant in reconstructed soils planted with grasses. Plant species were the main factor influencing α-diversity in natural and in reconstructed soils. Nitrogen deposition, pH, and plant species were the main factors influencing the β-diversity of the prokaryotic communities in natural and reconstructed soils. The results highlight the importance of nitrogen deposition and aboveground-belowground relationships in shaping soil microbial communities in natural and reconstructed soils. IMPORTANCE Covering over 800 km 2 , land disturbed by the exploitation of the oil sands in Canada has to be restored. Here, we take advantage of the proximity between these reconstructed ecosystems and the boreal forest surrounding the oil sand mining area to study soil microbial community structure and processes in both natural and nonnatural environments. By identifying key characteristics shaping the structure of soil microbial communities, this study improved our understanding of how vegetation, soil characteristics and microbial communities interact and drive soil functions. Copyright © 2017 American Society for Microbiology.

Species richness and soil properties in Pinus ponderosa forests: A structural equation modeling analysis

USGS Publications Warehouse

Laughlin, D.C.; Abella, S.R.; Covington, W.W.; Grace, J.B.

2007-01-01

Question: How are the effects of mineral soil properties on understory plant species richness propagated through a network of processes involving the forest overstory, soil organic matter, soil nitrogen, and understory plant abundance? Location: North-central Arizona, USA. Methods: We sampled 75 0.05-ha plots across a broad soil gradient in a Pinus ponderosa (ponderosa pine) forest ecosystem. We evaluated multivariate models of plant species richness using structural equation modeling. Results: Richness was highest at intermediate levels of understory plant cover, suggesting that both colonization success and competitive exclusion can limit richness in this system. We did not detect a reciprocal positive effect of richness on plant cover. Richness was strongly related to soil nitrogen in the model, with evidence for both a direct negative effect and an indirect non-linear relationship mediated through understory plant cover. Soil organic matter appeared to have a positive influence on understory richness that was independent of soil nitrogen. Richness was lowest where the forest overstory was densest, which can be explained through indirect effects on soil organic matter, soil nitrogen and understory cover. Finally, model results suggest a variety of direct and indirect processes whereby mineral soil properties can influence richness. Conclusions: Understory plant species richness and plant cover in P. ponderosa forests appear to be significantly influenced by soil organic matter and nitrogen, which are, in turn, related to overstory density and composition and mineral soil properties. Thus, soil properties can impose direct and indirect constraints on local species diversity in ponderosa pine forests. ?? IAVS; Opulus Press.

Soil microbial community structure: mechanical disturbance alters soil microbial community

USDA-ARS?s Scientific Manuscript database

Soil microbes are responsible for soil nutrient cycling in both perennial and annual management systems for beef cattle and grain production. In the Southern Plains of Oklahoma, producers plant winter wheat (Triticum aestivum) in rotation with winter canola (Brassica rapa). Producers in the Southern...

Soil fungal communities respond to grassland plant community richness and soil edaphics

USDA-ARS?s Scientific Manuscript database

Fungal communities in soil have significant influences on terrestrial ecosystem dynamics, yet our understanding of the drivers of fungal diversity and community structure in soil is limited. Fungal communities associated with the rhizosphere of four native perennial grassland plant species grown in ...

Anaerobic soil disinfestation and Brassica seed meal amendment alter soil microbiology and system resistance

USDA-ARS?s Scientific Manuscript database

Brassica seed meal amendments and anaerobic soil disinfestation control a spectrum of soil-borne plant pathogens via a diversity of mechanisms. Transformations in microbial community structure and function in certain instances were determinants of disease control and enhanced plant performance. Fo...

NEGLECTED COMPONENTS OF BIODIVERSITY: SOIL ORIBATID MITES, COMMUNITY STRUCTURE AND SOIL RECOVERY

EPA Science Inventory

Oribatid mites are an abundant and diverse component of soils in regional pine forests, and are valuable in characterizing the biodiversity of these forested lands. We sampled oribatid mites using soil cores and leaf litterbags, in young aggrading forest stands. Comparing these...

A Novel Growing Device Inspired by Plant Root Soil Penetration Behaviors

PubMed Central

Sadeghi, Ali; Tonazzini, Alice; Popova, Liyana; Mazzolai, Barbara

2014-01-01

Moving in an unstructured environment such as soil requires approaches that are constrained by the physics of this complex medium and can ensure energy efficiency and minimize friction while exploring and searching. Among living organisms, plants are the most efficient at soil exploration, and their roots show remarkable abilities that can be exploited in artificial systems. Energy efficiency and friction reduction are assured by a growth process wherein new cells are added at the root apex by mitosis while mature cells of the root remain stationary and in contact with the soil. We propose a new concept of root-like growing robots that is inspired by these plant root features. The device penetrates soil and develops its own structure using an additive layering technique: each layer of new material is deposited adjacent to the tip of the device. This deposition produces both a motive force at the tip and a hollow tubular structure that extends to the surface of the soil and is strongly anchored to the soil. The addition of material at the tip area facilitates soil penetration by omitting peripheral friction and thus decreasing the energy consumption down to 70% comparing with penetration by pushing into the soil from the base of the penetration system. The tubular structure provides a path for delivering materials and energy to the tip of the system and for collecting information for exploratory tasks. PMID:24587244

Influence of Precipitation Regime on Microbial Decomposition Patterns in Semi-Arid Ecosystems

NASA Astrophysics Data System (ADS)

Feris, K. P.; Jilek, C.; Huber, D. P.; Reinhardt, K.; deGraaff, M.; Lohse, K.; Germino, M.

2011-12-01

In water-limited semi-arid sagebrush steppe ecosystems predicted changes in climate may manifest as a shift from historically winter/snow-dominated precipitation regimes to one dominated by spring rains. In these ecosystems soil microorganisms play a vital role in linking the effects of water availability and plant productivity to biogeochemical cycling. Patterns of soil microbial catalyzed organic matter decomposition patters (i.e. patterns of extracellular enzyme activity (EEA)) are thought to depend upon the quantity and quality of soil organic matter (SOM), pH, and mean annual precipitation (Sinsabaugh, 2008), and less on the timing and magnitude of precipitation. However, sagebrush-steppe plant communities respond strongly to changes in the timing and magnitude of precipitation, and preliminary findings by our group suggest that corresponding changes in SOM quantity, quality, N-cycle dynamics, and soil structure are occurring. Therefore, we hypothesized: 1) Shifts in the timing and magnitude of precipitation would indirectly affect soil microbial decomposition patterns via responses in the plant community structure; and 2) Changes in precipitation patterns can directly affect soil microbial community structure and function, in effect uncoupling the interaction between plant community structure and soil community structure. We tested our hypotheses by determining the influence of experimentally manipulated timing and magnitude of precipitation on soil microbial EEA using standard flourometric assays in soils sampled under plant canopies and plant interspaces. We assessed this response in a mature (18 + years) ecohydrologic field experiment in eastern Idaho that annually imitates three possible post climatic-shift precipitation regimes (Ambient (AMB): no additional precipitation, ~200mm annually; Summer (SUMM): 200mm provisioned at 50mm bi-weekly starting in June; and Fall/Spring (F/S): 200mm provisioned over 1-2 weeks in October or April) (n=3). Within plant interspaces Beta glucosaminide activity increased by 18% in treatments receiving additional F/S precipitation, whereas alpha glucopyranoside activity was lower in the F/S and SUMM plots. Conversely, underplant canopies alpha glucopyranoside activity increased by 15% in the SUMM and F/S precipitation treatments. Across treatments and sampling types (i.e. plant canopy vs. interspace), cellobioside activity levels are consistently elevated in response to additional precipitation compared to those of the control plots. When coupled with recent preliminary findings by our group regarding changes in plant and microbial community structure and SOM, C-storage, and soil structural responses, these preliminary findings suggest that 1) microbial community structure and function respond both directly and indirectly to changes in climate, and 2) thus provide a mechanism for changes in plant community structure to feed-forward to affect soil carbon decomposition patterns and ultimately soil carbon storage potential.

A dynamic organic soil biogeochemical model for simulating the effects of wildfire on soil environmental conditions and carbon dynamics of black spruce forests

Treesearch

Shuhua Yi; A. David McGuire; Eric Kasischke; Jennifer Harden; Kristen Manies; Michelle Mack; Merritt Turetsky

2010-01-01

Ecosystem models have not comprehensively considered how interactions among fire disturbance, soil environmental conditions, and biogeochemical processes affect ecosystem dynamics in boreal forest ecosystems. In this study, we implemented a dynamic organic soil structure in the Terrestrial Ecosystem Model (DOS-TEM) to investigate the effects of fire on soil temperature...

Soil macroinvertebrate communities across a productivity gradient in deciduous forests of eastern North America

Treesearch

Evelyn S. Wenk; Mac A. Callaham; Joseph O' Brien; Paul J. Hanson

2016-01-01

Within the temperate, deciduous forests of the eastern US, diverse soil-fauna communities are structured by a combination of environmental gradients and interactions with other biota. The introduction of non-native soil taxa has altered communities and soil processes, and adds another degree of variability to these systems. We sampled soil macroinvertebrate abundance...

Compositional changes of soil organic matter with cropping time were more profound in subsoils and distinct between Phaeozem and Chernozem in Northeast China

USDA-ARS?s Scientific Manuscript database

Soil organic matter (SOM) contributes to soil processes and is found both in shallow and deep soil layers. Its activity can be affected by its chemical composition, yet knowledge is incomplete of how land use alters the structural composition of SOM throughout the profiles of different soil types. T...

Do anaerobic digestates promote dispersion, acidification and water repellency in soils?

NASA Astrophysics Data System (ADS)

Voelkner, Amrei; Holthusen, Dörthe; Horn, Rainer

2014-05-01

Digestates are used as organic fertilizer on agricultural land due to their high amounts of nutrients (e.g. potassium, sodium). It is commonly expected that the application of sludge derived from anaerobic digestion can influence the soil structure and soil stability. Due to the fact that digestates contain large quantities of monovalent salts and long-chained fatty acids, the consequence of sludge amendment can be soil degradation caused by acidification, dispersion and increased water-repellency. Thus, water infiltration can be impeded which results in a preservation of stable soil aggregates. However, a diminished water infiltration can support water erosion and preferential flow of easy soluble nutrients into the groundwater. Our research was conducted with different digestates derived from maize, wheat and sugar beet to examine occurring processes in soils of two different textures after the application of anaerobic sludges. Particularly, we focused on the wetting properties of the soil. For this purpose, the wetting behavior was investigated by determining the sorptivity-based Repellency Index with moist samples and the contact angle with homogenized, air-dried soil material. Further surveys were carried out to assess the flow behavior of digestates application and the deformation of the particle-to-particle association by microscaled shearing. Additionally, the acidification process in the soil as a result of sludge application was investigated. To account for the dispersive impact of digestates, the turbidity of soil suspensions was ascertained. We summarize from the results that the digestates have a clear impact on the water repellency of the soil. We recognized a shift to more hydrophobic conditions. Partially, the pH remains on a high level due to the alkaline digestate, but several samples show a decline of pH, depending on the soil texture, respectively. However, soil structure was weakened as was shown by an increase of turbidity. As a conclusion, we point out the necessity to take into account the impact which anaerobic digestates might have on soil structure and stability in addition to their fertilizing effect to sustain the soil in a good state.

Energy Transformations of Soil Organic Matter in a Changing World

NASA Astrophysics Data System (ADS)

Herrmann, A. M.; Coucheney, E.; Grice, S. M.; Ritz, K.; Harris, J.

2011-12-01

The role of soils in governing the terrestrial carbon balance is acknowledged as being important but remains poorly understood within the context of climate change. Soils exchange energy with their surroundings and are therefore open systems thermodynamically, but little is known how energy transformations of decomposition processes are affected by temperature. Soil organic matter and the soil biomass can be conceptualised as analogous to the 'fuel' and 'biological engine' of the earth, respectively, and are pivotal in driving the belowground carbon cycle. Thermodynamic principles of soil organic matter decomposition were evaluated by means of isothermal microcalorimetry (TAM Air, TA Instruments, Sollentuna Sweden: (i) Mineral forest soils from the Flakaliden long-term nitrogen fertilisation experiment (Sweden) were amended with a range of different substrates representing structurally simple to complex, ecologically pertinent organic matter and heat signatures were determined at temperatures between 5 and 25°C. (ii) Thermodynamic and resource-use efficiencies of the biomass were determined in arable soils which received contrasting long-term management regimes with respect to organic matter and nitrogen since 1956. The work showed that (i) structurally labile components have higher activation energy and temperature dependence than structurally more complex organic components. This is, however, in contrast to the thermodynamic argument which suggests the opposite that reactions metabolising structurally complex, aromatic components have higher temperature dependence than reactions metabolising structurally more labile components. (ii) Microbial communities exposed to long-term stress by heavy metal and low pH were less thermodynamic efficient and showed a decrease in resource-use efficiency in comparison with conventional input regimes. Differences in efficiencies were mirrored in both the phenotypic and functional profiles of the communities. We will present our findings illustrating the capacity of isothermal microcalorimetry to evaluate temperature dependencies of soil organic matter decomposition, associated energy transformations and thermodynamic principles in soil ecosystems.

Dissecting the multi-scale spatial relationship of earthworm assemblages with soil environmental variability.

PubMed

Jiménez, Juan J; Decaëns, Thibaud; Lavelle, Patrick; Rossi, Jean-Pierre

2014-12-05

Studying the drivers and determinants of species, population and community spatial patterns is central to ecology. The observed structure of community assemblages is the result of deterministic abiotic (environmental constraints) and biotic factors (positive and negative species interactions), as well as stochastic colonization events (historical contingency). We analyzed the role of multi-scale spatial component of soil environmental variability in structuring earthworm assemblages in a gallery forest from the Colombian "Llanos". We aimed to disentangle the spatial scales at which species assemblages are structured and determine whether these scales matched those expressed by soil environmental variables. We also tested the hypothesis of the "single tree effect" by exploring the spatial relationships between root-related variables and soil nutrient and physical variables in structuring earthworm assemblages. Multivariate ordination techniques and spatially explicit tools were used, namely cross-correlograms, Principal Coordinates of Neighbor Matrices (PCNM) and variation partitioning analyses. The relationship between the spatial organization of earthworm assemblages and soil environmental parameters revealed explicitly multi-scale responses. The soil environmental variables that explained nested population structures across the multi-spatial scale gradient differed for earthworms and assemblages at the very-fine- (<10 m) to medium-scale (10-20 m). The root traits were correlated with areas of high soil nutrient contents at a depth of 0-5 cm. Information on the scales of PCNM variables was obtained using variogram modeling. Based on the size of the plot, the PCNM variables were arbitrarily allocated to medium (>30 m), fine (10-20 m) and very fine scales (<10 m). Variation partitioning analysis revealed that the soil environmental variability explained from less than 1% to as much as 48% of the observed earthworm spatial variation. A large proportion of the spatial variation did not depend on the soil environmental variability for certain species. This finding could indicate the influence of contagious biotic interactions, stochastic factors, or unmeasured relevant soil environmental variables.

An ecosystem approach to assess soil quality in organically and conventionally managed farms in Iceland and Austria

NASA Astrophysics Data System (ADS)

van Leeuwen, J. P.; Lehtinen, T.; Lair, G. J.; Bloem, J.; Hemerik, L.; Ragnarsdóttir, K. V.; Gísladóttir, G.; Newton, J. S.; de Ruiter, P. C.

2014-06-01

Intensive agricultural production can be an important driver for the loss of long-term soil quality. For this reason, the European Critical Zone Observatory (CZO) network adopted four pairs of agricultural CZO sites that differ in their management: conventional or organic. The CZO sites include two pairs of grassland farms in Iceland and two pairs of arable farms in Austria. Conventional fields differed from the organic fields in the use of artificial fertilizers and pesticides. Soils of these eight farms were analysed in terms of their physical, chemical, and biological properties, including soil aggregate size distribution, soil organic matter contents, abundance of soil microbes and soil fauna, and taxonomic diversity of soil microarthropods. In Icelandic grasslands, organically farmed soils had larger mean weight diameters than the conventional farms, while there were no differences in the Austrian farms. Organic farming did neither systematically influence organic matter contents or composition, nor soil carbon and nitrogen contents. Also soil food web structures, in terms of presence of trophic groups of soil organisms, were highly similar among all farms, indicating a low sensitivity of trophic structure to land use or climate. However, soil organism biomass, especially of bacteria and nematodes, was consistently higher in organic farms than in conventional farms. Within the microarthropods, also taxonomic diversity was systematically higher in the organic farms compared to the conventional farms. This difference was found across countries, farm-, crop- and soil-types. The results do not show systematic differences in physical and chemical properties between organic and conventional farms, but confirm that organic farming can enhance soil organism biomass, and that microarthropod diversity is a sensitive and consistent indicator for land management.

Degradation of 4-chlorophenol and microbial diversity in soil inoculated with single Pseudomonas sp. CF600 and Stenotrophomonas maltophilia KB2.

PubMed

Nowak, Agnieszka; Mrozik, Agnieszka

2018-06-01

Soil contamination with chlorophenols is a serious problem all over the world due to their common use in different branches of industry and agriculture. The objective of this study was to determine whether bioaugmenting soil with single Pseudomonas sp. CF600 and Stenotrophomonas maltophilia KB2 and additional carbon sources such as phenol (P) and sodium benzoate (SB) could enhance the degradation of 4-chlorophenol (4-CP). During the degradation experiment, the number of bacteria as well as the structural and functional diversity of the soil microbial communities were determined. It was found that the most effective degradation of 4-CP in the soil was observed after it was inoculated with CF600 and the addition of SB. The biodegradation of five doses of 4-CP in this soil proceeded within 100 days. At the same time, the rate of the disappearance of 4-CP in the soil that had been bioaugmented with CF600 and contaminated with 4-CP and P was 5-6.5 times lower compared to its rate of disappearance in the soil that had been contaminated with 4-CP. The biodegradation of 4-CP in all of the treated and untreated soils was accompanied by a systematic decrease in the number of heterotrophic bacteria (THB) ranging between 13 and 40%. It was also proven that the tested aromatic compounds affected the soil microbial community structure through an increase in the marker fatty acids for Gram-negative bacteria (BG-) and fungi (F). The essential changes in the patterns of the fatty acid methyl esters (FAMEs) for the polluted soil included an increase in the fatty acid saturation and hydroxy fatty acid abundance. The obtained results also indicated that the introduction of CF600 into the soil contaminated with 4-CP and SB or P caused an increase in the functional diversity of the soil microorganisms. In contrast, in the soil that had been inoculated with KB2 and in the non-inoculated soil, the addition of 4-CP and P decreased the microbial activity. In conclusion, the inoculation of both strains into contaminated soil with aromatic compounds caused irreversible changes in the functional and structural diversity of the soil microbial communities. Copyright © 2018 Elsevier Ltd. All rights reserved.

Multivariate functions for predicting the sorption of 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5-tricyclohexane (RDX) among taxonomically distinct soils.

PubMed

Katseanes, Chelsea K; Chappell, Mark A; Hopkins, Bryan G; Durham, Brian D; Price, Cynthia L; Porter, Beth E; Miller, Lesley F

2016-11-01

After nearly a century of use in numerous munition platforms, TNT and RDX contamination has turned up largely in the environment due to ammunition manufacturing or as part of releases from low-order detonations during training activities. Although the basic knowledge governing the environmental fate of TNT and RDX are known, accurate predictions of TNT and RDX persistence in soil remain elusive, particularly given the universal heterogeneity of pedomorphic soil types. In this work, we proposed a new solution for modeling the sorption and persistence of these munition constituents as multivariate mathematical functions correlating soil attribute data over a variety of taxonomically distinct soil types to contaminant behavior, instead of a single constant or parameter of a specific absolute value. To test this idea, we conducted experiments measuring the sorption of TNT and RDX on taxonomically different soil types that were extensively physical and chemically characterized. Statistical decomposition of the log-transformed, and auto-scaled soil characterization data using the dimension-reduction technique PCA (principal component analysis) revealed a strong latent structure based in the multiple pairwise correlations among the soil properties. TNT and RDX sorption partitioning coefficients (KD-TNT and KD-RDX) were regressed against this latent structure using partial least squares regression (PLSR), generating a 3-factor, multivariate linear functions. Here, PLSR models predicted KD-TNT and KD-RDX values based on attributes contributing to endogenous alkaline/calcareous and soil fertility criteria, respectively, exhibited among the different soil types: We hypothesized that the latent structure arising from the strong covariance of full multivariate geochemical matrix describing taxonomically distinguished soil types may provide the means for potentially predicting complex phenomena in soils. The development of predictive multivariate models tuned to a local soil's taxonomic designation would have direct benefit to military range managers seeking to anticipate the environmental risks of training activities on impact sites. Published by Elsevier Ltd.

Influence of management history and landscape variables on soil organic carbon and soil redistribution

USGS Publications Warehouse

Venteris, E.R.; McCarty, G.W.; Ritchie, J.C.; Gish, T.

2004-01-01

Controlled studies to investigate the interaction between crop growth, soil properties, hydrology, and management practices are common in agronomy. These sites (much as with real world farmland) often have complex management histories and topographic variability that must be considered. In 1993 an interdisiplinary study was started for a 20-ha site in Beltsville, MD. Soil cores (271) were collected in 1999 in a 30-m grid (with 5-m nesting) and analyzed as part of the site characterization. Soil organic carbon (SOC) and 137Cesium (137Cs) were measured. Analysis of aerial photography from 1992 and of farm management records revealed that part of the site had been maintained as a swine pasture and the other portion as cropped land. Soil properties, particularly soil redistribution and SOC, show large differences in mean values between the two areas. Mass C is 0.8 kg m -2 greater in the pasture area than in the cropped portion. The pasture area is primarily a deposition site, whereas the crop area is dominated by erosion. Management influence is suggested, but topographic variability confounds interpretation. Soil organic carbon is spatially structured, with a regionalized variable of 120 m. 137Cs activity lacks spatial structure, suggesting disturbance of the profile by animal activity and past structures such as swine shelters and roads. Neither SOC nor 137Cs were strongly correlated to terrain parameters, crop yields, or a seasonal soil moisture index predicted from crop yields. SOC and 137Cs were weakly correlated (r2 ???0.2, F-test P-value 0.001), suggesting that soil transport controls, in part, SOC distribution. The study illustrates the importance of past site history when interpreting the landscape distribution of soil properties, especially those strongly influenced by human activity. Confounding variables, complex soil hydrology, and incomplete documentation of land use history make definitive interpretations of the processes behind the spatial distributions difficult. Such complexity may limit the accuracy of scaling approaches to mapping SOC and soil redistribution.

Soil microbial community structure and diversity are largely influenced by soil pH and nutrient quality in 78-year-old tree plantations

NASA Astrophysics Data System (ADS)

Zhou, Xiaoqi; Guo, Zhiying; Chen, Chengrong; Jia, Zhongjun

2017-04-01

Forest plantations have been recognised as a key strategy management tool for stocking carbon (C) in soils, thereby contributing to climate warming mitigation. However, long-term ecological consequences of anthropogenic forest plantations on the community structure and diversity of soil microorganisms and the underlying mechanisms in determining these patterns are poorly understood. In this study, we selected 78-year-old tree plantations that included three coniferous tree species (i.e. slash pine, hoop pine and kauri pine) and a eucalypt species in subtropical Australia. We investigated the patterns of community structure, and the diversity of soil bacteria and eukaryotes by using high-throughput sequencing of 16S rRNA and 18S rRNA genes. We also measured the potential methane oxidation capacity under different tree species. The results showed that slash pine and Eucalyptus significantly increased the dominant taxa of bacterial Acidobacteria and the dominant taxa of eukaryotic Ascomycota, and formed clusters of soil bacterial and eukaryotic communities, which were clearly different from the clusters under hoop pine and kauri pine. Soil pH and nutrient quality indicators such as C : nitrogen (N) and extractable organic C : extractable organic N were key factors in determining the patterns of soil bacterial and eukaryotic communities between the different tree species treatments. Slash pine and Eucalyptus had significantly lower soil bacterial and eukaryotic operational taxonomical unit numbers and lower diversity indices than kauri pine and hoop pine. A key factor limitation hypothesis was introduced, which gives a reasonable explanation for lower diversity indices under slash pine and Eucalyptus. In addition, slash pine and Eucalyptus had a higher soil methane oxidation capacity than the other tree species. These results suggest that significant changes in soil microbial communities may occur in response to chronic disturbance by tree plantations, and highlight the importance of soil pH and physiochemical characteristics in microbially mediated ecological processes in forested soils.

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.

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.

PubMed

Liu, Peng; Jia, Shuyu; He, Xiwei; Zhang, Xuxiang; Ye, Lin

2017-12-01

Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of Lime on characteristics of consolidation, strength, swelling and plasticity of fine grained soil

NASA Astrophysics Data System (ADS)

Estabragh, A. R.; Bordbar, A. T.; Parsaee, B.; Eskandari, Gh.

2009-04-01

Using Lime as an additive material to clayey soil is one of the best effective technique in building the soil structures to get some purposes such as soil stabilization, soil reinforcement and decreasing soil swelling. In this research the effect of Lime on geotechnical characteristics of a clayey soil was investigated. Soil specimen types used in this study were consisted of clayey soil as the control treatment and clay mixed with different weight fractions of lime, 4, 6, 8 & 10 percent. Some experiments such as CBR, atterburg limits, compaction, consolidation and swelling was conducted on specimens. Results revealed that adding lime to soil would change its physical and mechanical properties. Adding lime increase the compression strength and consolidation coefficient and decrease swelling potential and maximum dry density. According to the results, Atterburg experiments show that presence of lime in soil increase the liquid limit of low plasticity soil and decrease the liquid limit of high plasticity soil, but totally it decreases the plasticity index of soils. Key words: soil stabilization, lime, compression strength, swelling, atterburg limits, compaction

Aggregate Stability and Erodibility of Purple Soil on Sloping Farmland as affected by different Soil Thickness

NASA Astrophysics Data System (ADS)

Huang, Xinjun; Zhang, Qingwen; Chen, Shanghong; Dong, Yuequn; Xiao, Meijia; Hamed, Lamy Mamdoh Mohamed

2017-04-01

Soil thickness is basic limiting condition for purple soil, not only due to its effect on crop production, but also its effect on soil structure. Steady-state of soil thickness will be achieved over time, as result the soil aggregate which the key factor of soil erodibility can be enhanced as well. However, the effect of soil thickness on aggregates stability and the characteristics of soil erodibility in sloping land have not yet fully understood.A field survey was conducted in hilly area of Sichuan region located in southeast China to study the relationship between soil aggregate stability and soil erodibility on sloping farmland under different four thickness (100cm, 80cm, 60cm, 30cm) of purple soil. Based on two different sieving methods (Dry and Wet sieving), we analyzed soil aggregate stability and its effect on soil erodibility within depth of 0-30cm soil layers. The results indicated that: Water stable aggregate on sloping farmland was ranged between 37.9% to 58.6%, where it increased with increasing the soil thickness. Moreover, fractal dimension calculated from dry-sieving and wet-sieving was 2.06-2.49 and 2.70-2.85 respectively, where it decreased with decreasing the soil thickness. The overall soil erodibility was 0.05-1.00 and a negative significant correlation was found between soil aggregate stability and erodibility(P<0.01). Moreover, farmland with thick soil profile tended to be high in soil erodibility within the top soil layer (0-30cm). The results reveal that soil thickness can affect soil aggregate stability as well as erodibility. As soil thickness increased, the top soil became more stable and less erodible. Keywords：purple soil; soil thickness; soil aggregate；soil erodibility

Soil aggregation, erodibility, and erosion rates in mountain soils (NW Alps, Italy)

NASA Astrophysics Data System (ADS)

Stanchi, S.; Falsone, G.; Bonifacio, E.

2015-04-01

Erosion is a relevant soil degradation factor in mountain agrosilvopastoral ecosystems that can be enhanced by the abandonment of agricultural land and pastures left to natural evolution. The on-site and off-site consequences of soil erosion at the catchment and landscape scale are particularly relevant and may affect settlements at the interface with mountain ecosystems. RUSLE (Revised Universal Soil Loss Equation) estimates of soil erosion consider, among others, the soil erodibility factor (K), which depends on properties involved in structure and aggregation. A relationship between soil erodibility and aggregation should therefore be expected. However, erosion may limit the development of soil structure; hence aggregates should not only be related to erodibility but also partially mirror soil erosion rates. The aim of the research was to evaluate the agreement between aggregate stability and erosion-related variables and to discuss the possible reasons for discrepancies in the two kinds of land use considered (forest and pasture). Topsoil horizons were sampled in a mountain catchment under two vegetation covers (pasture vs. forest) and analyzed for total organic carbon, total extractable carbon, pH, and texture. Soil erodibility was computed, RUSLE erosion rate was estimated, and aggregate stability was determined by wet sieving. Aggregation and RUSLE-related parameters for the two vegetation covers were investigated through statistical tests such as ANOVA, correlation, and regression. Soil erodibility was in agreement with the aggregate stability parameters; i.e., the most erodible soils in terms of K values also displayed weaker aggregation. Despite this general observation, when estimating K from aggregate losses the ANOVA conducted on the regression residuals showed land-use-dependent trends (negative average residuals for forest soils, positive for pastures). Therefore, soil aggregation seemed to mirror the actual topsoil conditions better than soil erodibility. Several hypotheses for this behavior were discussed. A relevant effect of the physical protection of the organic matter by the aggregates that cannot be considered in K computation was finally hypothesized in the case of pastures, while in forests soil erodibility seemed to keep trace of past erosion and depletion of finer particles. A good relationship between RUSLE soil erosion rates and aggregate stability occurred in pastures, while no relationship was visible in forests. Therefore, soil aggregation seemed to capture aspects of actual vulnerability that are not visible through the erodibility estimate. Considering the relevance and extension of agrosilvopastoral ecosystems partly left to natural colonization, further studies on litter and humus protective action might improve the understanding of the relationship among erosion, erodibility, and structure.

De-icing salt contamination reduces urban tree performance in structural soil cells.

PubMed

Ordóñez-Barona, Camilo; Sabetski, Vadim; Millward, Andrew A; Steenberg, James

2018-03-01

Salts used for de-icing roads and sidewalks in northern climates can have a significant impact on water quality and vegetation. Sub-surface engineering systems, such as structural soil cells, can regulate water runoff and pollutants, and provide the necessary soil volume and irrigation to grow trees. However, the ability of such systems to manage de-icing salt contamination, and the impact of this contamination on the trees growing in them, have not been evaluated. We report on an field investigation of de-icing salt contamination in structural cells in two street-revitalization projects in Toronto, Canada, and the impact of this contamination on tree performance. We analyzed soil chemistry and collected tree attributes; these data were examined together to understand the effect of salinity on tree mortality rates and foliar condition. Data collected from continuous soil salinity loggers from April to June for one of the two sites were used to determine whether there was a long-term accumulation of salts in the soils. Results for both sites indicate that both sites displayed high salinity and alkalinity, with levels elevated beyond those suggested before those reported to cause negative tree effects. For one site, trees that were alive and trees that had a better foliar condition had significantly lower levels of soil salinity and alkalinity than other trees. High salinity and alkalinity in the soil were also associated with lower nutrient levels for both sites. Although tests for salinity accumulation in the soils of one site were negative, a longer monitoring of the soil conditions within the soil cells is warranted. Despite structural cells being increasingly utilized for their dual role in storm-water management and tree establishment, there may be a considerable trade-off between storm-water management and urban-forest function in northern climates where de-icing salt application continues to be commonplace. Copyright © 2017 Elsevier Ltd. All rights reserved.

Synchrotron-based micro and nanotomographic investigations of soil aggregate microbial and pore structure

NASA Astrophysics Data System (ADS)

Kemner, K. M.; O'Brien, S.; Whiteside, M. D.; Sholto-Douglas, D.; Antipova, O.; Bailey, V.; Boyanov, M.; Dohnalkova, A.; Gursoy, D.; Kovarik, L.; Lai, B.; Roehrig, C.; Vogt, S.

2017-12-01

Soil is a highly complex network of pore spaces, minerals, and organic matter (e.g., roots, fungi, and bacteria), making it physically heterogeneous over nano- to macro-scales. Such complexity arises from feedbacks between physical processes and biological activity that generate a dynamic, self-organizing 3D complex. Since we first demonstrated the utility of synchrotron-based transmission tomography to image internal soil aggregate structure [Kemner et al., 1998], we and many other researchers have made use of and have advanced the application of this technique. However, our understanding of how microbes and microbial metabolism are distributed throughout soil aggregates is limited, because no technique is available to image the soil pore network and the life that inhabits it. X-ray transmission microtomography can provide highly detailed 3D renderings of soil structure but cannot distinguish cells from other electron-light material such as air or water. However, the use of CdSe quantum dots (QDs) as a reporter of bacterial presence enables us to overcome this constraint, instilling bacterial cells with enough contrast to detect them and their metabolic functions in their opaque soil habitat, with hard x-rays capable of penetrating 3D soil structures at high resolution. Previous transmission tomographic imaging of soil aggregates with high energy synchrotron x-rays has demonstrated 700 nm3 voxel spatial resolution. These and recent results from nanotomographic x-ray transmission imaging of soil aggregates with 30 nm3 voxel resolution will be presented. In addition, results of submicron voxel-sized x-ray fluorescence 3D imaging to determine microbial distributions within soil aggregates and the critical role to be played by the upgrade of the Advanced Photon Source for 100-1000X increases in hard x-ray brilliance will also be presented. *Kemner, et al., SPIE 3449, 45-53, 1998

Comparative molecular analysis of chemolithoautotrophic bacterial diversity and community structure from coastal saline soils, Gujarat, India

PubMed Central

2012-01-01

Background Soils harbour high diversity of obligate as well as facultative chemolithoautotrophic bacteria that contribute significantly to CO2 dynamics in soil. In this study, we used culture dependent and independent methods to assess the community structure and diversity of chemolithoautotrophs in agricultural and coastal barren saline soils (low and high salinity). We studied the composition and distribution of chemolithoautotrophs by means of functional marker gene cbbL encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase and a phylogenetic marker 16S rRNA gene. The cbbL form IA and IC genes associated with carbon fixation were analyzed to gain insight into metabolic potential of chemolithoautotrophs in three soil types of coastal ecosystems which had a very different salt load and sulphur content. Results In cbbL libraries, the cbbL form IA was retrieved only from high saline soil whereas form IC was found in all three soil types. The form IC cbbL was also amplified from bacterial isolates obtained from all soil types. A number of novel monophyletic lineages affiliated with form IA and IC phylogenetic trees were found. These were distantly related to the known cbbL sequences from agroecosystem, volcanic ashes and marine environments. In 16S rRNA clone libraries, the agricultural soil was dominated by chemolithoautotrophs (Betaproteobacteria) whereas photoautotrophic Chloroflexi and sulphide oxidizers dominated saline ecosystems. Environmental specificity was apparently visible at both higher taxonomic levels (phylum) and lower taxonomic levels (genus and species). The differentiation in community structure and diversity in three soil ecosystems was supported by LIBSHUFF (P = 0.001) and UniFrac. Conclusion This study may provide fundamentally new insights into the role of chemolithoautotrophic and photoautotrophic bacterial diversity in biochemical carbon cycling in barren saline soils. The bacterial communities varied greatly among the three sites, probably because of differences in salinity, carbon and sulphur contents. The cbbL form IA-containing sulphide-oxidizing chemolithotrophs were found only in high saline soil clone library, thus giving the indication of sulphide availability in this soil ecosystem. This is the first comparative study of the community structure and diversity of chemolithoautotrophic bacteria in coastal agricultural and saline barren soils using functional (cbbL) and phylogenetic (16S rDNA) marker genes. PMID:22834535

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.

Correspondence between vegetation and soils in wetlands and nearby uplands

USGS Publications Warehouse

Scott, Michael L.; Slauson, William L.; Segelquist, Charles A.; Auble, Gregor T.

1989-01-01

The association between vegetation and soils from a geographically broad sampling of wetlands and adjoining uplands is reported for 38 hydric and 26 nonhydric soils, as recognized in the hydric soils list of the Soil Conservation Service. Wetlands represented in the study include estuaries, pitcher plant bogs, prairie depressional wetlands, and western riparian lands. The agreement between vegetation and soils is clear with few exceptions. In general, hydric soils support hydrophytic plant communities, and nonhydric soils support upland communities. Only 10% of the hydric soils sampled support upland communities and only 15% of the nonhydric soils support wetland communities. Exceptions to the correspondence between vegetation and soils are discussed; local hydrology, the transitional nature of some soils, and other determinants of wetland vegetation structure (e.g., salinity, disturbance) seem to account for many of the observed discrepancies. A method that simplifies the complexity of soils and vegetation cannot be expected to represent accurately all details of their interrelations.

Afforestation neutralizes soil pH.

PubMed

Hong, Songbai; Piao, Shilong; Chen, Anping; Liu, Yongwen; Liu, Lingli; Peng, Shushi; Sardans, Jordi; Sun, Yan; Peñuelas, Josep; Zeng, Hui

2018-02-06

Soil pH regulates soil biogeochemical processes and has cascading effects on terrestrial ecosystem structure and functions. Afforestation has been widely adopted to increase terrestrial carbon sequestration and enhance water and soil preservation. However, the effect of afforestation on soil pH is still poorly understood and inconclusive. Here we investigate the afforestation-caused soil pH changes with pairwise samplings from 549 afforested and 148 control plots in northern China. We find significant soil pH neutralization by afforestation-afforestation lowers pH in relatively alkaline soil but raises pH in relatively acid soil. The soil pH thresholds (T pH ), the point when afforestation changes from increasing to decreasing soil pH, are species-specific, ranging from 5.5 (Pinus koraiensis) to 7.3 (Populus spp.) with a mean of 6.3. These findings indicate that afforestation can modify soil pH if tree species and initial pH are properly matched, which may potentially improve soil fertility and promote ecosystem productivity.

Dynamics of Verticillium species microsclerotia in field soils in response to fumigation, cropping patterns, and flooding

USDA-ARS?s Scientific Manuscript database

Many soil-inhabiting fungi are capable of surviving the dynamic soil microenvironment through the formation of resilient resting structures, such as thick-walled spores, melanized hyphae, and sclerotia. Verticillium dahliae is a soil-inhabiting, economically significant plant pathogenic fungus that ...

Retention of Nickel in Soils: Sorption-Desorption and Extended X-ray Absorption Fine Structure Experiments

EPA Science Inventory

Adsorption and desorption of heavy metals in soils are primary factors that influence their bioavailability and mobility in the soil profile. To examine the characteristics of nickel (Ni) adsorption-desorption in soils, kinetic batch experiments were carried out followed by Ni re...

Impacts of deficit irrigation and altered rooting patterns on soil structure and associated soil properties

USDA-ARS?s Scientific Manuscript database

A better understanding of belowground systems and overall management impacts on soil health is needed to improve crop production and long-term sustainability under deficit irrigation. This study investigates effects of deficit irrigation on rooting patterns in maize and subsequent impacts on soil pr...

Patterns of soil community structure differ by scale and ecosystem type along a large-scale precipitation gradient

USDA-ARS?s Scientific Manuscript database

Climate models predict increased variability in precipitation regimes, which will likely increase frequency/duration of drought. Reductions in soil moisture affect physical and chemical characteristics of the soil habitat and can influence soil organisms such as mites and nematodes. These organisms ...

Soil microbial community structure and target organisms under different fumigation treatments

USDA-ARS?s Scientific Manuscript database

Several high-value crop producers in California rely heavily on soil fumigants to control key diseases, nematodes, weeds and volunteer crops. Fumigants with broad biocidal activity can affect both target and non-target soil organisms. The ability of non-target soil organisms to recover after fumigat...

Responses of redwood soil microbial community structure and N transformations to climate change

Treesearch

Damon C. Bradbury; Mary K. Firestone

2012-01-01

Soil microorganisms perform critical ecosystem functions, including decomposition, nitrogen (N) mineralization and nitrification. Soil temperature and water availability can be critical determinants of the rates of these processes as well as microbial community composition and structure. This research examined how changes in climate affect bacterial and fungal...

Uncovering trophic positions and food resources of soil animals using bulk natural stable isotope composition.

PubMed

Potapov, Anton M; Tiunov, Alexei V; Scheu, Stefan

2018-06-19

Despite the major importance of soil biota in nutrient and energy fluxes, interactions in soil food webs are poorly understood. Here we provide an overview of recent advances in uncovering the trophic structure of soil food webs using natural variations in stable isotope ratios. We discuss approaches of application, normalization and interpretation of stable isotope ratios along with methodological pitfalls. Analysis of published data from temperate forest ecosystems is used to outline emerging concepts and perspectives in soil food web research. In contrast to aboveground and aquatic food webs, trophic fractionation at the basal level of detrital food webs is large for carbon and small for nitrogen stable isotopes. Virtually all soil animals are enriched in 13 C as compared to plant litter. This 'detrital shift' likely reflects preferential uptake of 13 C-enriched microbial biomass and underlines the importance of microorganisms, in contrast to dead plant material, as a major food resource for the soil animal community. Soil organic matter is enriched in 15 N and 13 C relative to leaf litter. Decomposers inhabiting mineral soil layers therefore might be enriched in 15 N resulting in overlap in isotope ratios between soil-dwelling detritivores and litter-dwelling predators. By contrast, 13 C content varies little between detritivores in upper litter and in mineral soil, suggesting that they rely on similar basal resources, i.e. little decomposed organic matter. Comparing vertical isotope gradients in animals and in basal resources can be a valuable tool to assess trophic interactions and dynamics of organic matter in soil. As indicated by stable isotope composition, direct feeding on living plant material as well as on mycorrhizal fungi is likely rare among soil invertebrates. Plant carbon is taken up predominantly by saprotrophic microorganisms and channelled to higher trophic levels of the soil food web. However, feeding on photoautotrophic microorganisms and non-vascular plants may play an important role in fuelling soil food webs. The trophic niche of most high-rank animal taxa spans at least two trophic levels, implying the use of a wide range of resources. Therefore, to identify trophic species and links in food webs, low-rank taxonomic identification is required. Despite overlap in feeding strategies, stable isotope composition of the high-rank taxonomic groups reflects differences in trophic level and in the use of basal resources. Different taxonomic groups of predators and decomposers are likely linked to different pools of organic matter in soil, suggesting different functional roles and indicating that trophic niches in soil animal communities are phylogenetically structured. During last two decades studies using stable isotope analysis have elucidated the trophic structure of soil communities, clarified basal food resources of the soil food web and revealed links between above- and belowground ecosystem compartments. Extending the use of stable isotope analysis to a wider range of soil-dwelling organisms, including microfauna, and a larger array of ecosystems provides the perspective of a comprehensive understanding of the structure and functioning of soil food webs. © 2018 Cambridge Philosophical Society.

Fate and effect of imidacloprid on vermicompost-amended soils under dissimilar conditions: Risk for soil functions, structure, and bacterial abundance.

PubMed

Castillo Diaz, Jean Manuel; Martin-Laurent, Fabrice; Beguet, Jérèmie; Nogales, Rogelio; Romero, Esperanza

2017-02-01

The fate and impact of pesticide on soil depend partly on the agricultural practices, such as prior treatment with pesticide and/or organic amendments. As a means of determining how the previous soil conditions can affect the fate of imidacloprid (IMI) and its effect on soil functions, experiments were made with soil samples, double-amended or not with either vine-shoot (W) or olive cake (O) vermicompost or contaminated or not with IMI. These soil samples, incubated for 3months, were placed in two microcosms (M1 with the pre-amended soils and M2 with the pre-exposed soils), treated with IMI and amended with vermicomposts and then incubated for 3months. The IMI distribution on soil fractions, sorption processes, dissipation kinetics, and biochemical as well as genetic structure and bacterial abundance were determined to assess the fate and impact of IMI on the soil. The addition of W vermicompost to the soil reduced the IMI availability. The dissipation kinetic in soils from M1 and M2 followed, respectively, a single first-order and a double first-order in parallel models. The lowest IMI persistence corresponded to the soil from M2 amended with O-vermicompost with DT50 and DT90 values of 67d and 265d, while in the other soils 90% dissipation required >512d. The vermicomposts-amended contaminated soils increased the dehydrogenase activity by 2- and 4-fold respect the control soils. However, the urease activity decreased due to the IMI influence. The changes in the bacterial community in the contaminated soil amended with O-vermicompost during incubation were correlated with the dissipation rate constant of IMI, suggesting a better tolerance of microorganisms to IMI. Thus, in the soil contaminated with IMI, the amendment with the vermicompost from olive cake can mitigate the impact of this insecticide on soil functions and promote its depuration capability while minimizing environmental risks. Copyright © 2016 Elsevier B.V. All rights reserved.

Observing and modeling links between soil moisture, microbes and CH4 fluxes from forest soils

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Levy-Booth, David; Barker, Jason; Prescott, Cindy; Grayston, Sue

2017-04-01

Soil moisture is a key driver of methane (CH4) fluxes in forest soils, both of the net uptake of atmospheric CH4 and emission from the soil. Climate and land use change will alter spatial patterns of soil moisture as well as temporal variability impacting the net CH4 exchange. The impact on the resultant net CH4 exchange however is linked to the underlying spatial and temporal distribution of the soil microbial communities involved in CH4 cycling as well as the response of the soil microbial community to environmental changes. Significant progress has been made to target specific CH4 consuming and producing soil organisms, which is invaluable in order to understand the microbial regulation of the CH4 cycle in forest soils. However, it is not clear as to which extent soil moisture shapes the structure, function and abundance of CH4 specific microorganisms and how this is linked to observed net CH4 exchange under contrasting soil moisture regimes. Here we report on the results from a research project aiming to understand how the CH4 net exchange is shaped by the interactive effects soil moisture and the spatial distribution CH4 consuming (methanotrophs) and producing (methanogens). We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs and methanogens, soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient in a temperate rainforest on the Canadian Pacific coast. Furthermore, we conducted laboratory experiments to determine whether the net CH4 exchange from hydrologically contrasting forest soils responded differently to changes in soil moisture. Lastly, we modelled the microbial mediation of net CH4 exchange along the soil moisture gradient using structural equation modeling. Our study shows that it is possible to link spatial patterns of in situ net exchange of CH4 to microbial abundance of CH4 consuming and producing organisms. We also show that the microbial community responds different to environmental change dependent on the soil moisture regime. These results are important to include in future modeling efforts to predict changes in soil-atmosphere exchange of CH4 under global change.

Distribution of rock fragments and their effects on hillslope soil erosion in purple soil, China

NASA Astrophysics Data System (ADS)

Wang, Xiaoyan

2017-04-01

Purple soil is widely distributed in Sichuan Basin and Three Gorges Reservoir Area. Purple soil region is abundant in soil fertility and hydrothermal resources, playing an important role in the agricultural development of China. Soil erosion has long been recognized as a major environmental problem in the purple soil region where the population is large and slope farming is commonly practiced, and rainstorm is numerous. The existence of rock fragments is one of the most important characteristics of purple soil. Rock fragments at the soil surface or in the soil layer affect soil erosion processes by water in various direct and indirect ways, thus the erosion processes of soil containing rock fragments have unique features. Against the severe soil degradation by erosion of purple soil slope, carrying out the research about the characteristics of purple soil containing rock fragments and understanding the influence of rock fragments on soil erosion processes have important significance, which would promote the rational utilization of purple soil slope land resources and accurate prediction of purple soil loss. Therefore, the aims of this study were to investigate the distribution of rock fragments in purple soil slope and the impact of rock fragment content on soil physical properties and soil erosion. First, field sampling methods were used to survey the spatial variability of rock fragments in soil profiles and along slope and the physical properties of soils containing rock fragments. Secondly, indoor simulated rainfall experiments were used to exam the effect of rock fragments in the soil layer on soil erosion processes and the relationships between rainfall infiltration, change of surface flow velocity, surface runoff volume and sediment on one hand, and rock fragment content (Rv, 0% 30%, which was determined according the results of field investigation for rock fragment distribution) on the other were investigated. Thirdly, systematic analysis about the influence of rock fragment cover on purple soil slope erosion process were carried on, under different conditions with two kind of rock fragment positions (resting on soil surface and embedded into top soil layer), varied rock fragment coverage (Rc, 0% 40%), two kind of soils with textural porosity or structural porosity, and three kind of rainfall intensities (I, 1 mm/min, 1.5 mm/min and 2 mm/min). Simulated rainfall experiments in situ plots in the field, combined with simulated rainfall experiments in soil pans indoor, were used. The main conclusions of this dissertation are as following: 1. The spatial distribution characteristics of rock fragments in purple soil slope and its effects on the soil physical properties were clarified basically. 2. The mechanism of influence of rock fragments within top soil layer on soil erosion processes was understood and a threshold of rock fragment content on the infiltration was figured out. 3. The relationships between surface rock fragment cover and hillslope soil erosion in purple soil under different conditions with varied rock fragment positions, soil structures and rainfall intensities were obtained and the soil and water conservation function of surface rock fragment cover on reducing soil loss was affirmed.

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota.

PubMed

Leiva, Diego; Clavero-León, Claudia; Carú, Margarita; Orlando, Julieta

2016-11-01

Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Soil phosphorus depletion and shifts in plant communities change bacterial community structure in a long-term grassland management trial.

PubMed

Adair, Karen L; Wratten, Steve; Lear, Gavin

2013-06-01

Agricultural systems rely on healthy soils and their sustainability requires understanding the long-term impacts of agricultural practices on soils, including microbial communities. We examined the impact of 17 years of land management on soil bacterial communities in a New Zealand randomized-block pasture trial. Significant variation in bacterial community structure related to mowing and plant biomass removal, while nitrogen fertilizer had no effect. Changes in soil chemistry and legume abundance described 52% of the observed variation in the bacterial community structure. Legumes (Trifolium species) were absent in unmanaged plots but increased in abundance with management intensity; 11% of the variation in soil bacterial community structure was attributed to this shift in the plant community. Olsen P explained 10% of the observed heterogeneity, which is likely due to persistent biomass removal resulting in P limitation; Olsen P was significantly lower in plots with biomass removed (14 mg kg(-1) ± 1.3SE) compared with plots that were not mown, or where biomass was left after mowing (32 mg kg(-1) ± 1.6SE). Our results suggest that removal of plant biomass and associated phosphorus, as well as shifts in the plant community, have greater long-term impacts on soil bacterial community structure than application of nitrogen fertilizers. © 2013 John Wiley & Sons Ltd and Society for Applied Microbiology.

Assessing the fate of radioactive nickel in cultivated soil cores.

PubMed

Denys, Sébastien; Echevarria, Guillaume; Florentin, Louis; Leclerc, Elisabeth; Morel, Jean-Louis

2009-10-01

Parameters regarding fate of (63)Ni in the soil-plant system (soil: solution distribution coefficient, K(d) and soil plant concentration ratio, CR) are mostly determined in controlled pot experiments or from simple models involving a limited set of soil parameters. However, as migration of pollutants in soil is strongly linked to the water migration, variation of soil structure in the field and seasonal variation of evapotranspiration will affect these two parameters. The aim of this work was to explore to what extent the downward transfer of (63)Ni and its uptake by plants from surface-contaminated undisturbed soil cores under cultivation can be explained by isotopic dilution of this radionuclide in the pool of stable Ni of soils. Undisturbed soil cores (50 cm x 50 cm) were sampled from a brown rendzina (Rendzic Leptosol), a colluvial brown soil (Fluvic Cambisol) and an acidic brown soil (Dystric Cambisol) using PVC lysimeter tubes (three lysimeters sampled per soil type). Each core was equipped with a leachate collector. Cores were placed in a greenhouse and maize (DEA, Pioneer) was sown. After 44 days, an irrigation was simulated at the core surfaces to supply 10 000 Bq (63)NiCl(2). Maize was harvested 135 days after (63)Ni input and radioactivity determined in both vegetal and water samples. Effective uptake of (63)Ni by maize was calculated for leaves and kernels. Water drainage and leaching of (63)Ni were monitored over the course of the experiment. Values of K(d) in surface soil samples were calculated from measured parameters of isotopic exchange kinetics. Results confirmed that (63)Ni was strongly retained at the soil surface. Prediction of the (63)Ni downward transfer could not be reliably assessed using the K(d) values, since the soil structure, which controls local water fluxes, also affected both water and Ni transport. In terms of (63)Ni plant uptake, the effective uptake in undisturbed soil cores is controlled by isotope dilution as previously shown at the pot experiment scale.

Soil process-oriented modelling of within-field variability based on high-resolution 3D soil type distribution maps.

NASA Astrophysics Data System (ADS)

Bönecke, Eric; Lück, Erika; Gründling, Ralf; Rühlmann, Jörg; Franko, Uwe

2016-04-01

Today, the knowledge of within-field variability is essential for numerous purposes, including practical issues, such as precision and sustainable soil management. Therefore, process-oriented soil models have been applied for a considerable time to answer question of spatial soil nutrient and water dynamics, although, they can only be as consistent as their variation and resolution of soil input data. Traditional approaches, describe distribution of soil types, soil texture or other soil properties for greater soil units through generalised point information, e.g. from classical soil survey maps. Those simplifications are known to be afflicted with large uncertainties. Varying soil, crop or yield conditions are detected even within such homogenised soil units. However, recent advances of non-invasive soil survey and on-the-go monitoring techniques, made it possible to obtain vertical and horizontal dense information (3D) about various soil properties, particularly soil texture distribution which serves as an essential soil key variable affecting various other soil properties. Thus, in this study we based our simulations on detailed 3D soil type distribution (STD) maps (4x4 m) to adjacently built-up sufficient informative soil profiles including various soil physical and chemical properties. Our estimates of spatial STD are based on high-resolution lateral and vertical changes of electrical resistivity (ER), detected by a relatively new multi-sensor on-the-go ER monitoring device. We performed an algorithm including fuzzy-c-mean (FCM) logic and traditional soil classification to estimate STD from those inverted and layer-wise available ER data. STD is then used as key input parameter for our carbon, nitrogen and water transport model. We identified Pedological horizon depths and inferred hydrological soil variables (field capacity, permanent wilting point) from pedotransferfunctions (PTF) for each horizon. Furthermore, the spatial distribution of soil organic carbon (SOC), as essential input variable, was predicted by measured soil samples and associated to STD of the upper 30 cm. The comprehensive and high-resolution (4x4 m) soil profile information (up to 2 m soil depth) were then used to initialise a soil process model (Carbon and Nitrogen Dynamics - CANDY) for soil functional modelling (daily steps of matter fluxes, soil temperature and water balances). Our study was conducted on a practical field (~32,000 m²) of an agricultural farm in Central Germany with Chernozem soils under arid conditions (average rainfall < 550 mm). This soil region is known to have differences in soil structure mainly occurring within the subsoil, since topsoil conditions are described as homogenous. The modelled soil functions considered local climate information and practical farming activities. Results show, as expected, distinguished functional variability, both on spatial and temporal resolution for subsoil evident structures, e.g. visible differences for available water capacity within 0-100 cm but homogenous conditions for the topsoil.

Current advancements and challenges in soil-root interactions modelling

NASA Astrophysics Data System (ADS)

Schnepf, Andrea; Huber, Katrin; Abesha, Betiglu; Meunier, Felicien; Leitner, Daniel; Roose, Tiina; Javaux, Mathieu; Vanderborght, Jan; Vereecken, Harry

2015-04-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Current Advancements and Challenges in Soil-Root Interactions Modelling

NASA Astrophysics Data System (ADS)

Schnepf, A.; Huber, K.; Abesha, B.; Meunier, F.; Leitner, D.; Roose, T.; Javaux, M.; Vanderborght, J.; Vereecken, H.

2014-12-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Influence of crop rotation and tillage intensity on soil physical properties and functions

NASA Astrophysics Data System (ADS)

Krümmelbein, Julia

2013-04-01

Soil tillage intensity can vary concerning tillage depth, frequency, power input into the soil and degree of soil turn-over. Conventional tillage systems where a plough is regularly used to turn over the soil can be differentiated from reduced tillage systems without ploughing but with loosening the upper soil and no tillage systems. Between conventional tillage and no tillage is a wide range of more or less reduced tillage systems. In our case the different tillage intensities are not induced by different agricultural machinery or techniques, but result from varying crop rotations with more or less perennial crops and therefore lower or higher tillage frequency. Our experimental area constitutes of quite unstructured substrates, partly heavily compacted. The development of a functioning soil structure and accumulation of nutrients and organic matter are of high importance. Three different crop rotations induce varying tillage intensities and frequencies. The first crop rotation (Alfalfa monoculture) has only experienced seed bed preparation once and subsequently is wheeled once a year to cut and chaff the biomass. The second crop rotation contains perennial and annual crops and has therefore been tilled more often, while the third crop rotation consists only of annual crops with annual seedbed preparation. Our results show that reduced tillage intensity/frequency combined with the intense root growth of Alfalfa creates the most favourable soil physical state of the substrate compared to increased tillage and lower root growth intensity of the other crop rotations. Soil tillage disturbs soil structure development, especially when the substrate is mechanically unstable as in our case. For such problematic locations it is recommendable to reduce tillage intensity and/or frequency to allow the development of soil structure enhanced by root growth and thereby the accumulation of organic matter and nutrients within the rooting zone.

Wetting properties of fungi mycelium alter soil infiltration and soil water repellency in a γ-sterilized wettable and repellent soil.

PubMed

Chau, Henry Wai; Goh, Yit Kheng; Vujanovic, Vladimir; Si, Bing Cheng

2012-12-01

Soil water repellency (SWR) has a drastic impact on soil quality resulting in reduced infiltration, increased runoff, increased leaching, reduced plant growth, and increased soil erosion. One of the causes of SWR is hydrophobic fungal structures and exudates that change the soil-water relationship. The objective of this study was to determine whether SWR and infiltration could be manipulated through inoculation with fungi. The effect of fungi on SWR was investigated through inoculation of three fungal strains (hydrophilic -Fusarium proliferatum, chrono-amphiphilic -Trichoderma harzianum, and hydrophobic -Alternaria sp.) on a water repellent soil (WR-soil) and a wettable soil (W-soil). The change in SWR and infiltration was assessed by the water repellency index and cumulative infiltration respectively. F. proliferatum decreased the SWR on WR-soil and slightly increased SWR in W-soil, while Alternaria sp. increased SWR in both the W-soil and the WR-soil. Conversely T. harzianum increased the SWR in the W-soil and decreased the SWR in the WR-soil. All strains showed a decrease in infiltration in W-soil, while only the F. proliferatum and T. harzianum strain showed improvement in infiltration in the WR-soil. The ability of fungi to alter the SWR and enmesh soil particles results in changes to the infiltration dynamics in soil. Copyright © 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Microbial diversity affects self-organization of the soil–microbe system with consequences for function

PubMed Central

Crawford, John W.; Deacon, Lewis; Grinev, Dmitri; Harris, James A.; Ritz, Karl; Singh, Brajesh K.; Young, Iain

2012-01-01

Soils are complex ecosystems and the pore-scale physical structure regulates key processes that support terrestrial life. These include maintaining an appropriate mixture of air and water in soil, nutrient cycling and carbon sequestration. There is evidence that this structure is not random, although the organizing mechanism is not known. Using X-ray microtomography and controlled microcosms, we provide evidence that organization of pore-scale structure arises spontaneously out of the interaction between microbial activity, particle aggregation and resource flows in soil. A simple computational model shows that these interactions give rise to self-organization involving both physical particles and microbes that gives soil unique material properties. The consequence of self-organization for the functioning of soil is determined using lattice Boltzmann simulation of fluid flow through the observed structures, and predicts that the resultant micro-structural changes can significantly increase hydraulic conductivity. Manipulation of the diversity of the microbial community reveals a link between the measured change in micro-porosity and the ratio of fungal to bacterial biomass. We suggest that this behaviour may play an important role in the way that soil responds to management and climatic change, but that this capacity for self-organization has limits. PMID:22158839

Simazine biodegradation and community structures of ammonia-oxidizing microorganisms in bioaugmented soil: impact of ammonia and nitrate nitrogen sources.

PubMed

Wan, Rui; Yang, Yuyin; Sun, Weimin; Wang, Zhao; Xie, Shuguang

2014-02-01

The objective of the present study was to investigate the impact of ammonia and nitrate nitrogen sources on simazine biodegradation by Arthrobacter sp. strain SD1 and the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in non-agricultural soil. Soil microcosms with different treatments were constructed for herbicide biodegradation test. The relative abundance of the strain SD1 and the structures of AOA and AOB communities were assessed using quantitative PCR (q-PCR) and terminal restriction fragment length polymorphism (TRFLP), respectively. The co-existence of two inorganic nitrogen sources (ammonia and nitrate) had certain impact on simazine dissipation by the strain SD1. Bioaugmentation could induce a shift in the community structures of both AOA and AOB, but AOA were more responsive. Nitrogen application had significant impacts on AOA and AOB communities in bioaugmented soils. Moreover, in non-bioaugmented soil, the community structure of AOA, instead of AOB, could be quickly recovered after herbicide application. This study could add some new insights towards the impacts of nitrogen sources on s-triazine bioremediation and ammonia-oxidizing microorganisms in soil ecosystem.

Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates.

PubMed

Patel, Vrutika; Sharma, Anukriti; Lal, Rup; Al-Dhabi, Naif Abdullah; Madamwar, Datta

2016-03-22

Gauging the microbial community structures and functions become imperative to understand the ecological processes. To understand the impact of long-term oil contamination on microbial community structure soil samples were taken from oil fields located in different industrial regions across Kadi, near Ahmedabad, India. Soil collected was hence used for metagenomic DNA extraction to study the capabilities of intrinsic microbial community in tolerating the oil perturbation. Taxonomic profiling was carried out by two different complementary approaches i.e. 16S rDNA and lowest common ancestor. The community profiling revealed the enrichment of phylum "Proteobacteria" and genus "Chromobacterium," respectively for polluted soil sample. Our results indicated that soil microbial diversity (Shannon diversity index) decreased significantly with contamination. Further, assignment of obtained metagenome reads to Clusters of Orthologous Groups (COG) of protein and Kyoto Encyclopedia of Genes and Genomes (KEGG) hits revealed metabolic potential of indigenous microbial community. Enzymes were mapped on fatty acid biosynthesis pathway to elucidate their roles in possible catalytic reactions. To the best of our knowledge this is first study for influence of edible oil on soil microbial communities via shotgun sequencing. The results indicated that long-term oil contamination significantly affects soil microbial community structure by acting as an environmental filter to decrease the regional differences distinguishing soil microbial communities.

Visualizing the impact of living roots on rhizosphere soil structure using X-ray microtomography

NASA Astrophysics Data System (ADS)

Menon, M.; Berli, M.; Ghezzehei, T. A.; Nico, P.; Young, M. H.; Tyler, S. W.

2009-04-01

The rhizosphere is an interface between bulk soil and plant root and plays a critical role in root water and nutrient uptake. In this study, we used X-ray Computerized Microtomography (microCT) to visualize soil structure around living roots non-destructively and with high spatial resolution. Four different plant species (Helianthus annuus, Lupinus hartwegii, Vigna radiata and Phaseolus lunatus), grown in four different porous materials (glass beads, medium and coarse sand, loam aggregates), were scanned with 10 μm spatial resolution, using the microtomography beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA. Sample cross section images clearly show contacts between roots and soil particles, connecting water films, air-water interfaces as well as some cellular features of the plants taproots. We found with a simulation experiment, inflating a cylindrical micro-balloon in a pack of air-dry loam aggregates, that soil fracturing rather than compaction might occur around a taproot growing in dry soil. Form these preliminary experiments, we concluded that microCT has potential as a tool for a more process-based understanding of the role of rhizosphere soil structure on soil fertility, plant growth and the water balance at the earth-atmosphere interface.

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

PubMed

Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan

2015-06-16

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

Bioremediation using Novosphingobium strain DY4 for 2,4-dichlorophenoxyacetic acid-contaminated soil and impact on microbial community structure.

PubMed

Dai, Yu; Li, Ningning; Zhao, Qun; Xie, Shuguang

2015-04-01

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is commonly used for weed control. The ubiquity of 2,4-D has gained increasing environmental concerns. Biodegradation is an attractive way to clean up 2,4-D in contaminated soil. However, information on the bioaugmentation trial for remediating contaminated soil is still very limited. The impact of bioaugmentation using 2,4-D-degraders on soil microbial community remains unknown. The present study investigated the bioremediation potential of a novel degrader (strain DY4) for heavily 2,4-D-polluted soil and its bioaugmentation impact on microbial community structure. The strain DY4 was classified as a Novosphingobium species within class Alphaproteobacteria and harbored 2,4-D-degrading TfdAα gene. More than 50 and 95 % of the herbicide could be dissipated in bioaugmented soil (amended with 200 mg/kg 2,4-D) respectively in 3-4 and 5-7 days after inoculation of Novosphingobium strain DY4. A significant growth of the strain DY4 was observed in bioaugmented soil with the biodegradation of 2,4-D. Moreover, herbicide application significantly altered soil bacterial community structure but bioaumentation using the strain DY4 showed a relatively weak impact.

Bringing life to soil physical processes

NASA Astrophysics Data System (ADS)

Hallett, P. D.

2013-12-01

When Oklahoma's native prairie grass roots were replaced by corn, the greatest environmental (and social) disaster ever to hit America ensued. The soils lost structure, physical binding by roots was annihilated and when drought came the Great Dust Bowl commenced. This form of environmental disaster has repeated over history and although not always apparent, similar processes drive the degradation of seemingly productive farmland and forests. But just as negative impacts on biology are deleterious to soil physical properties, positive impacts could reverse these trends. In finding solutions to soil sustainability and food security, we should be able to exploit biological processes to improve soil physical properties. This talk will focus on a quantitative understanding of how biology changes soil physical behaviour. Like the Great Dust Bowl, it starts with reinforcement mechanisms by plant roots. We found that binding of soil by cereal (barley) roots within 5 weeks of planting can more than double soil shear strength, with greater plant density causing greater reinforcement. With time, however, the relative impact of root reinforcement diminishes due to root turnover and aging of the seedbed. From mechanical tests of individual roots, reasonable predictions of reinforcement by tree roots are possible with fibre bundle models. With herbaceous plants like cereals, however, the same parameters (root strength, stiffness, size and distribution) result in a poor prediction. We found that root type, root age and abiotic factors such as compaction and waterlogging affect mechanical behaviour, further complicating the understanding and prediction of root reinforcement. For soil physical stability, the interface between root and soil is an extremely important zone in terms of resistance of roots to pull-out and rhizosphere formation. Compounds analogous to root exudates have been found with rheological tests to initially decrease the shear stress where wet soils flow, but after decomposition of these exudates by microbes the shear stress increases. This suggests an initial dispersion, followed by aggregation of the soil, which explains the structural arrangement of soil particles in the rhizosphere observed by microscopy. Dispersion of soil minerals in the root zone is important to release bound nutrients from mineral surfaces. Using fracture mechanics we measured large impacts of biological exudates on the toughness and interparticle bond energy of soils. Now novel tests are being developed to quantify interparticle bonding by biological exudates on single and multiple particle contacts, including mechanical test specimens that can be inoculated with specific bacteria or fungi. This will allow for clay mineralogy, water potential and solution chemistry impacts on interparticle bonding to be quantified directly. Wettability experiments with the same samples measure hydrological properties such as contact angle. Basic information from these tests will help explain biological processes that drive soil structure formation and stabilisation, providing data for models of soil structure dynamics.

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

Not Available

This report was prepared at the request of the Lawrence Livermore Laboratory (LLL) to provide background information for analyzing soil-structure interaction by the frequency-independent impedance function approach. LLL is conducting such analyses as part of its seismic review of selected operating plants under the Systematic Evaluation Program for the US Nuclear Regulatory Commission. The analytical background and basic assumptionsof the impedance function theory are briefly reviewed, and the role of radiation damping in soil-structure interaction analysis is discussed. The validity of modeling soil-structure interaction by using frequency-independent functions is evaluated based on data from several field tests. Finally, the recommendedmore » procedures for performing soil-structure interaction analyses are discussed with emphasis on the modal superposition method.« less

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank

PubMed Central

Leite, Márcio F. A.; Pan, Yao; Bloem, Jaap; Berge, Hein ten; Kuramae, Eiko E.

2017-01-01

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake. PMID:28198425

Soil microbial succession along a chronosequence on a High Arctic glacier foreland, Ny-Ålesund, Svalbard: 10 years' change

NASA Astrophysics Data System (ADS)

Yoshitake, Shinpei; Uchida, Masaki; Iimura, Yasuo; Ohtsuka, Toshiyuki; Nakatsubo, Takayuki

2018-06-01

Rapid glacial retreat in the High Arctic causes the expansion of new habitats, but the successional trajectories of soil microbial communities are not fully understood. We examined microbial succession along a chronosequence twice with a 10-year interval in a High Arctic glacier foreland. Soil samples were collected from five study sites with different ages and phospholipid fatty acids analysis was conducted to investigate the microbial biomass and community structure. Microbial biomass did not differ significantly between the two sampling times but tended to increase with the chronosequence and showed a significant correlation with soil carbon (C) and nitrogen (N) content. Microbial community structure clearly differed along the chronosequence and was correlated with C and N content. The largest shift in community structure over 10 years was observed in the newly exposed sites after deglaciation. The accumulation of soil organic matter was regarded as an important determinant both of microbial biomass and community structure over the successional period. In contrast, the initial microbial community on the newly exposed soil changed rapidly even in the High Arctic, suggesting that some key soil processes such as C and N cycling can also shift within the relatively short period after rapid glacial retreat.

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank.

PubMed

Leite, Márcio F A; Pan, Yao; Bloem, Jaap; Berge, Hein Ten; Kuramae, Eiko E

2017-02-15

Use of organic amendments is a valuable strategy for crop production. However, it remains unclear how organic amendments shape both soil microbial community structure and activity, and how these changes impact nutrient mineralization rates. We evaluated the effect of various organic amendments, which range in Carbon/Nitrogen (C/N) ratio and degradability, on the soil microbiome in a mesocosm study at 32, 69 and 132 days. Soil samples were collected to determine community structure (assessed by 16S and 18S rRNA gene sequences), microbial biomass (fungi and bacteria), microbial activity (leucine incorporation and active hyphal length), and carbon and nitrogen mineralization rates. We considered the microbial soil DNA as the microbial seedbank. High C/N ratio favored fungal presence, while low C/N favored dominance of bacterial populations. Our results suggest that organic amendments shape the soil microbial community structure through a feedback mechanism by which microbial activity responds to changing organic inputs and rearranges composition of the microbial seedbank. We hypothesize that the microbial seedbank composition responds to changing organic inputs according to the resistance and resilience of individual species, while changes in microbial activity may result in increases or decreases in availability of various soil nutrients that affect plant nutrient uptake.

Soil properties and not inputs control carbon : nitrogen : phosphorus ratios in cropped soils in the long term

NASA Astrophysics Data System (ADS)

Frossard, Emmanuel; Buchmann, Nina; Bünemann, Else K.; Kiba, Delwende I.; Lompo, François; Oberson, Astrid; Tamburini, Federica; Traoré, Ouakoltio Y. A.

2016-02-01

Stoichiometric approaches have been applied to understand the relationship between soil organic matter dynamics and biological nutrient transformations. However, very few studies have explicitly considered the effects of agricultural management practices on the soil C : N : P ratio. The aim of this study was to assess how different input types and rates would affect the C : N : P molar ratios of bulk soil, organic matter and microbial biomass in cropped soils in the long term. Thus, we analysed the C, N, and P inputs and budgets as well as soil properties in three long-term experiments established on different soil types: the Saria soil fertility trial (Burkina Faso), the Wagga Wagga rotation/stubble management/soil preparation trial (Australia), and the DOK (bio-Dynamic, bio-Organic, and "Konventionell") cropping system trial (Switzerland). In each of these trials, there was a large range of C, N, and P inputs which had a strong impact on element concentrations in soils. However, although C : N : P ratios of the inputs were highly variable, they had only weak effects on soil C : N : P ratios. At Saria, a positive correlation was found between the N : P ratio of inputs and microbial biomass, while no relation was observed between the nutrient ratios of inputs and soil organic matter. At Wagga Wagga, the C : P ratio of inputs was significantly correlated to total soil C : P, N : P, and C : N ratios, but had no impact on the elemental composition of microbial biomass. In the DOK trial, a positive correlation was found between the C budget and the C to organic P ratio in soils, while the nutrient ratios of inputs were not related to those in the microbial biomass. We argue that these responses are due to differences in soil properties among sites. At Saria, the soil is dominated by quartz and some kaolinite, has a coarse texture, a fragile structure, and a low nutrient content. Thus, microorganisms feed on inputs (plant residues, manure). In contrast, the soil at Wagga Wagga contains illite and haematite, is richer in clay and nutrients, and has a stable structure. Thus, organic matter is protected from mineralization and can therefore accumulate, allowing microorganisms to feed on soil nutrients and to keep a constant C : N : P ratio. The DOK soil represents an intermediate situation, with high nutrient concentrations, but a rather fragile soil structure, where organic matter does not accumulate. We conclude that the study of C, N, and P ratios is important to understand the functioning of cropped soils in the long term, but that it must be coupled with a precise assessment of element inputs and budgets in the system and a good understanding of the ability of soils to stabilize C, N, and P compounds.

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.

Aggregation and C dynamics along an elevation gradient in carbonate-containing grassland soils of the Alps

NASA Astrophysics Data System (ADS)

Garcia-Franco, Noelia; Wiesmeier, Martin; Kiese, Ralf; Dannenmann, Michael; Wolf, Benjamin; Zistl-Schlingmann, Marcus; Kögel-Knabner, Ingrid

2017-04-01

C sequestration in mountainous grassland soils is regulated by physical, chemical and biological soil process. An improved knowledge of the relationship between these stabilization mechanisms is decisive to recommend the best management practices for climate change mitigation. In this regard, the identification of a successful indicator of soil structural improvement and C sequestration in mountainous grassland soils is necessary. Alpine and pre-alpine grassland soils in Bavaria represent a good example for mountainous grassland soils faced with climate change. We sampled grassland soils of the northern limestone alps in Bavaria along an elevation gradient from 550 to 1300 m above sea level. We analyzed C dynamics by a comparative analysis of the distribution of C according to aggregate size classes: large-macroaggregates (> 2000 µm), small-macroaggregates (250-2000 µm), microaggregates (63-250 µm), silt plus clay particles (<63 µm) and bulk soil. Our preliminary results showed higher C content and changed water-stable aggregate distribution in the high elevation sites compared to lower elevations. Magnesium carbonate seem to play an important role in stabilizing macroaggregates formed from fresh OM. In addition, the isolation of occluded microaggregates within macroaggregates will help us to improve our understanding on the effects of climate change on soil structure and on the sensitivity of different C stabilization mechanisms present in mountainous soils.

Oligotyping reveals stronger relationship of organic soil bacterial community structure with N-amendments and soil chemistry in comparison to that of mineral soil at Harvard Forest, MA, USA

Treesearch

Swathi A. Turlapati; Rakesh Minocha; Stephanie Long; Jordan Ramsdell; Subhash C. Minocha

2015-01-01

The impact of chronic nitrogen amendments on bacterial communities was evaluated at Harvard Forest, Petersham, MA, USA. Thirty soil samples (3 treatments × 2 soil horizons × 5 subplots) were collected in 2009 from untreated (control), low nitrogen-amended (LN; 50 kg NH4NO3ha-1yr

Relationships between soil organic matter, nutrients, bacterial community structure, and the performance of microbial fuel cells.

PubMed

Dunaj, Sara J; Vallino, Joseph J; Hines, Mark E; Gay, Marcus; Kobyljanec, Christine; Rooney-Varga, Juliette N

2012-02-07

Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful renewable resource: soil organic carbon. We analyzed bacterial community structure, MFC performance, and soil characteristics in different microhabitats within MFCs constructed from agricultural or forest soils in order to determine how soil type and bacterial dynamics influence MFC performance. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs. Bacterial community profile data indicate that the bacterial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These results suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic bacterial communities, while the quality of available organic matter may have played a significant role in supporting high performing bacterial communities.

Bacterial diversity and community structure in lettuce soil are shifted by cultivation time

NASA Astrophysics Data System (ADS)

Liu, Yiqian; Chang, Qing; Guo, Xu; Yi, Xinxin

2017-08-01

Compared with cereal production, vegetable production usually requires a greater degree of management and larger input of nutrients and irrigation, but these systems are not sustainable in the long term. This study aimed to what extent lettuce determine the bacterial community composition in the soil, during lettuce cultivation, pesticides and fertilizers were not apply to soil. Soil samples were collected from depths of 0-20cm and 20-40cm. A highthroughput sequencing approach was employed to investigate bacterial communities in lettuce-cultivated soil samples in a time-dependent manner. The dominant bacteria in the lettuce soil samples were mainly Proteobacteria, Actinobacteria, Chloroflexi, Nitrospirae, Firmicutes, Acidobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, Gemmatimo nadetes, Cyanobacteria. Proteobacteria was the most abundant phylum in the 6 soil samples. The relative abundance of Acidobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia and Cyanobacteria decreased through time of lettuce cultivation, but the relative abundance of Proteobacteria, Actinobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Nitrospirae increased over time. In the 0-20cm depth group and the 20-40cm depth soil, a similar pattern was observed that the percentage number of only shared OTUs between the early and late stage was lower than that between the early and middle stage soil, the result showed that lettuce growth can affect structure of soil bacterial communities.

Effects of biochar on dechlorination of hexachlorobenzene and the bacterial community in paddy soil.

PubMed

Song, Yang; Bian, Yongrong; Wang, Fang; Herzberger, Anna; Yang, Xinglun; Gu, Chenggang; Jiang, Xin

2017-11-01

Anaerobic reductive dechlorination is an important degradation pathway for chlorinated organic contaminants in paddy soil. This study investigated the effects of amending paddy soil with wheat straw biochar on both the dechlorination of hexachlorobenzene (HCB), a typical highly chlorinated contaminant, and on the structure of soil bacteria communities. Soil amendment of 0.1% biochar did not significantly affect the dechlorination of HCB in the soil. However, biochar amendment at higher application levels (5%) stimulated the dechlorination of HCB in the first month of anaerobic incubation and inhibited the dechlorination of HCB after that period. The stimulation effect may be ascribed to the graphite carbon and carbon-centered persistent radicals, which are redox active, in biochar. The inhibiting effect could be partly ascribed to the reduced bioavailability of HCB in biochar-amended soils. High-throughput sequencing revealed that the amendment of biochar changed the soil bacterial community structure but not the bacterial abundances and diversities. The relative abundance of Dehalococcoidaceae in the tested soils showed a significant relationship with the dechlorination percentages of HCB, indicating that Dehalococcoidaceae may be the main HCB-dechlorinating bacteria in the studied paddy soil. The results indicated that low application levels of biochar did not affect the dechlorination of HCB in the paddy soil, while high application levels of biochar mainly inhibited the dechlorination of HCB due to the reduced bioavailability of HCB and the reduced abundances of certain dechlorinating bacteria in the biochar-amended paddy soil. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

Proposal and Research Direction of Soil Mass Organic Reorganization

NASA Astrophysics Data System (ADS)

Zhang, Lu; Han, Jichang

2018-01-01

Land engineering as a new discipline has been temporarily outrageous. The proposition of soil body organic reorganization undoubtedly enriches the research content for the construction of land engineering disciplines. Soil body organic reconstruction is designed to study how to realize the ecological ecology of the land by studying the external force of nature, to study the influence of sunlight, wind and water on soil body, how to improve the soil physical structure, to further strengthen the research of biological enzymes and microbes, and promote the release and utilization of beneficial inert elements in soil body. The emerging of frontier scientific research issues with soil body organic reorganization to indicate directions for the future development of soil engineering.

Effects of vegetation structure on soil carbon, nutrients and greenhouse gas exchange in a savannah ecosystem of Mount Kilimanjaro Region

NASA Astrophysics Data System (ADS)

Becker, J.

2015-12-01

The savannah biome is a hotspot for biodiversity and wildlife conservation in Africa and recently got in the focus of research on carbon sequestration. Savannah ecosystems are under strong pressure from climate and land-use change, especially around populous areas like the Mt. Kilimanjaro region. Savannah vegetation consists of grassland with isolated trees and is therefore characterized by high spatial variation of canopy cover, aboveground biomass and root structure. The canopy structure is a major regulator for soil ecological parameters and soil-atmospheric trace gas exchange (CO2, N2O, CH4) in water limited environments. The spatial distribution of these parameters and the connection between above and belowground processes are important to understand and predict ecosystem changes and estimate its vulnerability. Our objective was to determine spatial trends and changes of soil parameters and relate their variability to the vegetation structure. We chose three trees from each of the two most dominant species (Acacia nilotica and Balanites aegyptiaca) in our research area. For each tree, we selected transects with nine sampling points of the same relative distances to the stem. At these each sampling point a soil core was taken and separated in 0-10 cm and 10-30 cm depth. We measured soil carbon (C) and nitrogen (N) storage, microbial biomass C and N, Natural δ13C, soil respiration, available nutrients, pH, cation exchange capacity (CEC) as well as root biomass and -density, soil temperature and soil water content. Concentrations and stocks of C and N fractions, CEC and K+ decreased up to 50% outside the crown covered area. Microbial C:N ratio and CO2 efflux was about 30% higher outside the crown. This indicates N limitation and low C use efficiency in soil outside the crown area. We conclude that the spatial structure of aboveground biomass in savanna ecosystems leads to a spatial variance in nutrient limitation. Therefore, the capability of a savanna ecosystem to act as a C sink is directly and indirectly dependent on the vegetation structure.

Invasive Plants Rapidly Reshape Soil Properties in a Grassland Ecosystem.

PubMed

Gibbons, Sean M; Lekberg, Ylva; Mummey, Daniel L; Sangwan, Naseer; Ramsey, Philip W; Gilbert, Jack A

2017-01-01

Plant invasions often reduce native plant diversity and increase net primary productivity. Invaded soils appear to differ from surrounding soils in ways that impede restoration of diverse native plant communities. We hypothesize that invader-mediated shifts in edaphic properties reproducibly alter soil microbial community structure and function. Here, we take a holistic approach, characterizing plant, prokaryotic, and fungal communities and soil physicochemical properties in field sites, invasion gradients, and experimental plots for three invasive plant species that cooccur in the Rocky Mountain West. Each invader had a unique impact on soil physicochemical properties. We found that invasions drove shifts in the abundances of specific microbial taxa, while overall belowground community structure and functional potential were fairly constant. Forb invaders were generally enriched in copiotrophic bacteria with higher 16S rRNA gene copy numbers and showed greater microbial carbohydrate and nitrogen metabolic potential. Older invasions had stronger effects on abiotic soil properties, indicative of multiyear successions. Overall, we show that plant invasions are idiosyncratic in their impact on soils and are directly responsible for driving reproducible shifts in the soil environment over multiyear time scales. IMPORTANCE In this study, we show how invasive plant species drive rapid shifts in the soil environment from surrounding native communities. Each of the three plant invaders had different but consistent effects on soils. Thus, there does not appear to be a one-size-fits-all strategy for how plant invaders alter grassland soil environments. This work represents a crucial step toward understanding how invaders might be able to prevent or impair native reestablishment by changing soil biotic and abiotic properties.

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.

PubMed

Flores-Rentería, Dulce; Curiel Yuste, Jorge; Rincón, Ana; Brearley, Francis Q; García-Gil, Juan Carlos; Valladares, Fernando

2015-05-01

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

Mouthing of Soil Contaminated Objects is Associated with Environmental Enteropathy in Young Children.

PubMed

Morita, Tomohiko; Perin, Jamie; Oldja, Lauren; Biswas, Shwapon; Sack, R Bradley; Ahmed, Shahnawaz; Haque, Rashidul; Bhuiyan, Nurul Amin; Parvin, Tahmina; Bhuyian, Sazzadul Islam; Akter, Mahmuda; Talukder, Kaisar A; Shahnaij, Mohammad; Faruque, Abu G; George, Christine Marie

2017-06-01

To characterise childhood mouthing behaviours and to investigate the association between object-to-mouth and food-to-mouth contacts, diarrhoea prevalence and environmental enteropathy. A prospective cohort study was conducted of 216 children ≤30 months of age in rural Bangladesh. Mouthing contacts with soil and food and objects with visible soil were assessed by 5-h structured observation. Stool was analysed for four faecal markers of intestinal inflammation: alpha-1-antitrypsin, myeloperoxidase, neopterin and calprotectin. Overall 82% of children were observed mouthing soil, objects with visible soil, or food with visible soil during the structured observation period. Sixty two percent of children were observed mouthing objects with visible soil, 63% were observed mouthing food with visible soil, and 18% were observed mouthing soil only. Children observed mouthing objects with visible soil had significantly elevated faecal calprotectin concentrations (206.81 μg/g, 95% confidence interval [CI]: 6.27, 407.36). There was also a marginally significant association between Escherichia coli counts in soil from a child's play space and the prevalence rate of diarrhoea (diarrhoea prevalence ratio: 2.03, 95% CI 0.97, 4.25). These findings provide further evidence to support the hypothesis that childhood mouthing behaviour in environments with faecal contamination can lead to environmental enteropathy in susceptible paediatric populations. Furthermore, these findings suggest that young children mouthing objects with soil, which occurred more frequently than soil directly (60% vs. 18%), was an important exposure route to faecal pathogens and a risk factor for environmental enteropathy. © 2017 John Wiley & Sons Ltd.

Quantification of spatial distribution and spread of bacteria in soil at microscale

NASA Astrophysics Data System (ADS)

Juyal, Archana; Eickhorst, Thilo; Falconer, Ruth; Baveye, Philippe; Otten, Wilfred

2015-04-01

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. Soil is a complex heterogeneous environment comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota including bacteria and fungi. Bacteria occupy a very small portion of available pore space in soil which demonstrates that their spatial arrangement in soil has a huge impact on the contact to their target and on the way they interact to carry out their functions. Due to limitation of techniques, there is scant information on spatial distribution of indigenous or introduced bacteria at microhabitat scale. There is a need to understand the interaction between soil structure and microorganisms including fungi for ecosystem-level processes such as carbon sequestration and improving the predictive models for soil management. In this work, a combination of techniques was used including X-ray CT to characterize the soil structure and in-situ detection via fluorescence microscopy to visualize and quantify bacteria in soil thin sections. Pseudomonas fluorescens bacteria were introduced in sterilized soil of aggregate size 1-2 mm and packed at bulk-densities 1.3 g cm-3 and 1.5 g cm-3. A subset of samples was fixed with paraformaldehyde and subsequently impregnated with resin. DAPI and fluorescence in situ hybridization (FISH) were used to visualize bacteria in thin sections of soil cores by epifluorescence microscopy to enumerate spatial distribution of bacteria in soil. The pore geometry of soil was quantified after X-ray microtomography scanning. The distribution of bacteria introduced locally reduced significantly (P

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

Sorption of Hydrophobic Organic Compounds on Natural Sorbents and Organoclays from Aqueous and Non-Aqueous Solutions: A Mini-Review

PubMed Central

Moyo, Francis; Tandlich, Roman; Wilhelmi, Brendan S.; Balaz, Stefan

2014-01-01

Renewed focus on the sorption of hydrophobic organic chemicals (HOCs) onto mineral surfaces and soil components is required due to the increased and wider range of organic pollutants being released into the environment. This mini-review examines the possibility of the contribution and mechanism of HOC sorption onto clay mineral sorbents such as kaolinite, and soil organic matter and the possible role of both in the prevention of environmental contamination by HOCs. Literature data indicates that certain siloxane surfaces can be hydrophobic. Therefore soils can retain HOCs even at low soil organic levels and the extent will depend on the structure of the pollutant and the type and concentration of clay minerals in the sorbent. Clay minerals are wettable by nonpolar solvents and so sorption of HOCs onto them from aqueous and non-aqueous solutions is possible. This is important for two reasons: firstly, the movement and remediation of soil environments will be a function of the concentration and type of clay minerals in the soil. Secondly, low-cost sorbents such as kaolinite and expandable clays can be added to soils or contaminated environments as temporary retention barriers for HOCs. Inorganic cations sorbed onto the kaolinite have a strong influence on the rate and extent of sorption of hydrophobic organic pollutants onto kaolinite. Structural sorbate classes that can be retained by the kaolinite matrix are limited by hydrogen bonding between hydroxyl groups of the octahedral alumosilicate sheet and the tetrahedral sheet with silicon. Soil organic carbon plays a key role in the sorption of HOCs onto soils, but the extent will be strongly affected by the structure of the organic soil matter and the presence of soot. Structural characterisation of soil organic matter in a particular soil should be conducted during a particular contamination event. Contamination by mining extractants and antibiotics will require renewed focus on the use of the QSAR approaches in the context of the sorption of HOCs onto clay minerals from aqueous and non-aqueous solutions. PMID:24821385

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.

Variation in Vegetation Structure and Soil Properties, and the Relation Between Understory Plants and Environmental Variables Under Different Phyllostachys pubescens Forests in Southeastern China

NASA Astrophysics Data System (ADS)

Zhang, Changshun; Xie, Gaodi; Fan, Shaohui; Zhen, Lin

2010-04-01

Biodiversity maintenance and soil improvement are key sustainable forestry objectives. Research on the effects of bamboo forest management on plant diversity and soil properties are therefore necessary in bamboo-growing regions, such as southeastern China’s Shunchang County, that have not been studied from this perspective. We analyzed the effects of different Phyllostachys pubescens proportions in managed forests on vegetation structure and soil properties using pure Cunninghamia lanceolata forests as a contrast, and analyzed the relation between understory plants and environmental variables (i.e., topography, stand and soil characteristics) by canonical correspondence analysis (CCA). The forest with 80% P. pubescens and 20% hardwoods (such as Phoebe bournei, Jatropha curcas, Schima superba) maintained the highest plant diversity and best soil properties, with significantly higher plant diversity than the C. lanceolata forest, and better soil physicochemical and biological properties. The distribution of understory plants is highly related to environmental factors. Silvicultural disturbance strongly influenced the ability of different bamboo forests to maintain biodiversity and soil quality under extensive management, and the forest responses to management were consistent with the intermediate-disturbance hypothesis (i.e., diversity and soil properties were best at intermediate disturbance levels). Our results suggest that biodiversity maintenance and soil improvement are important management goals for sustainable bamboo management. To achieve those objectives, managers should balance the inputs and outputs of nutrients and protect understory plants by using appropriate fertilizer (e.g., organic fertilizer), adjusting stand structure, modifying utilization model and the harvest time, and controlling the intensity of culms and shoots harvests.

Carbon stabilization and microbial growth in acidic mine soils after addition of different amendments for soil reclamation

NASA Astrophysics Data System (ADS)

Zornoza, Raúl; Acosta, Jose; Ángeles Muñoz, María; Martínez-Martínez, Silvia; Faz, Ángel; Bååth, Erland

2016-04-01

The extreme soil conditions in metalliferous mine soils have a negative influence on soil biological activity and therefore on soil carbon estabilization. Therefore, amendments are used to increase organic carbon content and activate microbial communities. In order to elucidate some of the factors controlling soil organic carbon stabilization in reclaimed acidic mine soils and its interrelationship with microbial growth and community structure, we performed an incubation experiment with four amendments: pig slurry (PS), pig manure (PM) and biochar (BC), applied with and without marble waste (MW; CaCO3). Results showed that PM and BC (alone or together with MW) contributed to an important increment in recalcitrant organic C, C/N ratio and aggregate stability. Bacterial and fungal growths were highly dependent on pH and labile organic C. PS supported the highest microbial growth; applied alone it stimulated fungal growth, and applied with MW it stimulated bacterial growth. BC promoted the lowest microbial growth, especially for fungi, with no significant increase in fungal biomass. MW+BC increased bacterial growth up to values similar to PM and MW+PM, suggesting that part of the biochar was degraded, at least in short-term mainly by bacteria rather than fungi. PM, MW+PS and MW+PM supported the highest microbial biomass and a similar community structure, related with the presence of high organic C and high pH, with immobilization of metals and increased soil quality. BC contributed to improved soil structure, increased recalcitrant organic C, and decreased metal mobility, with low stimulation of microbial growth.

Analysing Structure Dynamics in Arable Soils using X-ray Micro-Tomography

NASA Astrophysics Data System (ADS)

Schlüter, S.; Weller, U.; Vogel, H.-J.

2009-04-01

Structure is a dynamic property of soil. It interacts with many biotic and abiotic features and controls various soil functions. We analyzed soil structure within different plots of the ''Static Fertilisation Experiment'' at the agricultural research station in Bad Lauchstaedt (Germany) using X-ray micro tomography. The aim was to investigate in how far different levels of organic carbon, increased microbial activity and enhanced plant growth affects structural properties of an arable soil. Since 106 years one plot has experienced a constant application of farmyard manure and fertilisers, whereas the other has never been fertilised in this period. Intact soil cores from the chernozem soil at the two plots were taken from a depth of 5 to 15 cm (Ap-horizon) and 35 to 45 cm (Ah-horizon) to analyse structural changes with depth and in two different seasons (spring and summer) to investigate structure dynamics. The pore structure was analysed by quantifying the mean geometrical and topological characteristics of the pore network as a function of pore size. This was done by a combination of Minkowski functionals and morphological size distibution. For small structural features close to the image resolution the results clearly depend on the applied filtering technique and segmentation thresholds. Therefore the application of different image enhancement techniques is discussed. Furthermore, a new method for an automated determination of grey value thesholds for the segmentation of CT-images into pore space and solid is developed and evaluated. We highlight the relevance of image resolution for structure analysis. Results of the structure analysis reveal that the spring samples of the ploughed layer (Ap-horizon) from the fertilised plot have significantly higher macroporosities (P < 0.05) than those from the non-fertilised plot. The internal connectivity of the pore network is better in the fertilised plot and the pore size distribution was found to be different, too. The differences in porosity and pore connectivity increase from spring to summer. Both plots were compacted by a rolling machine in late winter. So the difference in structure dynamics is interpreted as an enhanced structure resiliency in the fertilised and carbon enriched plot after that compaction. A comparison with porosity features of a nearby reference profil under grassland demonstrates that the impact of tillage on pore structure is higher than the different contents in organic carbon. The carbon enriched horizon beneath the ploughed layer (Ah-horizon) shows no differences in pore size distribution and connectivity as a function of fertilisation. Thus, at that soil depth, no long-term effects of fertilization in terms of soil structure are detectable. Obviously, the highly different energy input during 106 years only affects the structure of the top soil.

[Effects of Organic and Inorganic Slow-Release Compound Fertilizer on Different Soils Microbial Community Structure].

PubMed

Wang, Fei; Yuan, Ting; Gu, Shou-kuan; Wang, Zheng-yin

2015-04-01

As a new style fertilizer, slow-control release fertilizer had been an important subject in recent years, but few researches were about soil microbial community structure diversity. Phospholipid fatty acid method was used to determined the microbial community structure diversity of acid soil and slight alkaline soil applied with slow-release compound fertilizer (SRF), chemical fertilizer (CF) and common compound fertilizer (CCF) at the 10th, 30th, 60th and 90th day under the constant temperature incubation condition. Results indicated that various bacteria (i. e 13:0, i14:0,14:0, i15:0, a15:0, i16:0, 16:12OH, 16:1w5c,16:0, i17:0, a17:0, cy17:0, 17:02OH, i18:0, 18:0 and cy19:0w8c), two actinomycetes (10Me17:0 and 10Me18:0) and only one fungus (18:1 w9c) were detected in two soils after applying slow-release compound fertilizer and other fertilizers during the whole incubation period. SRF could significantly increase the fungi PLFA content by 8.3% and 6.8% at the early stage (the 10th day and 30th day) compared with CF, as well as significantly increase by 22.7% and 17.1% at the late stage (the 60th day and 90th day) compared with CCF in acid soil. SRF significantly increased bacteria, fungi and gram positive bacteria compared with CF and CCF in incubation period (except at the 30th day) in slight alkaline soil. SRF could significantly improve the ratio of normal saturated fatty acid and monounsaturated fatty acid at the 30th day and 90th days in acid soil compared with no fertilizer (CK), CF and CCF, while as to slight alkaline soil, SRF was significantly greater than that of CK, CF and CCF only at the 60th day. SRF could significantly decrease the ratio of iso PLFA and anteiso PLFA in acid soil (in 30-90 days) and slight alkaline soil (in 10-60 days). For two soils PLFA varieties, contents and ratios of microbial community, slow-release compound fertilizer increased soil microbial PLFA varieties and contents, and decreased the influence to microbial survival environment, especially for the acid soil. Through the research of slow-release compound fertilizer on soil microbial community structure diversity, it could provide a scientific basis for widely application of slow-release compound fertilizer in agricultural production.

Earthquake Ground Motion Selection

DOT National Transportation Integrated Search

2012-05-01

Nonlinear analyses of soils, structures, and soil-structure systems offer the potential for more accurate characterization of geotechnical and structural response under strong earthquake shaking. The increasing use of advanced performance-based desig...

Soil Water Retention as Indicator for Soil Physical Quality - Examples from Two SoilTrEC European Critical Zone Observatories

NASA Astrophysics Data System (ADS)

Rousseva, Svetla; Kercheva, Milena; Shishkov, Toma; Dimitrov, Emil; Nenov, Martin; Lair, Georg J.; Moraetis, Daniel

2014-05-01

Soil water retention is of primary importance for majority of soil functions. The characteristics derived from Soil Water Retention Curve (SWRC) are directly related to soil structure and soil water regime and can be used as indicators for soil physical quality. The aim of this study is to present some parameters and relationships based on the SWRC data from the soil profiles characterising the European SoilTrEC Critical Zone Observatories Fuchsenbigl and Koiliaris. The studied soils are representative for highly productive soils managed as arable land in the frame of soil formation chronosequence at "Marchfeld" (Fuchsenbigl CZO), Austria and heavily impacted soils during centuries through intensive grazing and farming, under severe risk of desertification in context of climatic and lithological gradient at Koiliaris, Crete, Greece. Soil water retention at pF ≤ 2.52 was determined using the undisturbed soil cores (100 cm3 and 50 cm3) by a suction plate method. Water retention at pF = 4.2 was determined by a membrane press method and at pF ≥ 5.6 - by adsorption of water vapour at controlled relative humidity, both using ground soil samples. The soil physical quality parameter (S-parameter) was defined as the slope of the water retention curve at its inflection point (Dexter, 2006), determined with the obtained parameters of van Genuhten (1980) water retention equation. The S-parameter values were categorised to assess soil physical quality as follows: S < 0.020 very poor, 0.020 ≤ S < 0.035 poor, 0.035 ≤ S < 0.050 good, S ≥ 0.050 very good (Dexter, 2004). The results showed that most of the studied topsoil horizons have good physical quality according to both the S-parameter and the Plant-Available Water content (PAW), with the exception of the soils from croplands at CZO Fuxenbigl (F4, F5) which are with poor soil structure. The link between the S-parameter and the indicator of soil structure stability (water stable soil aggregates with size 1-3 mm) is not well defined. The scattering is due to high values of S in subsoil, which does not always coincide with favourable physical properties, as it can be seen from the relationship with the PAW content. It was found that values of S ≥ 0.05 correspond to PAW > 20 % vol. in the topsoil horizons. The high values of S in subsoil horizons are due to the low PAW and restrict the application of the S categories in these cases. Well defined links are found between the PAW content and the S-parameter when the data from the topsoil horizons are grouped in 2 groups according to the ratio between air-filled pores (at pF 2.52) and plant available water: <2 and ≥ 2. The authors acknowledge gratefully the European Commission Research Directorate-General for funding the SoilTrEC project (Contract No 244118) under its 7th Framework Programme.

Soil bacterial community and functional shifts in response to altered snowpack in moist acidic tundra of northern Alaska

NASA Astrophysics Data System (ADS)

Ricketts, Michael P.; Poretsky, Rachel S.; Welker, Jeffrey M.; Gonzalez-Meler, Miquel A.

2016-09-01

Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snow fence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of expected ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation, where deep snow ˜ 100 % and intermediate snow ˜ 50 % increased snowpack relative to the control, and low snow ˜ 25 % decreased snowpack relative to the control. Soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C concentration, nitrogen (N) concentration, and pH. Soil microbial community DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla (ranging from 82 to 96 % of total detected phyla per sample) and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (% C, % N, C : N, pH); however, a single predictor was not identified, suggesting that each bacterial phylum responds differently to soil characteristics. Overall, bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial functional potential was inferred using ancestral state reconstruction to approximate functional gene abundance, revealing a decreased abundance of genes required for soil organic matter (SOM) decomposition in the organic layers of the deep snow accumulation zones. These results suggest that predicted climate change scenarios may result in altered soil bacterial community structure and function, and indicate a reduction in decomposition potential, alleviated temperature limitations on extracellular enzymatic efficiency, or both. The fate of stored C in Arctic soils ultimately depends on the balance between these mechanisms.

Biochar amendment decreases soil microbial biomass and increases bacterial diversity in Moso bamboo (Phyllostachys edulis) plantations under simulated nitrogen deposition

NASA Astrophysics Data System (ADS)

Li, Quan; Lei, Zhaofeng; Song, Xinzhang; Zhang, Zhiting; Ying, Yeqing; Peng, Changhui

2018-04-01

Biochar amendment has been proposed as a strategy to improve acidic soils after overuse of nitrogen fertilizers. However, little is known of the role of biochar in soil microbial biomass carbon (MBC) and bacterial community structure and diversity after soil acidification induced by nitrogen (N) deposition. Using high-throughput sequencing of the 16S rRNA gene, we determined the effects of biochar amendment (BC0, 0 t bamboo biochar ha‑1 BC20, 20 t bamboo biochar ha‑1 and BC40, 40 t bamboo biochar ha‑1) on the soil bacterial community structure and diversity in Moso bamboo plantations that had received simulated N deposition (N30, 30 kg N ha‑1 yr‑1 N60, 60 kg N ha‑1 yr‑1 N90, 90 kg N ha‑1 yr‑1 and N-free) for 21 months. After treatment of N-free plots, BC20 significantly increased soil MBC and bacterial diversity, while BC40 significantly decreased soil MBC but increased bacterial diversity. When used to amend N30 and N60 plots, biochar significantly decreased soil MBC and the reducing effect increased with biochar amendment amount. However, these significant effects were not observed in N90 plots. Under N deposition, biochar amendment largely increased soil bacterial diversity, and these effects depended on the rates of N deposition and biochar amendment. Soil bacterial diversity was significantly related to the soil C/N ratio, pH, and soil organic carbon content. These findings suggest an optimal approach for using biochar to offset the effects of N deposition in plantation soils and provide a new perspective for understanding the potential role of biochar amendments in plantation soil.

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.

[Effect of soil phenolic acids on soil microbe of coal-mining depressed land after afforestation restoration by different tree species].

PubMed

Ji, Li; Yang, Li Xue

2017-12-01

Phenolic acids are one of the most important factors that influence microbial community structure. Investigating the dynamic changes of phenolic acids and their relationship with the microbial community structure in plantation soils with different tree species could contribute to better understanding and revealing the mechanisms of microbial community changes under afforestation restoration in coal-mining subsidence areas. In this study, plantations of three conifer and one deciduous species (Pinus koraiensis, Larix gmelinii, Pinus sylvestris var. mongolica, and Populus ussuriensis) were established on abandoned coal-mining subsidence areas in Baoshan District, Shuangyashan City. The contents of soil phenols, 11 types of phenolic acids, and microbial communities in all plots were determined. The results showed that the contents of soil complex phenol in plantations were significantly higher than that of abandoned land overall. Specifically, soils in larch and poplar plantations had higher contents of complex phenol, while soils in larch and Korean pine plantations had greater contents of total phenol. Moreover, soil in the P. koraiensis plantation had a higher content of water-soluble phenol compared with abandoned lands. The determination of 11 phenolic acids indicated that the contents of ferulic acid, abietic acid, β-sitosterol, oleanolic acid, shikimic acid, linoleic acid, and stearic acid were higher in plantation soils. Although soil phenol contents were not related with soil microbial biomass, the individual phenolic acids showed a significant relationship with soil microbes. Ferulic acid, abietic acid, and β-sitosterol showed significant promoting effects on soil microbial biomass, and they showed positive correlations with fungi and fungi/bacteria ratio. These three phenolic acids had higher contents in the poplar plantation, suggesting that poplar affo-restation had a beneficial effect on soil quality in coal-mining subsidence areas.

Pore-scale investigation on the response of heterotrophic respiration to moisture conditions in heterogeneous soils

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

Yan, Zhifeng; Liu, Chongxuan; Todd-Brown, Katherine E.

The relationship between microbial respiration rate and soil moisture content is an important property for understanding and predicting soil organic carbon degradation, CO 2 production and emission, and their subsequent effects on climate change. This paper reports a pore-scale modeling study to investigate the response of heterotrophic respiration to moisture conditions in soils and to evaluate various factors that affect this response. X-ray computed tomography was used to derive soil pore structures, which were then used for pore-scale model investigation. The pore-scale results were then averaged to calculate the effective respiration rates as a function of water content in soils.more » The calculated effective respiration rate first increases and then decreases with increasing soil water content, showing a maximum respiration rate at water saturation degree of 0.75 that is consistent with field and laboratory observations. The relationship between the respiration rate and moisture content is affected by various factors, including pore-scale organic carbon bioavailability, the rate of oxygen delivery, soil pore structure and physical heterogeneity, soil clay content, and microbial drought resistivity. Simulations also illustrates that a larger fraction of CO 2 produced from microbial respiration can be accumulated inside soil cores under higher saturation conditions, implying that CO 2 flux measured on the top of soil cores may underestimate or overestimate true soil respiration rates under dynamic moisture conditions. Overall, this study provides mechanistic insights into the soil respiration response to the change in moisture conditions, and reveals a complex relationship between heterotrophic microbial respiration rate and moisture content in soils that is affected by various hydrological, geochemical, and biophysical factors.« less

Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure.

PubMed

Ishaq, Suzanne L; Johnson, Stephen P; Miller, Zach J; Lehnhoff, Erik A; Olivo, Sarah; Yeoman, Carl J; Menalled, Fabian D

2017-02-01

Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P < 0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P < 0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.

Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.

PubMed

Chaudhary, Doongar R; Kim, Jinhyun; Kang, Hojeong

2018-04-01

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

PubMed Central

Lim, Hyoun Soo; Hong, Soon Gyu; Kim, Ji Hee; Lee, Joohan; Choi, Taejin; Ahn, Tae Seok; Kim, Ok-Sun

2015-01-01

Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment. PMID:25799273

A metrics for soil hydrological processes and their intrinsic dimensionality in heterogeneous systems

NASA Astrophysics Data System (ADS)

Lischeid, G.; Hohenbrink, T.; Schindler, U.

2012-04-01

Hydrology is based on the observation that catchments process input signals, e.g., precipitation, in a highly deterministic way. Thus, the Darcy or the Richards equation can be applied to model water fluxes in the saturated or vadose zone, respectively. Soils and aquifers usually exhibit substantial spatial heterogeneities at different scales that can, in principle, be represented by corresponding parameterisations of the models. In practice, however, data are hardly available at the required spatial resolution, and accounting for observed heterogeneities of soil and aquifer structure renders models very time and CPU consuming. We hypothesize that the intrinsic dimensionality of soil hydrological processes, which is induced by spatial heterogeneities, actually is very low and that soil hydrological processes in heterogeneous soils follow approximately the same trajectory. That means, the way how the soil transforms any hydrological input signals is the same for different soil textures and structures. Different soils differ only with respect to the extent of transformation of input signals. In a first step, we analysed the output of a soil hydrological model, based on the Richards equation, for homogeneous soils down to 5 m depth for different soil textures. A matrix of time series of soil matrix potential and soil water content at 10 cm depth intervals was set up. The intrinsic dimensionality of that matrix was assessed using the Correlation Dimension and a non-linear principal component approach. The latter provided a metrics for the extent of transformation ("damping") of the input signal. In a second step, model outputs for heterogeneous soils were analysed. In a last step, the same approaches were applied to 55 time series of observed soil water content from 15 sites and different depths. In all cases, the intrinsic dimensionality in fact was very close to unity, confirming our hypothesis. The metrics provided a very efficient tool to quantify the observed behaviour, depending on depth and soil heterogeneity: Different soils differed primarily with respect to the extent of damping per depth interval rather than to the kind of damping. We will show how that metrics can be used in a very efficient way for representing soil heterogeneities in simulation models.

How far can we prevent further physical soil degradation in the future?

NASA Astrophysics Data System (ADS)

Horn, Rainer

2017-04-01

Arable as well as forest soils are exposed to increasing external stresses, which coincide with a further and deeper reaching soil degradation, which may result in an aggravation of hydraulic, gaseous, thermal but also physicochemical and chemical soil functions. The decline coincides with a simultaneous reduction in useable land areas and worsens food production amongst others. Therefore, it is mandatory, that stable soil structure from the surface down to depth prevents soil compaction, sustains water infiltration, reduces rates of soil erosion by water and wind in each case to the minimum possible under the soil, terrain, land use, and climatic conditions in which the soils occur. It improves organic carbon storage in soils and optimizes microbial activity and functions. These benefits coincide with sustainable soil properties and soil management systems, which prevent - deep mechanical stress propagation which can cause irreversible soil deformation, - loss of surface soil layers with coinciding organic and mineral nutrient pool available for microbial processing and plant uptake, - Truncation of soil horizons, or damage on private and public infrastructures (roads, houses) and downstream fields. In order to prevent negative impacts on soils, it is recommended, that A) concerning prevention of soil compaction - stresses applied to soils shall not exceed the mechanical soil stability to maintain the actual functioning of chemical, physical and biological processes and to utilize their resilience (i.e. the elasticity), - land use management strategies have to be related to the actual soil properties in order to optimize plant growth, yield, filtering and buffering of infiltrating water, and carbon sequestration. B) soil erosion by - water, wind, and tillage is counteracted by an adequate surface soil stability including a site specific residue management (e.g. conservation tillage), controlled traffic and harvesting, ecological grassland use strategies (e.g. fodder production and harvesting, adequate animal grazing), - wind is furthermore minimized by adequate hedgerow plantations, continuous cover crop growth, optimized particle bindings by water, infiltrating organic acids, appropriate grazing intensity. Agroforestry can be considered as an additional positive measure to reduce soil erosion risks generally and to ameliorate degraded sites. C) -plant cover on slopes remains untouched, overgrazing and consecutive soil homogenization especially under moist climatic conditions must be prevented but adjusted to the actual structure stability of the hillsides. The communication of these findings followed by application of such measures can help farmers and foresters as well as landowners to prevent (further) physical soil degradation in the future.

Microbial community responses in forest mineral soil to compaction, organic matter removal, and vegetation control

Treesearch

Matt D. Busse; Samual E. Beattie; Robert F. Powers; Felipe G. Sanchez; Allan E. Tiarks

2006-01-01

We tested three disturbance hypotheses in young conifer plantations: H1: soil compaction and removal of surface organic matter produces sustained changes in microbial community size, activity, and structure in mineral soil; H2: microbial community characteristics in mineral soil are linked to the recovery of plant diversity...

Determination of field-effective soil properties in the tidewater region of North Carolina

Treesearch

J. McFero Grace; R.W. Skaggs

2013-01-01

Soils vary spatially in texture, structure, depth of horizons, and macropores, which can lead to a large variation in soil physical properties. In particular, saturated hydraulic conductivity (Ksat) and drainable porosity are critical properties required to model field hydrology in poorly drained lands. These soil-property values can be measured...

Chemical structure of soil organic matter in slickspots as investigated by advanced solid-state NMR

USDA-ARS?s Scientific Manuscript database

Slickspot soils are saline, and knowledge of their humic chemistry would contribute to our limited understanding how salinity affects soil C and N stocks. We characterized humic acids (HAs) from slickspot soils with solid-state 13C nuclear magnetic resonance (NMR). Expanding on previous use of cross...

Using synchrotron-based X-ray micro-computed tomography and high-performance pore-scale simulation to evaluate hydraulic properties in biochar-amended soils

NASA Astrophysics Data System (ADS)

Zhou, H.; Yu, X.; Chen, C.; Zeng, L.; Lu, S.; Wu, L.

2016-12-01

In this research, we combined synchrotron-based X-ray micro-computed tomography (SR-mCT), with three-dimensional lattice Bolzmann (LB) method, to quantify how the change in pore space architecture affected macroscopic hydraulic of two clayey soils amended with biochar. SR-mCT was used to characterize pore structures of the soils before and after biochar addition. The high-resolution soil pore structures were then directly used as internal boundary conditions for three-dimensional water flow simulations with the LB method, which was accelerated by graphics processing unit (GPU) parallel computing. It was shown that, due to the changes in soil pore geometry, the application of biochar increased the soil permeability by at least 1 order of magnitude, and decreased the tortuosity by 20-30%. This work was the first physics based modeling study on the effect of biochar amendment on soil hydraulic properties. The developed theories and techniques have promising potential in understanding the mechanisms of water and nutrient transport in soil at the pore scale.

Chemical migration during soil water retention curve evaluation.

PubMed

Pires, Luiz F; Villanueva, Felipe C A; Dias, Nivea M P; Bacchi, Osny O Santos; Reichardt, Klaus

2011-09-01

Wetting and drying (W-D) cycles can induce important elemental migrations in soils. The main purpose of this work was to study the possible existence of soil chemical elemental migrations in samples submitted to repeated W-D cycles during evaluations of soil water retention curve (SWRC). The experimental measurements were carried out by Atomic Absorption Spectrometry (AAS) for Ca(2+), Mg(2+) and K(+) on samples of three different Brazilian tropical soils (Geric Ferralsol, Eutric Nitosol and Rhodic Ferralsol). Results demonstrate an increase in the electrical conductivity of the water extracted from the samples and significant losses of Ca(2+), Mg(2+) and K(+) during the applications of up to nine W-D cycles. It was also observed differences in SWRC for all soils when samples submitted to the application of several W-D cycles were compared with samples not submitted to it. These differences occurred at the region of both structural and textural pores. A possible explanation for these results could be the soil chemical migration during the sequences of W-D cycles, which can affect the soil structure development.

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

PLFA profiling of microbial community structure and seasonal shifts in soils of a Douglas-fir chronosequence

Treesearch

Jennifer Moore-Kucera; Richard P. Dick

2008-01-01

The impact and frequency of forest harvesting could significantly affect soil microbial community (SMC) structure and functioning. The ability of soil microorganisms to perform biogeochemical processes is critical for sustaining forest productivity and has a direct impact on decomposition dynamics and carbon storage potential. The Wind River Canopy Crane Research...

Dynaflow User’s Guide

DTIC Science & Technology

1988-11-01

264 ANALYSIS RESTART. ............. ..... ....... 269 1.0 TITLE CARD. .............. ............. 271 2.0 CONTROL CARDS...stress soil model will provide a tool for such analysis of waterfront structures. To understand the significance of liquefaction, it is important to note...Implementing this effective stress soil model into a finite element computer program would allow analysis of soil and structure together. TECHNICAL BACKGROUND

Microbial community structure and abundance in the rhizosphere and bulk soil of a tomato cropping system that includes cover crops

USDA-ARS?s Scientific Manuscript database

In this report we use Terminal Restriction Fragment Length Polymorphisms (TRFLP) in a tomato production system to “finger printing” the soil microbial community structure with Phylum specific primer sets. Factors influencing the soil microbes are a cover crop of Hairy Vetch (Vicia villosa) or Rye (...

Using the Subsurface Soil Sounding Radar for Investigating the Structure and Total Electron Content of the Martian Ionosphere

NASA Astrophysics Data System (ADS)

Smirnov, V. M.; Yushkova, O. V.; Marchuk, V. N.

2018-05-01

The possibilities of using the Martian soil subsurface sounding radar for investigating the structure of the plasma shell surrounding the planet have been considered. Based on the numerical modeling results and actual soil sounding data, it has been shown that the soil sounding mode of the radio-locating MARSIS radar can be used to assess the structure of the Martian ionosphere. As the emitted signals pass to the planet's surface, it is possible to use the reflected signals to estimate the total electron content of the Martian ionosphere along the flight track of the spacecraft.

Soil Microbial Properties and Plant Growth Responses to Carbon and Water Addition in a Temperate Steppe: The Importance of Nutrient Availability

PubMed Central

Guo, Chengyuan; Wang, Renzhong; Xiao, Chunwang

2012-01-01

Background Global climatic change is generally expected to stimulate net primary production, and consequently increase soil carbon (C) input. The enhanced C input together with potentially increased precipitation may affect soil microbial processes and plant growth. Methodology/Principal Findings To examine the effects of C and water additions on soil microbial properties and plant growth, we conducted an experiment lasting two years in a temperate steppe of northeastern China. We found that soil C and water additions significantly affected microbial properties and stimulated plant growth. Carbon addition significantly increased soil microbial biomass and activity but had a limited effect on microbial community structure. Water addition significantly increased soil microbial activity in the first year but the response to water decreased in the second year. The water-induced changes of microbial activity could be ascribed to decreased soil nitrogen (N) availability and to the shift in soil microbial community structure. However, no water effect on soil microbial activity was visible under C addition during the two years, likely because C addition alleviated nutrient limitation of soil microbes. In addition, C and water additions interacted to affect plant functional group composition. Water addition significantly increased the ratio of grass to forb biomass in C addition plots but showed only minor effects under ambient C levels. Our results suggest that soil microbial activity and plant growth are limited by nutrient (C and N) and water availability, and highlight the importance of nutrient availability in modulating the responses of soil microbes and plants to potentially increased precipitation in the temperate steppe. Conclusions/Significance Increased soil C input and precipitation would show significant effects on soil microbial properties and plant growth in the temperate steppe. These findings will improve our understanding of the responses of soil microbes and plants to the indirect and direct climate change effects. PMID:22496905

Evaluating equilibrium and non-equilibrium transport of bromide and isoproturon in disturbed and undisturbed soil columns.

PubMed

Dousset, S; Thevenot, M; Pot, V; Simunek, J; Andreux, F

2007-12-07

In this study, displacement experiments of isoproturon were conducted in disturbed and undisturbed columns of a silty clay loam soil under similar rainfall intensities. Solute transport occurred under saturated conditions in the undisturbed soil and under unsaturated conditions in the sieved soil because of a greater bulk density of the compacted undisturbed soil compared to the sieved soil. The objective of this work was to determine transport characteristics of isoproturon relative to bromide tracer. Triplicate column experiments were performed with sieved (structure partially destroyed to simulate conventional tillage) and undisturbed (structure preserved) soils. Bromide experimental breakthrough curves were analyzed using convective-dispersive and dual-permeability (DP) models (HYDRUS-1D). Isoproturon breakthrough curves (BTCs) were analyzed using the DP model that considered either chemical equilibrium or non-equilibrium transport. The DP model described the bromide elution curves of the sieved soil columns well, whereas it overestimated the tailing of the bromide BTCs of the undisturbed soil columns. A higher degree of physical non-equilibrium was found in the undisturbed soil, where 56% of total water was contained in the slow-flow matrix, compared to 26% in the sieved soil. Isoproturon BTCs were best described in both sieved and undisturbed soil columns using the DP model combined with the chemical non-equilibrium. Higher degradation rates were obtained in the transport experiments than in batch studies, for both soils. This was likely caused by hysteresis in sorption of isoproturon. However, it cannot be ruled out that higher degradation rates were due, at least in part, to the adopted first-order model. Results showed that for similar rainfall intensity, physical and chemical non-equilibrium were greater in the saturated undisturbed soil than in the unsaturated sieved soil. Results also suggested faster transport of isoproturon in the undisturbed soil due to higher preferential flow and lower fraction of equilibrium sorption sites.

Evaluating equilibrium and non-equilibrium transport of bromide and isoproturon in disturbed and undisturbed soil columns

NASA Astrophysics Data System (ADS)

Dousset, S.; Thevenot, M.; Pot, V.; Šimunek, J.; Andreux, F.

2007-12-01

In this study, displacement experiments of isoproturon were conducted in disturbed and undisturbed columns of a silty clay loam soil under similar rainfall intensities. Solute transport occurred under saturated conditions in the undisturbed soil and under unsaturated conditions in the sieved soil because of a greater bulk density of the compacted undisturbed soil compared to the sieved soil. The objective of this work was to determine transport characteristics of isoproturon relative to bromide tracer. Triplicate column experiments were performed with sieved (structure partially destroyed to simulate conventional tillage) and undisturbed (structure preserved) soils. Bromide experimental breakthrough curves were analyzed using convective-dispersive and dual-permeability (DP) models (HYDRUS-1D). Isoproturon breakthrough curves (BTCs) were analyzed using the DP model that considered either chemical equilibrium or non-equilibrium transport. The DP model described the bromide elution curves of the sieved soil columns well, whereas it overestimated the tailing of the bromide BTCs of the undisturbed soil columns. A higher degree of physical non-equilibrium was found in the undisturbed soil, where 56% of total water was contained in the slow-flow matrix, compared to 26% in the sieved soil. Isoproturon BTCs were best described in both sieved and undisturbed soil columns using the DP model combined with the chemical non-equilibrium. Higher degradation rates were obtained in the transport experiments than in batch studies, for both soils. This was likely caused by hysteresis in sorption of isoproturon. However, it cannot be ruled out that higher degradation rates were due, at least in part, to the adopted first-order model. Results showed that for similar rainfall intensity, physical and chemical non-equilibrium were greater in the saturated undisturbed soil than in the unsaturated sieved soil. Results also suggested faster transport of isoproturon in the undisturbed soil due to higher preferential flow and lower fraction of equilibrium sorption sites.

Modeling soil processes - are we lost in diversity?

NASA Astrophysics Data System (ADS)

Vogel, Hans-Joerg; Schlüter, Steffen

2015-04-01

Soils are among the most complex environmental systems. Soil functions - e.g. production of biomass, habitat for organisms, reactor for and storage of organic matter, filter for ground water - emerge from a multitude of processes interacting at different scales. It still remains a challenge to model and predict these functions including their stability and resilience towards external perturbations. As an inherent property of complex systems it is prohibitive to unravel all the relevant process in all detail to derive soil functions and their dynamics from first principles. Hence, when modeling soil processes and their interactions one is close to be lost in the overwhelming diversity and spatial heterogeneity of soil properties. In this contribution we suggest to look for characteristic similarities within the hyperdimensional state space of soil properties. The underlying hypothesis is that this state space is not evenly and/or randomly populated but that processes of self organization produce attractors of physical, chemical and biological properties which can be identified. (The formation of characteristic soil horizons is an obvious example). To render such a concept operational a suitable and limited set of indicators is required. Ideally, such indicators are i) related to soil functions, ii) are measurable and iii) are integral measures of the relevant physical, chemical and biological soil properties. This would allow for identifying suitable attractors. We will discuss possible indicators and will focus on soil structure as an especially promising candidate. It governs the availability of water and gas, it effects the spatial distribution of organic matter and, moreover, it forms the habitat of soil organisms and it is formed by soil biota. Quantification of soil structural properties became possible only recently with the development of more powerful tools for non-invasive imaging. Future research need to demonstrate in how far these tools can be used to identify functional soil types (i.e. attractors) allowing for modeling soil processes at an integral level. We provide an example from the 100-years fertilization experiment in Bad-Lauchstädt.

The structure of bacterial communities in natural and anthropogenic brown forest soils of the Botanical Garden on Murav'eva-Amurskogo Peninsula

NASA Astrophysics Data System (ADS)

Kovaleva, G. V.; Dobrovol'Skaya, T. G.; Golovacheva, A. V.

2007-05-01

The microbiological characterization of the brown forest soils in the territory of the Botanical Garden-Institute of the Far East Division of the Russian Academy of Sciences in southern Primor’e is given. The high humus content and weakly acid reaction of these soils were shown to provide the optimal conditions for the development of bacteria. In the brown forest soils differing in the thickness of the humus horizons, all the ecologic-trophic groups of bacteria were present and the bacterial communities were highly diverse. The structure of the bacterial communities was identical in all the organomineral horizons of the soils and varied greatly by the seasons. In the anthropogenically disturbed soils, the share of corynebacteria, which are resistant to stress and capable of the destruction of xenobiotics, decreased.

Analysis of soils - Part II: Determination of oligosaccharides in soils by MALDI-time-of-flight mass spectrometry

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

Schuerch, S.; Howald, M.; Schlunegger, U.P.

1995-12-31

Polysaccharides are the most abundant organic compounds in nature. Decomposition of plant and animal residues leads to a high polysaccharide content in soils. The decomposition of carbohydrates and subsequent mineralization of the products are part of the cycle of life on earth. In extracts of soils collected in the Valle Onsernone (Ticino, Switzerland), oligosaccharides of different size and structure have been identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The selected soils show identical climatic parameters and pedological factors, whereas the age of fallow land is the only varying factor. Identification and structure elucidation of the oligosaccharides is performedmore » by substrate-specific enzymatic hydrolysis. Moreover the appearance and the distribution of the oligosaccharides is correlated to soil genesis.« less

Stream Flow Prediction by Remote Sensing and Genetic Programming

NASA Technical Reports Server (NTRS)

Chang, Ni-Bin

2009-01-01

A genetic programming (GP)-based, nonlinear modeling structure relates soil moisture with synthetic-aperture-radar (SAR) images to present representative soil moisture estimates at the watershed scale. Surface soil moisture measurement is difficult to obtain over a large area due to a variety of soil permeability values and soil textures. Point measurements can be used on a small-scale area, but it is impossible to acquire such information effectively in large-scale watersheds. This model exhibits the capacity to assimilate SAR images and relevant geoenvironmental parameters to measure soil moisture.

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

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

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

DOE PAGES

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; ...

2017-09-28

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but onlymore » in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Finally, combining such an approach with broader knowledge of thresholding behavior – here related to active layer depth – would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.« less

Soil respiration across a permafrost transition zone: spatial structure and environmental correlates

NASA Astrophysics Data System (ADS)

Stegen, James C.; Anderson, Carolyn G.; Bond-Lamberty, Ben; Crump, Alex R.; Chen, Xingyuan; Hess, Nancy

2017-09-01

Soil respiration is a key ecosystem function whereby shifts in respiration rates can shift systems from carbon sinks to sources. Soil respiration in permafrost-associated systems is particularly important given climate change driven permafrost thaw that leads to significant uncertainty in resulting ecosystem carbon dynamics. Here we characterize the spatial structure and environmental drivers of soil respiration across a permafrost transition zone. We find that soil respiration is characterized by a non-linear threshold that occurs at active-layer depths greater than 140 cm. We also find that within each season, tree basal area is a dominant driver of soil respiration regardless of spatial scale, but only in spatial domains with significant spatial variability in basal area. Our analyses further show that spatial variation (the coefficient of variation) and mean-variance power-law scaling of soil respiration in our boreal system are consistent with previous work in other ecosystems (e.g., tropical forests) and in population ecology, respectively. Comparing our results to those in other ecosystems suggests that temporally stable features such as tree-stand structure are often primary drivers of spatial variation in soil respiration. If so, this provides an opportunity to better estimate the magnitude and spatial variation in soil respiration through remote sensing. Combining such an approach with broader knowledge of thresholding behavior - here related to active layer depth - would provide empirical constraints on models aimed at predicting ecosystem responses to ongoing permafrost thaw.

Contributions of root and shoot derived-C to soil organic matter throughout an agricultural soil profile assessed by compound-specific 13C analysis

NASA Astrophysics Data System (ADS)

Mendez-Millan, Mercedes; Dignac, Marie-France; Rumpel, Cornelia; Rasse, Daniel P.; Derenne, Sylvie

2010-05-01

The turnover of soil organic matter (SOM) is generally studied in the topsoil horizons, where the highest concentrations of organic carbon (OC) are found. Subsoils, although containing lower amounts of organic carbon compared to topsoils, greatly contribute to the total carbon stocks within a soil profile. An increase in SOM aliphaticity was observed during SOM degradation, and also down the soil profile, suggesting that the stable pool of SOM is enriched in aliphatic structures. These alkyl-C structures might mainly derive from cutins and suberins, two biomacromolecules, which contain biomarkers specific for shoot and root plant biomass. The aim of this study was to use cutin and suberin structural units to follow the incorporation of plant biomass originating from roots and shoots throughout an agricultural soil profile. We measured the 13C natural abundance of root and shoot biomarkers in samples taken from 15 to 105 cm depth in a C3/C4 chronosequence. After 9 years of maize (C4) cropping, the distribution of root biomarkers (diacids) significantly changed and their concentration increased compared to the wheat (CC3) soil. The largest increase was observed at 60-75 cm where diacids reached up to 134 ?g/gOC compared to 23 ?g/gOC in the wheat soil. Higher inputs from maize root biomass are also suggested by an average 13C enrichment of the root markers in the maize compared to the wheat soil.

[Population structure of soil arthropod in different age Pinus massoniana plantations].

PubMed

Tan, Bo; Wu, Fu-zhong; Yang, Wan-qin; Zhang, Jian; Xu, Zhen-feng; Liu, Yang; Gou, Xiao-lin

2013-04-01

An investigation was conducted on the population structure of soil arthropod community in the 3-, 8-, 14-, 31-, and 40-years old Pinus massoniana plantations in the upper reaches of the Yangtze River in spring (May) and autumn (October), 2011, aimed to search for the scientific management of the plantation. A total of 4045 soil arthropods were collected, belonging to 57 families. Both the individual density and the taxonomic group number of the soil arthropod community decreased obviously with increasing soil depth, and this trend increased with increasing stand age. The dominant groups and ordinary groups of the soil arthropod community varied greatly with the stand age of P. massoniana plantation, and a significant difference (P<0.05) was observed in the individual density and taxonomic group number among different age P. massoniana plantations. In comparison with other stand age P. massoniana plantations, 3years old P. massoniana plantation had a significant difference in the structure and diversity of soil arthropod community, and the similarity index of the soil arthropod community was lower. The individual density, taxonomic group number, and diversity of soil arthropod community were the highest in 8-years old P. massoniana plantation, and then, decreased obviously with increasing stand age. It was suggested that the land fertility of the P. massoniana plantations could be degraded with increasing stand age, and it would be appropriate to make artificial regulation and restoration in 8-years old P. massoniana plantation.

Compaction of forest soil by logging machinery favours occurrence of prokaryotes.

PubMed

Schnurr-Pütz, Silvia; Bååth, Erland; Guggenberger, Georg; Drake, Harold L; Küsel, Kirsten

2006-12-01

Soil compaction caused by passage of logging machinery reduces the soil air capacity. Changed abiotic factors might induce a change in the soil microbial community and favour organisms capable of tolerating anoxic conditions. The goals of this study were to resolve differences between soil microbial communities obtained from wheel-tracks (i.e. compacted) and their adjacent undisturbed sites, and to evaluate differences in potential anaerobic microbial activities of these contrasting soils. Soil samples obtained from compacted soil had a greater bulk density and a higher pH than uncompacted soil. Analyses of phospholipid fatty acids demonstrated that the eukaryotic/prokaryotic ratio in compacted soils was lower than that of uncompacted soils, suggesting that fungi were not favoured by the in situ conditions produced by compaction. Indeed, most-probable-number (MPN) estimates of nitrous oxide-producing denitrifiers, acetate- and lactate-utilizing iron and sulfate reducers, and methanogens were higher in compacted than in uncompacted soils obtained from one site that had large differences in bulk density. Compacted soils from this site yielded higher iron-reducing, sulfate-reducing and methanogenic potentials than did uncompacted soils. MPN estimates of H2-utilizing acetogens in compacted and uncompacted soils were similar. These results indicate that compaction of forest soil alters the structure and function of the soil microbial community and favours occurrence of prokaryotes.

[Effects of biochar on microbial ecology in agriculture soil: a review].

PubMed

Ding, Yan-Li; Liu, Jie; Wang, Ying-Ying

2013-11-01

Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.