Amplicons and isolates: Rhizobium diversity in fields under conventional and organic management

AbstractBackgroundThe influence of farming on plant, animal and microbial biodiversity has been carefully studied and much debated. Here, we compare an isolate-based study of 196 Rhizobium strains to amplicon-based MAUI-seq analysis of rhizobia from 17,000 white clover root nodules. We use these data to investigate the influence of soil properties, geographic distance, and field management on Rhizobium nodule populations.ResultsOverall, there was good agreement between the two approaches and the precise allele frequency estimates from the large-scale MAUI-seq amplicon data allowed detailed comparisons of rhizobium populations between individual plots and fields. A few specific chromosomal core-gene alleles were significantly correlated with soil clay content, and core-gene allele profiles became increasingly distinct with geographic distance. Field management was associated with striking differences in Rhizobium diversity, where organic fields showed significantly higher diversity levels than conventionally managed trials.ConclusionsOur results indicate that MAUI-seq is suitable and robust for assessing nodule Rhizobium diversity. We further observe possible profound effects of field management on microbial diversity, which could impact plant health and productivity and warrant further investigation.

Download Full-text

Transfer Learning for Soil Spectroscopy Based on Convolutional Neural Networks and Its Application in Soil Clay Content Mapping Using Hyperspectral Imagery

Sensors ◽

10.3390/s18093169 ◽

2018 ◽

Vol 18 (9) ◽

pp. 3169 ◽

Cited By ~ 23

Author(s):

Lanfa Liu ◽

Min Ji ◽

Manfred Buchroithner

Keyword(s):

Transfer Learning ◽

Large Scale ◽

Clay Content ◽

Hyperspectral Data ◽

Coefficient Of Determination ◽

Organic Soils ◽

Calibration Model ◽

Field Samples ◽

Soil Clay ◽

Soil Clay Content

Soil spectra are often measured in the laboratory, and there is an increasing number of large-scale soil spectral libraries establishing across the world. However, calibration models developed from soil libraries are difficult to apply to spectral data acquired from the field or space. Transfer learning has the potential to bridge the gap and make the calibration model transferrable from one sensor to another. The objective of this study is to explore the potential of transfer learning for soil spectroscopy and its performance on soil clay content estimation using hyperspectral data. First, a one-dimensional convolutional neural network (1D-CNN) is used on Land Use/Land Cover Area Frame Survey (LUCAS) mineral soils. To evaluate whether the pre-trained 1D-CNN model was transferrable, LUCAS organic soils were used to fine-tune and validate the model. The fine-tuned model achieved a good accuracy (coefficient of determination (R2) = 0.756, root-mean-square error (RMSE) = 7.07 and ratio of percent deviation (RPD) = 2.26) for the estimation of clay content. Spectral index, as suggested as a simple transferrable feature, was also explored on LUCAS data, but did not performed well on the estimation of clay content. Then, the pre-trained 1D-CNN model was further fine-tuned by field samples collect in the study area with spectra extracted from HyMap imagery, achieved an accuracy of R2 = 0.601, RMSE = 8.62 and RPD = 1.54. Finally, the soil clay map was generated with the fine-tuned 1D-CNN model and hyperspectral data.

Download Full-text

Remaining phosphorus and sodium fluoride pH in soils with different clay contents and clay mineralogies

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2004000300006 ◽

2004 ◽

Vol 39 (3) ◽

pp. 241-246 ◽

Cited By ~ 6

Author(s):

Marcelo Eduardo Alves ◽

Arquimedes Lavorenti

Keyword(s):

Buffer Capacity ◽

Ammonium Oxalate ◽

Clay Mineralogy ◽

Clay Content ◽

Response Curves ◽

Solution Ph ◽

Ph Values ◽

Soil Clay ◽

Soil Clay Content ◽

Discriminatory Capacity

The remaining phosphorus (Prem) has been used for estimating the phosphorus buffer capacity (PBC) of soils of some Brazilian regions. Furthermore, the remaining phosphorus can also be used for estimating P, S and Zn soil critical levels determined with PBC-sensible extractants and for defining P and S levels to be used not only in P and S adsorption studies but also for the establishment of P and S response curves. The objective of this work was to evaluate the effects of soil clay content and clay mineralogy on Prem and its relationship with pH values measured in saturated NaF solution (pH NaF). Ammonium-oxalate-extractable aluminum exerts the major impacts on both Prem and pH NaF, which, in turn, are less dependent on soil clay content. Although Prem and pH NaF have consistent correlation, the former has a soil-PBC discriminatory capacity much greater than pH NaF.

Download Full-text

P-sorption and desorption in Savanna Brazilian soils as a support for phosphorus fertilizer management

Ciência e Agrotecnologia ◽

10.1590/s1413-70542013000600005 ◽

2013 ◽

Vol 37 (6) ◽

pp. 521-530 ◽

Cited By ~ 17

Author(s):

Flávio Araújo Pinto ◽

Edicarlos Damacena de Souza ◽

Helder Barbosa Paulino ◽

Nilton Curi ◽

Marco Aurélio Carbone Carneiro

Keyword(s):

Clay Content ◽

Soil Characteristics ◽

Fertilizer Management ◽

Phosphorus Fertilizer ◽

Phosphorus Adsorption ◽

P Sorption ◽

Brazilian Soils ◽

Soil Clay ◽

Sand Base ◽

Soil Clay Content

Phosphorus (P) sorption by soils is a phenomenon that varies depending on soil characteristics, influencing its intensity and magnitude, which makes it a source or drain of P. The objective of this study was to determine the Maximum Phosphorus Adsorption Capacity (MPAC) and desorption of P from soils under native Savanna Brazilian and verify the correlation between MPAC and P Capacity Factor (PCF) with the chemical and physical properties of these soils. The study was conducted in seven soils under native Savannas. The Langmuir isotherms were adjusted from the values obtained in sorption assays, being evaluated the MPAC, the energy adsorption (EA) and PCF, which was calculated according to the levels of P-adsorbed and P-sorbed. Values of MPAC were classified as high in most soils, ranging from 283 up to 2635 mg kg-1 of P in the soil and were correlated with soil organic matter, clay, silt, sand, base saturation and pH. The PCF was higher in soils where the MPAC was also higher. The use of only one attribute of soil (clay content) as a criterion for the recommendation of phosphated fertilization, as routinely done, is susceptible to errors, needing the use of more attributes for a more accurate recommendation, as a function of the complexity of the interactions involved in the process.

Download Full-text

Surface soil clay content mapping at large scales using multispectral (VNIR–SWIR) ASTER data

International Journal of Remote Sensing ◽

10.1080/01431161.2018.1528018 ◽

2018 ◽

Vol 40 (4) ◽

pp. 1506-1533

Author(s):

Anis Gasmi ◽

Cécile Gomez ◽

Philippe Lagacherie ◽

Hédi Zouari

Keyword(s):

Surface Soil ◽

Clay Content ◽

Aster Data ◽

Soil Clay ◽

Soil Clay Content

Download Full-text

Factors Affecting Microbial Formation of Nitrate-Nitrogen in Soil and Their Effects on Fertilizer Nitrogen Use Efficiency

The Scientific World JOURNAL ◽

10.1100/tsw.2001.308 ◽

2001 ◽

Vol 1 ◽

pp. 122-129 ◽

Cited By ~ 7

Author(s):

Alan Olness ◽

Dian Lopez ◽

David Archer ◽

Jason Cordes ◽

Colin Sweeney ◽

...

Keyword(s):

Organic Matter ◽

Decision Aid ◽

Pore Space ◽

Organic Matter Content ◽

Clay Content ◽

Matter Content ◽

N Fertilizer ◽

Nitrate N ◽

Soil Clay ◽

Soil Clay Content

Mineralization of soil organic matter is governed by predictable factors with nitrate-N as the end product. Crop production interrupts the natural balance, accelerates mineralization of N, and elevates levels of nitrate-N in soil. Six factors determine nitrate-N levels in soils: soil clay content, bulk density, organic matter content, pH, temperature, and rainfall. Maximal rates of N mineralization require an optimal level of air-filled pore space. Optimal air-filled pore space depends on soil clay content, soil organic matter content, soil bulk density, and rainfall. Pore space is partitioned into water- and air-filled space. A maximal rate of nitrate formation occurs at a pH of 6.7 and rather modest mineralization rates occur at pH 5.0 and 8.0. Predictions of the soil nitrate-N concentrations with a relative precision of 1 to 4 μg N g–1of soil were obtained with a computerized N fertilizer decision aid. Grain yields obtained using the N fertilizer decision aid were not measurably different from those using adjacent farmer practices, but N fertilizer use was reduced by >10%. Predicting mineralization in this manner allows optimal N applications to be determined for site-specific soil and weather conditions.

Download Full-text

Determination of the Environmental Factors that Affect the Growth and Survival of Greek Fir Seedlings

Land ◽

10.3390/land9040100 ◽

2020 ◽

Vol 9 (4) ◽

pp. 100

Author(s):

Vassilis Detsis ◽

Georgios Efthimiou ◽

Olga Theodoropoulou ◽

Stavroula Siorokou

Keyword(s):

Regression Model ◽

Mixed Model ◽

Linear Mixed Model ◽

Clay Content ◽

Weather Conditions ◽

Apical Growth ◽

Growth And Survival ◽

Initial Height ◽

Soil Clay ◽

Soil Clay Content

Forests in the montane-Mediterranean zone have only recently began to be affected by wildfires, therefore the knowledge necessary for restoration projects is missing. The aim of the study was to assess the effects of factors related to seedling attributes, weather conditions and site suitability on seedling performance. The characterisation of sites was based on bedrock and soil clay content as well as pre-fire vegetation. Apical growth and survival of seedlings was monitored for four years in Parnitha National Park. The parameters of a linear mixed model were estimated using annual apical growth of seedlings surviving in the end of the study as the dependent variable and type of site, rainfall, initial seedling height and age as explanatory ones. A quantile regression model using all the data available was estimated for each year of study, taking into account only initial height and site type as well as a logistic regression model of survival. The findings indicate that the growth of Greek fir seedlings depends on May rainfall mediated by soil clay content, which in turn depends on bedrock, which is consistent with the “inverse texture hypothesis”. Sites with low soil clay content were always more beneficial for survival, which was stronger affected by summer–autumn rainfall. In both contexts, drought stress due to soil clay content fades with increasing age. Sites that were not fir dominated prior to fire proved unsuitable also for planting fir seedlings. A minor part of the observed variability could be associated with the initial height of seedlings, especially for seedlings showing high rates of apical growth.

Download Full-text

Effects of Soil Clay Content on Water Balance and Productivity in Rainfed Lowland Rice Ecosystem in Northeast Thailand

Plant Production Science ◽

10.1626/pps.10.232 ◽

2007 ◽

Vol 10 (2) ◽

pp. 232-241 ◽

Cited By ~ 26

Author(s):

Mitsuru Tsubo ◽

Shu Fukai ◽

Jayampathi Basnayake ◽

To Phuc Tuong ◽

Bas Bouman ◽

...

Keyword(s):

Water Balance ◽

Clay Content ◽

Lowland Rice ◽

Northeast Thailand ◽

Rainfed Lowland ◽

Soil Clay ◽

Soil Clay Content ◽

Rice Ecosystem

Download Full-text

Soil Clay Content Mapping Using a Time Series of Landsat TM Data in Semi-Arid Lands

Remote Sensing ◽

10.3390/rs70506059 ◽

2015 ◽

Vol 7 (5) ◽

pp. 6059-6078 ◽

Cited By ~ 24

Author(s):

Marouen Shabou ◽

Bernard Mougenot ◽

Zohra Chabaane ◽

Christian Walter ◽

Gilles Boulet ◽

...

Keyword(s):

Time Series ◽

Clay Content ◽

Arid Lands ◽

Landsat Tm ◽

Soil Clay ◽

Soil Clay Content ◽

Semi Arid

Download Full-text

Soil clay content, rainfall, and toposequence positions determining spatial variation in field water availability as estimated by a water balance model for rainfed lowland rice

Crop and Pasture Science ◽

10.1071/cp12108 ◽

2012 ◽

Vol 63 (6) ◽

pp. 529 ◽

Cited By ~ 7

Author(s):

T. Inthavong ◽

M. Tsubo ◽

S. Fukai

Keyword(s):

Water Balance ◽

Water Availability ◽

Clay Content ◽

Lowland Rice ◽

Balance Model ◽

Yield Reduction ◽

Growing Period ◽

Rainfed Lowland ◽

Soil Clay ◽

Soil Clay Content

Drought is a major limiting factor for the production of rainfed rice in the Mekong Region. Thus, estimation of the length of growing period (LGP) based on estimation of the development of water deficit is essential for sound planning of agricultural development. A recently developed soil-water balance model was used to quantify the availability of water for rice crops and yield reduction due to water deficit. Field water availability is known to be largely affected by soil type and rainfall pattern, and their separate effects were investigated in this study of a spatial analysis of LGP, using inputs for rainfed lowland rice in Savannakhet province in central Laos. The analysis showed that the start of growing period (SGP) and end of growing period (EGP) were affected largely by geographical variations in rainfall and soil clay content, respectively. Also, the areas having relatively short LGP were generally associated with large yield reduction because of low water availability associated with coarse-textured soils. At local scale, field water availability varied from upper to lower positions of a sloping land (toposequence) in the rainfed lowland ecosystem of the Mekong region, causing variation in yield within the toposequence. Using the level of field water determined around flowering time at different toposequence positions in 45 farms, estimated yield reduction was compared in seven main rice-growing districts of the province. Variability of yield loss, associated with variation in water availability, was larger across the toposequence positions than across districts, showing the importance of local variability in determining yield in rainfed lowland rice. The present approach of a combination of simulation model and GIS is adopted for characterisation of the water environment for rainfed lowland rice in other parts of Laos, as well as in neighbouring Thailand and Cambodia.

Download Full-text

Can soil clay content predict ammonia volatilization losses from subsurface-banded urea in eastern Canadian soils?

Canadian Journal of Soil Science ◽

10.1139/cjss-2018-0036 ◽

2018 ◽

Vol 98 (3) ◽

pp. 556-565 ◽

Cited By ~ 6

Author(s):

D.E. Pelster ◽

M.H. Chantigny ◽

D.A. Angers ◽

N. Bertrand ◽

J.D. MacDonald ◽

...

Keyword(s):

Cation Exchange ◽

Negative Relationship ◽

Clay Content ◽

Soil Mesocosms ◽

Dynamic Chamber ◽

Canadian Soils ◽

Soil Clay ◽

Soil Clay Content ◽

Physical And Chemical ◽

Water Extractable

To determine how soil physical and chemical characteristics affect NH3 volatilization, we measured NH3 losses from eight different eastern Canadian soils with various soil clay contents and cation exchange capacities (CEC). Losses were measured from soil mesocosms banded (0.05 m depth) with urea (equivalent of 140 kg N ha−1) in a dynamic chamber system fitted with an acid trap; with soil properties measured in parallel mesocosms. Regression analysis indicated a negative relationship between 28 d of NH3 volatilization losses and soil clay content (P < 0.001; R2 = 0.978), CEC (P < 0.001; R2 = 0.941), and buffer capacity (P = 0.006; R2 = 0.772), and positive relations with maximum change in soil pH (P = 0.015; R2 = 0.670) and maximum water-extractable NH4+ (P = 0.010; R2 = 0.721). A 90% reduction in NH3 losses occurred when clay content increased from 10% to 20%. Also, the correlation between water-extractable NH4+ and NH3 loss and a lack of correlation between salt-extractable (1 mol L−1 KCl) NH4+ and NH3 loss indicate that NH4+ bound to cation exchange sites does not contribute to the rapid NH3 volatilization. However, more research on soils of different mineralogy is required to ascertain whether this holds in other regions as well.

Download Full-text