Released this past November, the list is based on data collected from the Web of Science and highlights some of the world’s most influential scientific minds by naming the researchers whose publications over the previous decade have included a high number of Highly Cited Papers placing them among the top 1% most-cited.
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We wish to congratulate all of the researchers named and especially our authors on this amazing accomplishment! We are happy and proud to share in their success!
IntechOpen is proud to announce that 191 of our authors have made the Clarivate™ Highly Cited Researchers List for 2020, ranking them among the top 1% most-cited.
\n\n
Throughout the years, the list has named a total of 261 IntechOpen authors as Highly Cited. Of those researchers, 69 have been featured on the list multiple times.
\n\n\n\n
Released this past November, the list is based on data collected from the Web of Science and highlights some of the world’s most influential scientific minds by naming the researchers whose publications over the previous decade have included a high number of Highly Cited Papers placing them among the top 1% most-cited.
\n\n
We wish to congratulate all of the researchers named and especially our authors on this amazing accomplishment! We are happy and proud to share in their success!
Note: Edited in March 2021
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\r\n\tThe ecology of skinks has been studied in recent years (about two decades). Foraging mode has been shown to be a persuasive evolutionary force molding the diet, ecology, behavior, anatomy, biomechanics, life history, and physiology of skinks and lizards.
\r\n
\r\n\tThis volume will review the state of our knowledge on the effects of foraging mode on these and other organismal systems to show how skinks and lizards have evolved with foraging mode over a wide taxonomic survey of skink and lizard groups. This review will reveal the continuous nature of foraging strategies in skinks and lizards (especially skinks and lizards living in tropical regions), providing the general reader with an up-to-date review of the field, and will equip researchers with new insights and future directions for the sit-and-wait vs. wide foraging paradigm.
\r\n
\r\n\tThis volume will serve as a reference book for Ph.D. students, herpetologists, evolutionary biologists, animal behaviorists, and conservational ecologists. \r\n\t
",isbn:null,printIsbn:"979-953-307-X-X",pdfIsbn:null,doi:null,price:0,priceEur:0,priceUsd:0,slug:null,numberOfPages:0,isOpenForSubmission:!1,isSalesforceBook:!1,hash:"287b982cd93fa41c914d5d42c3cb6895",bookSignature:"Associate Prof. Binh Ngo",publishedDate:null,coverURL:"https://cdn.intechopen.com/books/images_new/11089.jpg",keywords:"Diet, Foraging Mode, Behavior, Life History, Microhabitat Use, Reproduction, Skink Ecology, Feeding Ecology, Reproductive Biology, Skinks, Lizards, Reptiles",numberOfDownloads:null,numberOfWosCitations:0,numberOfCrossrefCitations:null,numberOfDimensionsCitations:null,numberOfTotalCitations:null,isAvailableForWebshopOrdering:!0,dateEndFirstStepPublish:"September 30th 2021",dateEndSecondStepPublish:"October 28th 2021",dateEndThirdStepPublish:"December 27th 2021",dateEndFourthStepPublish:"March 17th 2022",dateEndFifthStepPublish:"May 16th 2022",remainingDaysToSecondStep:"7 months",secondStepPassed:!0,currentStepOfPublishingProcess:5,editedByType:null,kuFlag:!1,biosketch:"Dr. Ngo has received his Ph.D. in Zoology from National Cheng Kung University, Taiwan (2015), and has over five years of experience teaching Zoology, Ecology, and Animal Behavior. Dr. Ngo's research focuses primarily on behavioral ecology, bioacoustics, population biology, community ecology, conservation ecology, log-normal distributions, and site occupancy of amphibians and reptiles living in tropical regions.",coeditorOneBiosketch:null,coeditorTwoBiosketch:null,coeditorThreeBiosketch:null,coeditorFourBiosketch:null,coeditorFiveBiosketch:null,editors:[{id:"416568",title:"Associate Prof.",name:"Binh",middleName:null,surname:"V. Ngo",slug:"binh-v.-ngo",fullName:"Binh V. Ngo",profilePictureURL:"https://mts.intechopen.com/storage/users/416568/images/system/416568.jpg",biography:"BINH V. NGO is an Associate Professor of Biology and a senior lecturer at the College of Education, Hue University, Vietnam, where he has taught Zoology, Ecology, and Animal Behavior over the last 6 y. He received his Ph.D. in Zoology from National Cheng Kung University, Taiwan (2015). 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1. Introduction
The analysis of the Partial Discharges (PD) phenomenon, which manifests itself in the existing imperfections into the insulation of high voltage equipment have received global acceptance as an important tool for the predictive diagnosis of the operational conditions of these, allowing taking measures that can safeguard both the material and the power supply quality of the electrical system.
PD are short duration impulsive signals and, consequently, these can be detected in a wide frequency range, from a few kHz to GHz. Normally, there is a direct relationship between the frequency range where there is a higher incidence of PD pulses and the type of high-voltage equipment evaluated, e.g. transformers and generators usually emit pulses from a few tens of kHz up to about 30 MHz [1], whereas Gas Insulated Substations (GIS) are affected by very fast pulses ranging from 300 MHz to 3 GHz and for cables the spectrum covers frequencies from 300 MHz to 1 GHz.
Figure 1 shows two examples of measured PD pulses in two different HV equipment, a GIS and a hydro generator. Note the marked white noise presence. The pulses normally have an exponentially damped oscillatory shape or only an exponentially damped shape [2].
The proper diagnosis of equipment is closely related to the peak amplitude and shape of the pulses detected. Therefore, it is important to preserve the amplitude characteristics of the signal (especially the peaks), providing higher Signal to Noise Ratio (SNR) and lower Amplitude Error (EA).
The application of FFT and STFT filtering is not as effective in the treatment of non-stationary, transient, and stochastic signals as the PD [3], since these transforms do not allow a location in the time and frequency domain in the same way as the wavelet transform does [4, 5] (with better resolution in frequency and worse resolution in time for the low frequency components of the signal; and worse resolution in frequency and better resolution in time for the high frequency components of the signal). Therefore, the performance of these methods becomes limited in comparison with the wavelet denoising, which presents a capacity of self-adaptation to the signal.
Partial discharges, almost entirely, are electrically detected and quantified, exposing them to the extensive noise interferences that may compromise the PD signals measurement, limiting the diagnosis accuracy. Different signal processing tools have been used to extract the PD signals from these noise sources; among them, it is possible to highlight the Wavelet Transform (WT). The filtering by wavelet processing is recommended in the extraction of PD signals immersed in Gaussian noise [1, 6].
An efficient application of wavelet processing depends on the careful selection of the parameters that will concentrate the coefficients on the most suitable decomposition levels to minimize the PD signal information loss. Among these, we have the applied WT, the number of decomposition levels, the wavelet functions used in each of these levels, the method of estimating the threshold value of the obtained coefficients and the threshold function.
The choice of most of these parameters has already been widely explored in several works meant to PD processing [2, 6, 7, 8, 9, 10, 11, 12, 13]. However, with respect to threshold functions, most studies do not focus on PD signals denoising but on audio signals [14, 15, 16, 17, 18], Electrocardiogram (ECG) [19, 20, 21] or images [22, 23, 24, 25, 26, 27, 28]. Therefore, there is a lack of a dedicated threshold function to improve the PD pulses denoising, in order to increase the precision in the diagnosis of High Voltage (HV) equipment.
Based on the WT filtering theory, this chapter will be described the development of a wavelet threshold function aiming to improve the noise reduction in PD measurements. The logistic function serves as an inspiration to this new function [29], which is well known for its usefulness in numerous areas. Since it is customary to associate functions of this type with something that refers them to the name of their developers (e.g., [25]), it was designated as Fleming threshold function.
The denoising performance of the proposed threshold function was compared with the traditional Hard and Soft functions and with twelve other thresholding functions. For a fair analysis of the filtering results, were used 2064 simulated and measured PD pulses contaminated with uniform white noise, Gaussian white noise, and Amplitude Modulated (AM) noise. The results showed that our proposal is able to overcome, qualitatively, and quantitatively, all the confronted functions.
2. Wavelet domain detection
Noise degrades the accuracy and precision of analysis, in addition to reducing the detection limit of the instrument applied in the PD measurements. Often the WT is a tool designed to attenuate continuous random noise (white noise), because after the decomposition of a signal in the wavelet domain can be noted that the average density of the coefficients is inversely proportional to the dyadic scale 1/2j (j indicates the level of decomposition), i.e., half of the number of extreme local coefficients do not spread from a 1/2j scale to the next 1/2j+1 scale, distributing it uniformly across the scales. As the wavelet coefficients distribution pattern of the PD signal (which tends to have its energy concentrated in few decomposition levels) differs from the noise pattern, it becomes easy to identify and separate the PD signals from the noise [30, 31, 32]. However, in wavelet denoising, the noise attenuation occurs not only to the white noise but also to the noise with frequency components that do not match the frequency components of the PD pulses.
Basically, the wavelet shrinkage denoising process involves three steps [13, 31]:
Determine the WT decomposition tree (discrete WT, wavelet packet transform, stationary WT or dual-tree complex WT) to be applied, the number of decomposition levels J and the wavelet function that will be employed on each of the j levels (where j =1,2,⋯,J), and then perform the decomposition of the analyzed signal into its wavelet coefficients;
Calculate the threshold values using one of the threshold selection rules, which depend on statistical estimation of the noise level present in the signal. Apply the calculated value in a threshold function to thus reduce the coefficients of the noise figure and preserve the signal coefficients of interest, in our case the PD pulse;
Reconstruct the signal by applying the Inverse Wavelet Transform (corresponding to the decomposition tree selected in the first step) in the threshold coefficients, to obtain the filtered signal in the time domain.
Figure 2 illustrates each of these steps involved in the wavelet denoising processing of a digitalized signal.
Figure 2.
Signal denoising steps by wavelet transform.
Figure 3.
Logistic function.
As several parameters are involved, they should be carefully selected according to the signal characteristics, in order to maximize their wavelet coefficients above the noise level. Thus, filtering performance is closely related to each of these parameters and some of these will have a greater influence on the quality of the result. The determination of these parameters shows to be an optimization challenge [33]. In this chapter, we will focus our attention on the improvement of the threshold function applied in the second step.
3. Fleming threshold function
In most of the wavelet denoising literature, especially those focused in the treatment of PD signals, the choice of the threshold function normally falls between the Hard and the Soft functions. Moreover, it is well known that for PD pulse filtering the Hard function tends to preserve more of the signal information, providing a higher SNR and a lower Amplitude Error (AE). However, the Hard estimate has discontinuities, being not differentiable, which ends up causing instability problems and sensitivity to small changes in the data pseudo-Gibbs effect. The Soft function is weakly differentiable and produces a high attenuation of the coefficients and, therefore, the reduction of the amplitude in the resulting signal.
In an attempt to get around these problems, many alternatives are being proposed. The main idea is to generate a high-derivative order thresholding function, which contributes to its use in optimization algorithms that look for the optimal parameters to be applied in the thresholding of each signal [34]. Therefore, the function becomes adaptable to the signal to be processed, improving the quality of the denoised signal.
When analyzing the threshold functions applied, whether in the area of PD, audio, ECG, or image processing, it is remarkable that those seek improvements by combining both, the preservation properties of the coefficients and magnitudes provided by the Hard function, as well as the differentiation and smoothness provided by the Soft function. In image processing, the smoothness property is interesting so that the resulting image shows more pleasant contours. In signal processing, such as audio, ECG, and PD pulse processing, it is important to achieve better preservation of signal magnitude (peak) and signal noise ratio.
For this reason, many authors have explored functions that correspond to an interpolation of the Soft and Hard alternatives. As an example, it is possible to mention functions such as: the Garrote described by Nasiri et al. in [19]; the Non Negative Garrote described in [12]; the Adaptive Shirinkage showed by Partha Ray in [35]; the Liu developed by Shan Liu in [16]; the Hui presented in [36]; Stein and Semi-Soft shown in [12]; and the functions described by Zhang et al. in [37, 38]. However, the majority of the functions cannot adapt to the different signals due to the fixed transition curve on the threshold value. In these functions, there is still a greater tendency to smooth the coefficients than to preserve them, not realizing that for PD signals it is appropriate for the function to be closer to the Hard them to the Soft threshold function, but still preserving some of the smoothness (differentiability) in the transition of the threshold value, which will allow an improvement in the EQM and CC.
Following this line of reasoning, we propose a new threshold function similar to the Hard but being differentiable for higher orders and being able to adjust to each signal. This proposal is based on the well-known logistic function, shown in Figure 2, widely used in artificial neural networks, demography, economics, probability, statistics, chemistry, etc. Eq. (1) represents the logistic function, where H is the maximum value of the curve, α controls the slope of this curve and x corresponds to the value of x at the midpoint of the sigmoid curve dictated by the numerator value (Figure 3). When the x value tends to +∞ the curve approaches H and when it tends to −∞ it approaches to zero.
fx=H1+e−αx−x0E1
Eq. (1) enabled us to develop the threshold function for filtering signals in such a way that it circumvents the problems previously described. As the objective in the thresholding process is to preserve the coefficients above the threshold value, it is easy to see that the maximum value H will be the decomposed wavelet coefficient wj,k (which corresponds to the variable x). Thus, the function will maintain symmetry when we vary the inclination constant c of the curve. Finally, it is necessary to move the function along the abscissa axis so that the graph shown in Figure 2 leaves the ordinate axis and stays over the threshold value, this is done by subtracting the variable x from the value where we want to move the function (x0), i.e., the value of the coefficients wj,k must be subtracted from the threshold value λ. By making these adaptations, we obtain the following threshold function:
ηfωj,kλc=ωj,k1+e−cωj,k−λ=ωj,k1+ec−ωj,k+λE2
For a more efficient implementation, in which it is not necessary to worry about the fact that the coefficient wj,k is positive or negative, Eq. (2) can be rewritten using the signum (sign) function, which returns +1 if the value is positive and −1 if the value is negative. Thus, we have:
ηfωj,kλc=ωj,k1+ec−signωj,k×ωj,k+λE3
With high c values, the curve inclination on the threshold point is such that it approaches the Hard function, but with a smoother (differentiable) transition. For low c values, the inclination of the function will act with less intensity on the coefficients below the threshold value and with greater intensity on the coefficients above this value, i.e., a large part of noisy coefficients may pass and there will be information losses on those coefficients that represent the signal of interest, in our case the PD pulse. With the appropriate choice of the c value for each processed signal, it is possible to obtain a significant improvement in the result of the PD wavelet denoising in relation to the Hard and the Soft functions.
Considering a threshold value λ=1, Figure 4 shows the behavior of the proposed threshold function (called the Fleming function) for different c values (3, 10, 20, 30, 50, 80, 100 e 200). With very low values of c there is the possibility of passing a large number of noisy coefficients, so it is indicated that the value of the constant be greater than or equal to 5.
Figure 4.
Behavior of the Fleming threshold function to λ=1.
In a PD evaluation, most measurements provide signals with amplitude around mV. Thus, if the WT technique is applied to filter the signals, its decomposed coefficients will also be in the mV range and by using a threshold rule (in our case scaledep) the threshold value λ will be small and usually smaller than 1, mainly for coefficients that contain more noise than the PD components. When we evaluate the threshold function for a small threshold value (e.g., λ=0,05), the accuracy with which the coefficients are attenuated becomes lower, as illustrated in Figure 5. Note that even for c=200, most of the noisy coefficients can pass, different than what was seen for the threshold value λ=1.
Figure 5.
Behavior of the Fleming threshold function to λ=0,05.
One solution to overcome this problem was to adapt Eq. (3) according to the threshold value when it is considered small (understand as small as λ<0,5), by simply changing the c constant that controls the inclination proportionally to the λ threshold values. With this, we can rewrite Eq. (3) as follows:
thus, when λ<0,5 the lower the λ threshold value, the greater the rigor in discarding the coefficients (closer to the Hard function), with a significant improvement in the function’s behavior, as shown in Figure 6.
Figure 6.
Behavior of the modified Fleming threshold function to λ=0,05.
Therefore, in Eq. (4) we have a function capable of adapting to different types of wavelet coefficients, varying between the Soft and the Hard threshold functions according to the c inclination value defined. Thus, there is a need to define how (and which) the inclination value should be applied to the coefficients.
3.1 Relevant wavelet coefficient identification
From the idea of identifying the most important coefficients to form the PD signal, used for the SNRBWS method, we were able to perform a variant on the threshold function. In this case, we chose to use kurtosis (Ku) as a statistical measure of the probability distribution’s flatness [39] of the ωj,kwavelet coefficient, because the tapered this curve, the farther from the Normal probability distribution (Gaussian), which is characteristic of the white noise presence. Therefore, kurtosis will serve as an indicator to know if we have noisy coefficients (kurtosis close to 3) or PD components (high kurtosis ≥3).
Figure 7 shows the detail coefficients at level j=1 and the detail coefficients at level j=6 with their respective histograms. Notice that in Figure 7(a), formed almost exclusively by noise components, the histogram is very close to the Normal probability distribution, a fact that is confirmed by the kurtosis value equal to 2.9687; in the Figure 7(b) the coefficients have significant information about the PD pulse and the histogram is more tapered (leptokurtic), moving away from the Normal distribution, as indicated by the kurtosis value of 9.9612.
Figure 7.
Wavelet coefficients and histograms of a real PD pulse: (a) first detail coefficient (kurtosis = 2.9687); (b) sixth detail coefficient (kurtosis = 9.9612).
Then, to fulfill the task of identifying the most relevant coefficients to form the PD signal, it is enough to assume the following the condition regarding the kurtosis value: if the kurtosis of the coefficient is greater than 4, it must be considered important and the threshold function will make use of a lower c inclination constant, allowing the passage of more coefficients, otherwise it will be considered as noisy coefficients and a much higher inclination constant must be assigned (in case c=1020), eliminating a greater amount of noise, which approximates our function of the Hard. In equational terms, we have the Eq. (5):
In order to perform the evaluation of the Fleming thresholding functions, we took 2064 signals and submitted to the wavelet denoising processes. Among these signals, we included real PD measurements from HV equipment and PD simulated with different levels of uniform white, Gaussian white and AM noise (created of the same way described in [40]). For each data, we compare the performance of our proposal against the classical Hard and Soft thresholding, along with 12 other thresholding functions mentioned in the Section 4.
In addition to thresholding, the wavelet shrinkage process also requires the choice of the decomposition tree, the mother wavelet, the decomposition levels number and the threshold value λ estimation method. As our goal is to evaluate only the thresholding functions performance, we change only these and keep fixed the other wavelet parameters necessary to the signal filtering. We chose to use the FWT structure, due to the ease of its implementation and because it is widely applied in the treatment of PD signals. We use the SNRBWS method to select the mother wavelet and the NWDLS method to find the decomposition levels number. In the threshold value estimative, we chose the scaledep method [3, 40, 41].
Since the Fleming function depends on an c inclination constant, which controls how the decomposed wavelet coefficients are eliminated or attenuated, we also compare the results for different values of this constant.
The comparisons were done using statistical parameters as Absolute Mean Error (AME), Mean Square Error (MSE), Root Mean Square Error (RMSE), Correlation Coefficient (CC), Normalized Correlation Coefficient (NCC), Energy Difference (EnD), Signal to Noise Ratio (SNR), Signal to Noise Ratio Difference (DSNR), Noise Level Reduction (NLR), kurtosis difference (∆k); and local similarity criteria that involve maximum Magnitude Error (MEmax), minimum Magnitude Error (MEmin), maximum Peak Time Variation (PTVmax), minimum Peak Time Variation (PTVmin) and Rise Time Variation (RTV). Some of these parameters are used to form a fitness function (JApt), composed by global similarity criteria (csg) and local similarity criteria (csl), that can determine the best filtering result. All these criteria were described in [42].
4.1 Investigating the better inclination value c
In a first analysis, it was investigated, through the JApt fitness criterion, what is the best c inclination value to be used in each alternative of the Fleming thresholding. Table 1 evinced that c=5 produces the highest amount of best results per threshold function. In Table 2 both methods produce best results with a lower constant, in case c=10 to Fleming and c=5 to Fleming 2. In this way, it is possible to recommend not to use inclination values higher than 10.
Function
Best JApt results percentage
Inclination constant c
5
10
30
50
100
200
300
500
1000
Fleming
47,09
25,00
8,96
4,12
3,63
1,50
1,07
1,16
7,46
Fleming 2
65,16
11,82
5,52
2,37
1,79
1,55
0,78
1,16
9,84
Table 1.
Best results percentage (by JApt) comparison between Fleming functions to various inclination constants.
Function
Mean JApt results
Inclination constant c
5
10
30
50
100
200
300
500
1000
Fleming
2,71
3,12
1,02
0,09
0,73
0,49
0,07
0,93
0,96
Fleming 2
1,34
1,06
0,92
0,89
0,88
0,88
0,88
0,89
0,88
Table 2.
Mean value results (by JApt) comparison between Fleming functions to various inclination constants.
4.2 Comparison between Fleming, Hard and Soft threshold functions
The main objective of building a dedicated threshold function is to make it able to produce results superior to those of conventional functions. As seen, the most applied functions in wavelet coefficient filtering are Hard and Soft, not only for PD signals, but also for image processing, audio signals, etc.
First, we show in Figure 8 the results of the comparison between the first proposed alternative using c=5 against Hard and Soft functions. According to the JApt, we find that the proposed function achieves a higher percentage of better results than the Hard and Soft. As expected, due to its simplicity, the Soft thresholding is the fastest in runtime.
Figure 8.
Comparison of the better denoising results obtained between the Hard, Soft and Fleming threshold functions.
We then compare in Figure 9 the second alternative proposed with the Hard and Soft functions. Note that there is a significant improvement in the number of better results, achieving superior performance in the EMA and ∆k criteria, which did not occur with the first alternative of our function.
Figure 9.
Comparison of the better denoising results obtained between the Hard, Soft and Fleming 2 threshold functions.
Therefore, is evidenced by the superiority of the proposed alternatives in relation to the amount of better results obtained compared to the usual Hard and Soft methodologies. The only drawback is that our second proposal needs a little more time to be processed, but it is a relatively low price to be paid to achieve better results in reducing noisy components of PD signals. Also, note that, compared with the Soft function, the Hard thresholding tends to provide a better preservation of the PD pulses amplitudes and of the SNR, which confirms the statements made in the literature [3, 22].
In Figure 10 is shown a signal consisting of 3 simulated PD pulses wrapped in white noise and in AM noise, which was created as performed in [3]. In addition, note the filtering results for the Hard, Soft, Fleming and Fleming 2 thresholding. The Soft function tends to considerably attenuate the pulses peak amplitudes; the Hard function shows greater preservation of these amplitudes; the Fleming function allows the passage of a little more noise with negligible amplitudes, but it achieves better preservation of the amplitudes than the Hard and Soft, while the Fleming 2 function is able to solve Fleming’s problem by identifying the coefficients of greater importance. In this way, the Fleming 2 method presents better amplitudes preservation than the other functions and still manages to eliminate the low amplitude noise seen with the use of the Fleming. The filtering improvement is also indicated by the fitness function, with higher value (JApt = 16.4607) for the filtering result using the Fleming 2 thresholding.
Figure 10.
Comparison of the better denoising results obtained between the Hard, Soft, Fleming and Fleming 2 threshold functions to a simulated PD signal.
4.3 Comparison between all threshold functions
With the results described in the previous subsection, we have a quantitative idea of the used method’s capacity, but only with the average results is possible to have a real sense of the quality of each one. Taking advantage of the opportunity, we implement the various wavelet thresholding methods (mentioned in Section 4), including the: Adapt Shrink, Garrote, Hui, Liu, Non Negative Garrote (NNG), Semi Soft (SS), Stein, Zhang 1 (Z1), Zhang 2 (Z2), Zhang 3 (Z3), Zhang 4 (Z4), and Zhang 5 (Z5). The required variables for each of these alternatives were designated according to the specifications provided by the respective authors in the works that describe them.
Similarly to what was done in Table 1, we made a percentage evaluation of the amount of best results considering all threshold functions and the proposed Fleming functions (compared for a constant c = 5). From Tables 3 and 4, the bold values evidence that the Fleming threshold had a superior performance when compared to the other alternatives. In terms of fitness, the one with the highest amount of better filtering results was Fleming. The Stein function outperforms the others in execution time. The Soft function ends up losing space in practically all the evaluated criteria, confirming that it is not suitable to treat PD signals, due to the high attenuation generated in the wavelet coefficients processing.
Parameter
Threshold function
Hard
Soft
Fleming
Fleming 2
Adapt shrink
Garrote
Hui
Liu
AME
1,07
0,39
9,01
31,49
5,23
4,80
13,08
6,73
MSE
0,19
0,00
10,22
33,38
7,99
9,25
8,43
5,33
RMSE
0,19
0,00
10,22
33,38
7,99
9,25
8,43
5,33
CC
0,87
0,00
16,57
39,87
3,83
11,97
7,27
2,76
NCC
0,97
0,00
17,59
40,26
3,15
11,92
6,98
2,91
EnD
18,51
0,48
18,12
14,73
1,79
8,91
1,89
9,93
SNR
2,37
0,00
21,17
42,49
0,15
3,39
1,55
2,23
DSNR
2,37
0,00
21,17
42,49
0,15
3,39
1,55
2,23
NLR
0,00
0,00
0,00
0,00
0,00
0,00
0,00
0,00
MEmax
9,40
0,19
20,78
17,78
1,07
8,48
0,24
6,10
MEmin
8,19
0,10
18,70
19,04
2,28
10,17
1,31
8,28
PTVmax
0,73
0,00
6,15
3,20
2,96
5,43
0,48
2,57
PTVmin
1,16
0,00
7,27
4,36
2,86
5,09
0,58
2,96
DM
0,48
0,00
4,36
4,02
1,79
3,39
2,18
0,78
RTV
2,28
0,05
9,01
8,19
1,79
3,05
3,34
2,71
csg
3,25
0,10
20,01
35,71
0,78
5,62
4,89
5,96
csl
11,09
0,10
19,04
20,83
0,68
9,64
1,41
7,66
∆k
9,06
0,68
13,86
18,75
4,46
4,89
11,39
6,10
JApt
3,68
0,00
19,23
35,03
0,73
5,18
4,41
7,12
texec
1,60
3,59
4,22
0,00
18,27
0,15
0,10
4,51
Table 3.
Percentage of best results by evaluation parameters for all threshold functions.
Parameter
Threshold function
NNG
SS
Stein
Z1
Z2
Z3
Z4
Z5
AME
0,97
1,02
6,35
1,31
4,36
4,12
7,03
3,05
MSE
2,28
1,11
6,83
1,11
5,14
3,05
2,37
3,29
RMSE
1,70
1,11
7,41
1,11
5,14
2,96
2,37
3,39
CC
1,70
0,39
5,14
1,60
1,55
2,03
0,00
4,46
NCC
1,31
0,39
5,28
1,55
1,07
1,89
0,00
4,75
EnD
2,03
0,48
5,43
2,86
3,59
4,12
1,55
5,57
SNR
1,31
0,78
5,33
0,87
0,05
0,97
0,00
17,34
DSNR
1,21
0,78
5,43
0,87
0,05
0,97
0,00
17,34
NLR
0,00
0,00
0,00
26,26
0,00
0,00
0,00
73,74
MEmax
1,70
0,15
5,81
9,06
1,36
4,36
0,24
13,28
MEmin
1,11
0,05
11,05
5,18
2,71
5,28
0,15
6,40
PTVmax
0,00
1,16
1,79
6,15
5,33
20,16
2,52
41,38
PTVmin
0,00
1,16
1,26
6,06
4,99
18,90
1,31
42,05
DM
0,00
1,79
0,68
7,36
2,42
12,74
37,26
20,74
RTV
0,00
2,66
3,34
4,65
4,65
14,24
18,94
21,08
csg
4,02
2,57
7,95
0,24
1,07
3,59
0,00
4,26
csl
1,55
1,02
8,62
4,55
1,41
4,89
0,78
6,73
∆k
3,49
3,44
6,59
2,81
2,96
6,06
0,29
5,18
JApt
4,41
2,33
8,19
0,44
0,87
4,36
0,00
4,02
texec
0,24
2,37
9,93
18,02
0,00
3,05
0,58
33,38
Table 4.
Percentage of best results by evaluation parameters for all threshold functions.
Also was evaluated the average results of the evaluation parameters, according to the Tables 5 and 6. Note that the fitness JApt = 3,20 of the Fleming function (using c = 10) is the highest among all the others, being followed by the Garrote and the Hard functions. Thus, the proposed alternatives achieve the objective of overcoming other methods, also providing a better qualitative result in the treatment of PD pulses.
Parameter
Threshold function
Hard
Soft
Fleming
Fleming 2
Adapt shrink
Garrote
Hui
Liu
AME
0,021
0,020
0,021
0,021
0,021
0,023
0,023
0,019
MSE
0,020
0,017
0,020
0,020
0,017
0,021
0,025
0,016
RMSE
0,029
0,031
0,029
0,029
0,030
0,030
0,038
0,028
CC
0,770
0,736
0,790
0,787
0,761
0,773
0,713
0,775
NCC
0,769
0,733
0,789
0,786
0,759
0,773
0,706
0,773
EnD
0,302
0,525
0,267
0,283
0,472
0,364
0,571
0,294
SNR
6,47
1,22
6,82
6,83
2,57
6,51
0,00
5,40
DSNR
3,05
−2,20
3,40
3,41
−0,85
3,09
−3,42
1,98
NLR
−37,33
−36,57
−37,55
−37,52
−36,86
−38,26
−36,40
−37,16
MEmax
14,13
39,75
12,97
14,77
35,08
13,78
43,78
20,53
MEmin
16,11
35,57
13,20
16,24
30,09
14,03
40,20
17,37
PTVmax
15,71
11,44
11,66
16,28
13,97
13,29
12,45
9,08
PTVmin
23,06
20,14
19,93
23,93
23,45
22,07
23,58
16,49
DM
4536,233
4536,207
4536,231
4536,188
4536,217
4536,216
4536,227
4536,236
RTV
11,31
9,87
12,64
11,64
13,94
15,11
10,78
9,53
csg
3,81
−5,27
5,99
4,31
3,88
3,19
3,86
2,69
csl
2,92
3,59
2,87
2,97
24,71
22,80
31,21
25,11
∆k
23,67
30,79
20,46
23,78
−4,51
1,08
−10,83
−0,55
JApt
0,88
−8,86
3,12
1,33
0,456
0,456
0,458
0,456
texec
0,459
0,455
0,48
0,461
−0,63
4,27
−6,97
2,15
Table 5.
Average results by evaluation parameters for all threshold functions.
Parameter
Threshold function
NNG
SS
Stein
Z1
Z2
Z3
Z4
Z5
AME
0,019
0,020
0,019
0,022
0,020
0,011
0,036
0,072
MSE
0,016
0,017
0,016
0,017
0,016
0,002
0,172
0,247
RMSE
0,028
0,031
0,028
0,032
0,029
0,017
0,058
0,092
CC
0,762
0,736
0,762
0,624
0,767
0,753
0,122
0,575
NCC
0,759
0,733
0,759
0,623
0,764
0,751
0,117
0,575
EnD
0,357
0,525
0,357
3269
0,477
0,359
0,978
10,527
SNR
4,18
1,23
4,18
2,84
2,52
−78,15
−16,80
4,09
DSNR
0,76
−2,19
0,76
−0,58
−0,90
−81,57
−20,22
0,67
NLR
−36,97
−36,57
−36,97
−43,48
−36,80
45,31
−34,20
−47,92
MEmax
26,41
39,72
26,41
27,26
35,11
98,39
89,02
39,01
MEmin
22,50
35,53
22,50
30,88
30,66
95,69
87,53
61,48
PTVmax
9,92
11,44
9,92
18,99
11,24
10,64
132,89
20,63
PTVmin
17,34
19,80
17,34
23,76
18,87
18,12
174,24
28,26
DM
4536,237
4536,233
4536,237
4536,195
4536,231
4536,246
4536,136
4536,172
RTV
9,57
9,87
9,57
15,23
11,57
9,07
14,38
20,10
csg
−0,58
−5,26
−0,58
−6,30
−1,44
−84,39
−35,96
−8,89
csl
2,90
3,58
2,90
4,26
3,49
5,86
12,31
5,33
∆k
27,85
30,79
27,85
31,62
26,35
30,61
43,79
36,17
JApt
−3,48
−8,84
−3,48
−10,56
−4,93
−90,25
−48,27
−14,22
texec
0,457
0,455
0,455
0,457
0,464
0,456
0,456
0,456
Table 6.
Average results by evaluation parameters for all threshold functions.
Figure 11 exemplifies the wavelet shrinkage process using each of the thresholding functions discussed above for a PD signal measured from a hydro generator. In this case, note that the functions we have created are superior in preserving the amplitudes of the signals and eliminating the present noise, especially the filtering using the Fleming 2 function, which obtained the highest level of JApt compared to the other functions, followed by Fleming, Garrote and Hard functions. The Soft and the other thresholding alternatives end up causing deformations of the pulses waveforms and greater attenuation of these peak amplitudes. The Zhang 1 and Zhang 5 functions allow most of the noise to pass through the denoising process and the Zhang 4 function ends up eliminating the PD signal that we are interested in obtaining.
Figure 11.
Comparison of the better denoising results obtained between the all evaluated threshold functions to a measured PD signal from a hydro generator.
5. Conclusions
Was presented a new threshold function called Fleming, which combines the quality of a strongly differentiable function and a more flexible alternative, enabling its optimization to provide better results in the PD signals treatment, in order to preserve its important characteristics for the diagnosis of the HV equipment subjected to the partial discharge analysis. The proposal inspired by the well-known logistic function [29], which depends on a parameter that controls the inclination of the curve in the threshold value (calculated a priori). Also was created a variant of this same function, using a simple idea, but little investigated in the literature: identifying the decomposed coefficients with the greatest contribution in the desired signal recovering [3].
With the results described in Section 5, in which hundreds of signals (measured and simulated) were evaluated, the ability of the Fleming function and its Fleming 2 variant to overcome the most common functions such as Hard and Soft, as well as twelve other alternatives presented in some publications [15, 19, 22, 35, 36, 37, 38]. The Fleming function can be applied with different inclination values, but for PD signals, the ideal is that these values are limited between 5 and 10 to provide the best results.
The Fleming 2 alternative showed the highest percentage of the best results and the Fleming alternative showed the highest average value in terms of amplitude. Thus, if the goal is to achieve a higher number of better results, the indicated is to threshold the wavelet coefficients using the Fleming 2 function, but if the idea is to achieve better average results, consider using the Fleming function. As for the average processing time, these functions are relatively fast when compared to the other evaluated functions, not falling far behind the classic ones Hard and Soft.
The application of the developed thresholding functions is extensible to other types of signals, such as acoustic emissions, electrocardiogram signals, image processing, among others. However, in each case it would be necessary to investigate the appropriate values of the inclination parameter c.
\n',keywords:"wavelet transform, threshold function, partial discharge, signal denoising",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/73875.pdf",chapterXML:"https://mts.intechopen.com/source/xml/73875.xml",downloadPdfUrl:"/chapter/pdf-download/73875",previewPdfUrl:"/chapter/pdf-preview/73875",totalDownloads:376,totalViews:0,totalCrossrefCites:0,totalDimensionsCites:1,totalAltmetricsMentions:0,impactScore:0,impactScorePercentile:48,impactScoreQuartile:2,hasAltmetrics:0,dateSubmitted:"June 16th 2020",dateReviewed:"September 18th 2020",datePrePublished:"November 2nd 2020",datePublished:"February 24th 2021",dateFinished:"November 2nd 2020",readingETA:"0",abstract:"Based on the wavelet transform filtering theory, the chapter will describe the elaboration of a wavelet threshold function intended for the denoising of the partial discharge phenomenon measurements. This new function, conveniently named Fleming threshold, is based on the logistic function, which is well known for its utility in several important areas. In the development is shown some variations in the application of the Fleming function, in an attempt to identify the decomposition levels where the thresholding process must be more stringent and those where it can be more lenient, which increases its effectiveness in the removal of noisy coefficients. The proposed function and its variants demonstrate excellent results compared to other wavelet thresholding methods already described in the literature, including the famous Hard and Soft functions.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/73875",risUrl:"/chapter/ris/73875",book:{id:"10065",slug:"wavelet-theory"},signatures:"Caio F.F.C. Cunha, Mariane R. Petraglia, André T. Carvalho and Antonio C.S. Lima",authors:[{id:"1553",title:"Prof.",name:"Mariane",middleName:null,surname:"Petraglia",fullName:"Mariane Petraglia",slug:"mariane-petraglia",email:"mariane@pads.ufrj.br",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:{name:"Federal University of Rio de Janeiro",institutionURL:null,country:{name:"Brazil"}}},{id:"272211",title:"Dr.",name:"Caio Fleming",middleName:"Ferreira De Carvalho",surname:"Cunha",fullName:"Caio Fleming Cunha",slug:"caio-fleming-cunha",email:"caioflemin@gmail.com",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null},{id:"324697",title:"Dr.",name:"André",middleName:null,surname:"Carvalho",fullName:"André Carvalho",slug:"andre-carvalho",email:"tomaz@cepel.br",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null},{id:"324699",title:"Prof.",name:"Antonio Carlos",middleName:"Siqueira",surname:"S. Lima",fullName:"Antonio Carlos S. Lima",slug:"antonio-carlos-s.-lima",email:"acsl@dee.ufrj.br",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null}],sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Wavelet domain detection",level:"1"},{id:"sec_3",title:"3. Fleming threshold function",level:"1"},{id:"sec_3_2",title:"3.1 Relevant wavelet coefficient identification",level:"2"},{id:"sec_5",title:"4. Fleming threshold function",level:"1"},{id:"sec_5_2",title:"4.1 Investigating the better inclination value c",level:"2"},{id:"sec_6_2",title:"4.2 Comparison between Fleming, Hard and Soft threshold functions",level:"2"},{id:"sec_7_2",title:"4.3 Comparison between all threshold functions",level:"2"},{id:"sec_9",title:"5. Conclusions",level:"1"}],chapterReferences:[{id:"B1",body:'Carvalho A T, Lima A C, Cunha C F, Mariane R P. 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COPPE/UFRJ, Federal University of Rio de Janeiro, Brazil
CEPEL/ELETROBRAS, Electrical Energy Research Center, Brazil
'},{corresp:null,contributorFullName:"Mariane R. Petraglia",address:null,affiliation:'
COPPE/UFRJ, Federal University of Rio de Janeiro, Brazil
'},{corresp:null,contributorFullName:"André T. Carvalho",address:null,affiliation:'
CEPEL/ELETROBRAS, Electrical Energy Research Center, Brazil
COPPE/UFRJ, Federal University of Rio de Janeiro, Brazil
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1. Introduction
The well know endophytic plant growth promoting bacterium Xanthobacter autotrophicus, was described as Corynebacterium autotrophicus due its specific genetic qualities to grow under chemolithoautotrophically and for being able to fix molecular nitrogen (N2) as nitrogen source [1]: X. autotrophicus are rods, according to growth condition show pleomorphism depends on the species and the carbon and nitrogen source on which they are grown. X. autotrophicus is a Gram-type negative rods with high concentrations of polyphosphate granule belongs phylogenetically to the family Hyphomicrobiaceae in the class Alphaproteobacterial, grow heterotrophically under aerobic or microaerophilic conditions with acids, alcohols, and selectively with some carbohydrates as energy and carbon source like: fructose, galactose, mannose and sucrose [2, 3, 4, 5, 6, 7].
The endophyte plant growth promoting bacteria: X. autotrophicus can fix dinitrogen under heterotrophic and thioautotrophic conditions is able to grow with H2 plus O2 or H2 + Na2S2O3 as energy source and with CO2 as only inorganic carbon source [8, 9, 10] at reduced O2 tension [11, 12] in the absence of organic or inorganic nitrogen (N) compounds as aminoamides, peptides, proteins, nucleotides, well known sources as NH4+ (ammonia) or NO3− (nitrate) at the soil [13] and culture artificial media [14]. On the basis of their numbers, X. autotrophicus should be regarded as an associative symbiosis diazotroph due although entering roots of wheat (Triticum aestivum), bean (Phaseolus vulgaris), root beet (Beta vulgaris), rice (Oriza sativa) [15] tomato (Solanum lycopersicum), lettuce (Lactuca sativa) [16, 17] does not form nodules the way do symbiotic N2-fixing bacteria in legume as Bradyrhizobium japonicum does. The special position of X. autotrophicus among the chemolithoautotrophic and other the N2-fixing aerobic bacteria [1, 11], X. autotrophicus is able to grow with H2/CO2/O2 or to have high hydrogenase activity [10, 18], beside reaction of nitrogenase as the other well-known genera: Azotobacter, Derxia, Bradyrhizobium and Rhizobium [19, 20]. Originally, one key taxonomic property for discriminating X. autotrophicus from other genera yellow pigmented zeaxanthin dirhamnoside bacteria, including diazotrophs [2]. Xanthobacter strains can be isolated easily if certain conditions are applied: no other or very limiting sources of nitrogen other than N2 or H2/CO2/O2/N2 [9, 11] as gas phase providing an electron donor, a carbon source, electron acceptors, in liquid media; yellow colonies are showed on nutrient agar plates [1, 6]. Because its metabolic diversity Xanthobacter species are widespread in natural habitats [21] as is showed in Table 1.
Biochemical characteristics
1.
2.
3.
Cell morphology: rods
−
−
−
Morphology as rod on free carbon and nitrogen media
+
+
+
Slime production
+
+
+
Zeaxanthine dirhamnoside (yellow)
+
+
+
Zeaxanthine (orange, pinkish)
−
−
−
Motility under autotrophic growth conditions
−d
−d
−d
Vitamins required for growth
+
+
+
Sensitivity to chloramphenicol
−
−
−
Under autotrophic growth at 35°C
+
+
+
Utilization of hexoses
+
+
+
Growth on nutrient broth
+
+
+
Growth on glutamine as carbon source
+
+
+
Growth on citrate
+
+
+
Degradation of aromatic compounds
+
+
+
Degradation of cyclohexene (and derivatives)
+
+
+
Utilization of methanol
+
+
+
Utilization of hydrocarbons
+
+
+
Table 1.
Main biochemical characteristics among some species of the genus Xanthobacter.a
1 = X. autotrophicus in the reference; 2 = X. autotrophicus; 3 = X. autotrophicus repetitions.
Symbols and abbreviations: +, positive; (+), positive except for some unusual strains; −, negative; (−), negative except for some unusual strains; +/− not determined; TCA = tricarboxylic acid.
2. Phylogeny and taxonomy of Xanthobacter spp
The phylogenetic position of Xanthobacter based on 16S rRNA sequence analysis published in Bergey’s Manual of Systematic Bacteriology, showed that genus Xanthobacter is part of phylum Proteobacteria, class Alpha proteobacteria order Rhizobiales family Xanthobacteraceae. However, using phylogenetic trees constructed on the basis of 16S rRNA sequence comparisons, the type strains of Aquabacter spiritensis and Azorhizobium caulinodans are intermingled with the otherwise well-defined genus cluster Xanthobacter, Aquabacter and Azorhizobium (both single species genera are recognized as separate genera V and VI within the same family Hyphomicrobiaceae, some of the key properties described for the type species X. autotrophicus it is suggested to keep the separate genera names despite the 16S rRNA sequence similarity [22]. The 16S rRNA sequence is more than 98% similar to those of X. flavus and X. autotrophicus strains as is showed in Figure 1 [2, 6, 8, 23, 27]. The morphology and some of the physiological proprieties are different to separate species, supported by the low below 50% DNA-DNA hybridization data as well as tricarboxylic acid or TCA cycle intermediate; (1) synthesis of the water insoluble zeaxanthin dirhamnoside, showed by the yellow colonies; (2) normally to grow chemolithoautotrophically; and (3) able to fix dinitrogen under microaerophilic chemolithoautotrophic or heterotrophic conditions [1, 28]. Other characteristics are given in Table 1, Xanthobacter is free-living in soil and water as well as root-associated but never noduling, exhibits acetylene reduction as an indirect technique for nitrogen fixing capacity. Other features of Xanthobacter a are the h i g h G+C related with some flavobacteria and Cytophaga spp: (1) antibiotic pattern sensitivity [17] (2) positive reaction for catalase, oxidase and phosphatase acid and alkaline types; (3) negative reaction for methyl red, gas from carbohydrates, and the Voges-Proskauer test; and (4) containing ubiquinones Q10 and Q8 like is in Beijerinckia, and Azotobacter, are important for truly identification of these species, demonstration of the pigment zeaxanthin dirhamnoside and acquisition of the 16S rDNA sequence are important [2, 6, 21].
Figure 1.
Photographs of X. autotrophicus (a) macroscopic morphology in a mineral medium without sucrose either ammonium nitrate (MMWSA) under autotrophic conditions after 30 h incubation at 35°C, (b) and (c) microscopic morphology of X. autotrophicus according at Gram negative in MMWSA under the same incubation condition (photos from Environmental Laboratory-UMSNH, Sánchez-Yañez et al., 2020).
3. Taxonomy
The most identifications of environmental isolates are done by 16S rRNA sequence analysis, in a first common identification step, diagnostic taxonomic properties are: (1) yellow, “fried egg” shaped colonies with several amounts of slime production under cultivation media specific conditions; (2) rods, some species have strong polymorphic, branched, twisted cell morphology growing on nutrient agar with larger amounts of polyphosphate granula, can lead to the false impression of a Gram-positive staining reaction; however all Xanthobacter stain are truly Gram negative when is using a counterstain in polyphosphate-free cells of X. autotrophicus [2, 22, 24].
4. Isolation cultivation and axenic culture
Selective enrichment cultures. For isolation purposes, the use of free carbon and nitrogen agar medium as a selective medium is recommended for recovering Xanthobacter from; soil, upper layers of marine or freshwater sediments, lake water, steam and root of aal types of plants. Because of slime formation by X. autotrophicus of agar plates free carbon and nitrogen source. Frequently, other oligotrophic organisms grow as contaminants in the slimy colonies of Xanthobacter easy to separate in nutrient agar the following basal medium can be used for autotrophic as well as heterotrophic growth except when urea is used as nitrogen source. No vitamins or additions of yeast extract as growth factor are required for most X. autotrophicus, enrichment 100 mg of yeast extract per liter to the mineral medium can reduce an extended lag time for autotrophic growth under free carbon and nitrogen-fixing. In order to demostrate its capacity for fixing N2 is important not to add any inorganic or organic nitrogen source. During isolation, a vitamin solution any mixture containing biotin can enrichment to stimulate is growth, absence of ammonium, or amino acids, peptide, protein as any organic nitrogen source [29, 30]. For heterotrophic growth, common carbon sources are used: 0.5% sugars, 0.3% (v/v) alcohols or 0.4–0.8% organic acids. For growth under non-N2-fixing conditions, 0.1% of ammonium chloride or sulfate is common. The exact composition of this medium is not critical, and good results have been obtained with free sucrose and nitrogen agar medium, for storge sterile soil is one the easy and best one to preserve viability for relative long period of time. X. autotrophicus, studied in more detail, most of the strains tested grow at pH 5.0–8.5 while pH recommend is about 6.8–7.2 and its temperature 30–37°C. The morphological features of Xanthobacter can be used initially for identification. Colony morphology depends on the type of carbon and nitrogen source and growth conditions. On most carbohydrates, the colonies of main species are large from 1 to 5 mm in diameter, smooth, convex, circular, filiform, opaque, and typically egg-yolk yellow color due to zeaxanthin dirhamnoside (see Figure 2a). The colonies become less yellow and less opaque as the amount of slime increases. The production of slime on nutrient agar plates frequently results in colonies resembling fried eggs [15]. Zeaxanthin dirhamnoside is water-insoluble, in contrast to the reddish/pinkish/brown pigment or to the yellow-green diffusing pigments with fluorescence of Beijerinckia and Derxia the other yellowish diazotroph isolated with well-known methods. The latter fact also makes it easy to distinguish Xanthobacter from Derxia colonies, which turn brown with age besides other morphological and biochemistry characteristics [5, 31]. Xanthobacter strains are sensitive to wide range of antibiotics, but the response depends on the method applied broth cultures or the use of Difco (Dispense-O-Disk minifilters). X. autotrophicus was sensitive to ampicillin, penicillin, chloramphenicol, erythromycin, novobiocin, and polymyxin B, but they were resistant to erythromycin and bacitracin. Few strains can grow on violet red-bile medium (Oxoid), deoxycholate medium (Oxoid), tellurate agar (Difco), and mineral medium supplemented with crystal violet red colonies [6, 32, 33].
Figure 2.
Phylogeny and taxonomy of Xanthobacter spp.
4.1 Methods of storage
Xanthobacter cultures are grown on chemolithoautotrophic agar slants stored 1.5 years at 4°C after sealing the tubes tightly with parafilm. Also, liquid cultures grown under chemolithoautotrophic conditions mineral medium with 0.02% (w/v) yeast extract have been kept for more than 15 months at 4°C and, of course if glycerol is used as suspended solution at 40–60% (v/v) final, at –20°C and –75°C for more than 8 years. For long-term storage, cultures should be lyophilized on skim milk at 10% now sterile soil is an easy and safe technique [34, 35].
5. Autotrophy and nitrogen fixation capability
X. autotrophicus can use H2 from thiosulfate as source of energy for CO2 fixation, when grown heterotrophically in the presence of gas mixture, Xanthobacter species fix CO2 mainly via the ribulose-biphosphate pathway but phosphoenolpyruvate carboxylase activity also has been reported. Have shown that the fixation of CO2 plays an important role in the degradation of aliphatic epoxides and ketones by novel carboxylases [5, 8, 10, 24]. X. autotrophicus fixes N2 under heterotrophic growth conditions with sucrose as a carbon source; however, N2 fixation was showed for several strains of X. autotrophicus with 15N2 incorporation into cell protein [12, 18]. The biochemical studies on the enzyme and its relationship to oxygen have been restricted to X. autotrophicus. The nitrogenase in these two strains is similar to that in other aerobic diazotrophs [2, 6, 36, 37]. There is strong variation among the strains in respect to the optimal O2 concentration for growth under N2-fixing conditions, for X. autotrophicus. The optimal partial pressures of O2 for acetylene reduction are 5 and 2.5 kPa to 0.36 kPa. However, the alternative vanadium nitrogenase system could not yet be shown through substantial ethane synthesis or improving its growth when vanadium is added to molybdenum deprived medium [1, 14, 38].
6. Natural habitats
The known habitats of Xanthobacter are depending on its physiological properties, underline its catabolic versatility [39]. The sources for isolated strains include oil-contaminated soil and sludge from Japan [5], marine sediments, water and sediment samples from fresh- water lakes, soil of flooded rice fields, rhizosphere of wetland street ditches and wet meadow soil and garden soil from Europe, South Africa, North America, and Asia, sewage samples [3, 13, 40] and tree leaves [20, 41]. Xanthobacter is ubiquitous in microaerophilic environments with decaying organic material or matter [19] containing sufficient concentrations of H2 and CO2 and other metabolic compounds products of anaerobic microbial activity, such as organic acids and alcohols. Xanthobacter species are important in the microaerophilic interface between the anaerobic and aerobic habitats. Therefore, it is very likely that Xanthobacter, and possibly also other N2-fixing Knallgas bacteria, can be found in habitats other not yet known [42, 43]. According to literature, no thermophilic, psychrophilic, or halophilic strains have been isolated [44]. Furthermore, it is not clear whether Xanthobacter contributes significantly as an associative bacterium to the nitrogen cycle in agriculture issues, even though in greenhouse experiments [17, 45, 46], X. autotrophicus strains isolated from several environmental samples have been shown to stimulate and growth yields of rice, tomato and lettuce at reduced dose of nitrogen or phosphate fertilizer [1, 17, 38, 47].
6.1 Ecological interactions with other domestic plants
In Japan was reported a survey of N2-fixing bacteria from roots of rice, with strains called group 2 were X. autotrophicus and other isolated Xanthobacter-like of group 5, which could be a new genus [22, 31, 48, 49]. Some of these isolations were identified as a X. flavus on the basis of morphological and physiological properties. Up to 25% of the nitrogen fixed by soil bacteria was incorporated into rice plants and other reported. In one soil like soils of Kasakh, Armenia Xanthobacter was up 40–70% were N2-fixing population they may contribute to N balance in the soil of paddy rice. Also was demonstrated that strains close to X. autotrophicus could be found in the sediment of patty rice fields in Arkansas, United States, with more than 105 cells per g dry weight of roots in the rhizosphere of rice clearly as an endophyte [50]. A positive interaction among Xanthobacter and some domestic crops due to enhance biomass of plant as well as nitrogen content compared to those crops without Xanthobacter at limited dose of nitrogen fertilizer [17, 40]. Therefore, Xanthobacter can be classified as an associative diazotroph [19, 38, 44, 51, 52]. The possible role of Xanthobacter as a contributor of fixed N2, a growth factor stimulant on bean [45] lettuce, tomato, rice, rootbeet, wheat, plants, and an associative N2 fixer through either the phyllosphere or even stems nodules if in the future Azorhizobium is incorporated into the genus Xanthobacter needs to be investigate [20, 41, 53]. These studies should examine: (1) the role of the slime produced by Xanthobacter in its adherence to the rhizosphere and phyllosphere an involvement of slime in adherence processes was shown for various anaerobic bacteria; (2) the possible role of the polyglutamine polymer produced under high-nitrogen conditions directly after nitrogen fertilization [7, 38, 54] and (3) the role of plant growth stimulant formation by root and stem-associated Xanthobacter cells [13, 28, 55, 56, 57]. It has been reported than cultures of X. autotrophicus are producing indoleacetic acid when grown in medium with tryptophan [3]. Until now there are no reports about Xanthobacter isolated associated with any plant disease [18].
6.2 Biofertilizer application of endophytic plant growth promoting bacteria in modern sustainable agriculture
Biofertilizer is key action of organic farming and a main element for the economy in general modern agricultural production on a world scale [55, 56, 58, 59]. The biofertilizers play an important role in improving the fertility of the soil [60, 61]. In addition, their application in soil improves the structure of the soil minimizes the sole application of chemical fertilizer. Grain yield and harvest index also increase with use of biofertilizers. Inoculation with Azotobacter + Rhizobium + mycorrhizae gave the highest increase in straw and grain yield of wheat plants with rock phosphate as a P fertilizer. Azolla is inexpensive, economical, friendly, which provide benefit in terms of carbon and nitrogen enrichment of soil [62]. Some commercially available biofertilizers are also used for the crop. Raj [63] recorded that microorganism: B. subtilis, Thiobacillus thioxidans, and Saccharomyces) can be used as bio-fertilizers for solubilization of fixed micronutrients like Zn (zinc). As well for biological control, a modern approach of disease management a key role in sustainable agriculture [64, 65, 66]. Biofertilizers can be defined as carriers that contain living endophytic plant growth promoting bacteria (EPGPB) and/or microorganisms (EPGPM); when they are applied to seeds, plant surfaces, to soil, or to hydroponic agricultural system, they colonize the root system or interior of the plant, and to stimulate plant growth by increasing the demanding or availability of macro or micro minerals: nitrogen (N), phosphorus (P), potassium (K), cupper (Cu), iron (Fe), etc., to the host plant [67, 68]. According to Mishra et al. [69], biofertilizer could be mixture of active or latent microbial cell for several important mechanisms to improve plant growth and yield as the well-known: nitrogen fixing, phosphate solubilizing, or cellulolytic microorganisms for applications to soil, seed, roots, or composting involving any microbial process with the aims for enhancing plant growth, augment the availability of nutrients that can then be easily absorbed by the plants, as well as for biological control of plant pathogenic agents. Malusá and Vassilev [70] proposed that a biofertilizer is the formulated product containing one or more microorganisms that enhance the mineral availability for health growth and yield profitable performance of the plants by either replacing soil nutrients and/or by making nutrients more available to plants and/or by increasing plant availability to basic minerals [66, 71].
Biofertilizer products are usually based on the EPGPB or PGPM can be classified into three main types of microorganisms: arbuscular mycorrhizal fungi or AMF [72], plant growth promoting rhizobacteria or PGPR [73], and nitrogen fixing rhizobia and free nitrogen fixing bacteria for non-leguminous plant [74, 75] which are applied and approved as beneficial for domestic crops growth based in mineral nutritional, underline reported that PGPR are recommend worldwide as biofertilizers, contributing to maintain profitable yield without soil deterioration and preventing environmental pollution. Hence, with the potential contribution of the PGPR, to sustainable agriculture and forestry when pandemic condition of COVID 19 caused economic world depress [76, 77]. Sufficient densities of PGPR and/or EPGPB like X. autotrophicus in biofertilizer provide a beneficial role in creating a proper rhizosphere for plant growth and converting nutritionally important elements through biological process, for example increasing the availability of N, P, K, as well as inhibiting pathogens growth [67, 71].
The increasing availability of N, P, and K is enhancing soil fertility, to improve antagonistic capacity of PGPR or EPGPB to biocontrol of plant pathogens agents [58] as well as the survival time in all types of soil [78]. Previous studies show that a biofertilizer prepared by mixing all types of PGPR with composts or carriers could enhance growth- promoting effects and biocontrol of plants [79]. Bacillus spp [80] and Pseudomonas spp [81] are two PGPR that have been reported to effective biocontrol agents. Among these bacteria species, Bacillus subtilis, B. amyloliquefacients, and B. cereus are the most effective species for controlling plant diseases in domestic crops by several mechanisms [82]. Due endospores of the genus and species of Bacillus are tolerant to adverse environmental conditions allows PGPR, to survive and even to grow in a wide range of soils, thus facilitating the effective formulation of biofertilizer [83]. Based in this biochemicals qualities as well as the biorestauration of hyper fertilized or deteriorated soil [43, 74, 84, 85]. However, X. autotrophicus has many biological mechanisms to avoid environmental stress without any specific resistance structure a quality of this genus and specie [3, 21, 35] that has been useful to treat environments contaminated by chemical agents [86].
6.2.1 Biofertilizer (X. autotrophicus) for bioremediation of environment polluted by chemical agents
In that sense EPGPB (likes PGPM or/and PGPR can be classified as biofertilizers when they sustainable options to plant nourishment and enrichment source that would useful for bioremediation and/or phytoremediation (double actions plants and biofertilizer) for soil contaminated by chemical agents [87, 88]. There for X. autotrophicus is has been applied in bioaugmentation trials for cleaning up any environmental impacted by chemical agents [86] which due to powerful genetic capacity is able to degradate a wide range of chemical agents under several environmental conditions either soil and or water in that sense it been reported that X. autotrophicus is able to biodegradate of 1,2- dichloroethane (DCE) one of the largest chlorinated industrial chemical, most of it being used for synthesis of vinyl chloride and smaller amounts for ethylene diamine and other chemicals. It was also used as a solvent. Groundwater contamination is mainly due to leakages and improper waste disposal. X. autotrophicus can attack DCE by using some specific enzimes under oxic conditions was investigated in the 1980s [89, 90] required for prolonged groundwater bioremediation polluted by DCE. Such systems are operated under non-sterile conditions, and long-term survival of enzymes would require separate enzyme production and a process allowing for physical separation of the biocatalyst from groundwater. There may be attractive application opportunities if biotransformation of synthetic chemicals in waste streams leads to products that can be recycled, e.g., when a wastewater product can cleaning up. This issue that received attention during the development of strains of X. autotrophicus growing on 1,2,3-trichloropropane (TCP) and another xenobiotic compound that polluted wastewater [86, 90, 91, 92].
A bioformulation is not effective until it does not have an impact in field conditions, market existence and reliability and cost effectiveness [93]. Production of bioformulation is not only dependent on the detailed knowledge of microbial as well as plant physiology, but a number of technological challenges are also involved such as fermentation process, formulation type, population of microbe, and delivery systems [94]. Barea [59] has published that in order to get better bioformulation for any domestic crops is important to understand the interaction among EPGPB or PGPM. To reproduce those microorganisms is important the chemical composition of broth media as well as the main and best conditions for each microorganisms need to get enough amount of them for bioformulation applying in open agriculture [95]. Including legal and ecological permission for safe crops production. A key quality of any bioformulation has to be water soluble to make sure a positive effect on any domestic crop Himel et al. [96] and Bateman [97] underline for those bioformulation which are applying in in aerosol based on a droplet size that is sufficient to inoculate seeds and plants with excellent results. For bioformulations applied foliarly, it is important to consider all environmental factors: solar radiation, high temperatures, ultraviolet light, etc. that limit the survival of beneficial plant microorganisms [98]. In this sense, the type of bioformulations must be appropriate to the form and vehicle that transport the beneficial plant microorganisms according to the recommended application directly to the soil, to the seeds or plants so that the forecast of the result favors agricultural production or control of some disease or pest [99]. Therefore, it is important research for the innovation of bioformulation suitable for agricultural crops [58] that comply with the quality and legality standards to satisfy the world market demand for safe food without risk of environmental damage [100]. A fundamental aspect for the world market of biological inoculants has been the necessary implementation of microbiological quality controls with reliable protocols that are endorsed by laws in the world that protect those farmers who, when applying them, have the confidence that they will have positive results in production. agriculture, due in part to the unfortunate experience of bioformulations without microbiological or legal quality that have caused a rejection of some sectors involved in sustainable agricultural production, an aspect that has not yet been resolved in the world [68]. In an integral sense that the biotechnology of the formulation of inoculants requires solid research for the best selection of microorganisms that promote plant growth, as well as the protocols of legal and ethical microbiological quality in the generation of bioformulations that give confidence to be used in the world for a sustainable and harmless agricultural production in harmony with the environment [85].
7. Effect of Xanthobacter autotrophicus on the growth of Triticum aestivum and other domestic plants
Triticum aestivum is the main cereal consumed by the human population of the world, around 51% of human demand intake of calories and proteins. The annual production of this crop is ~630 million tons, being the major grown cereal worldwide with ~740 million ha harvested annually [101]. It is reported that the dynamics of colonization of endophytic genus plant growth promoting bacteria (EPGPB) like X. autotrophicus on the sphermosphere/rhizosphere in gramineae is reported, based in other genera and species different than Xanthobacter [49, 102, 103]. In that sense the response of domestic plants to X. autotrophicus is scarce [18] so research in progress indicates [16, 17, 45, 46] that it may be an excellent option for the sustainable production of domestic crops [67, 104, 105, 106] however it is believed that it may be similar to other genera and species of EPGB, of the known like Azospirillum, Azotobacter, Bacillus which are able to move from outside to into the root system [18, 107]. In the case of T. aestivum has a positive response to X. autotrophicus since can invade the interior of the root system where it transforms organic compounds derived from photosynthesis into phytohormons, to optimize the reduced dose of nitrogen fertilizer [46]. It has been showed that can invade the root of T. aestivum including other types of domestic crops [17, 45, 60]. This biochemical characteristic of X. autotrophicus was confirmed by its growth dependent on the nutritional richness of the rhizosphere of T. aestivum, attributable to certain organic acids, amino acids including other organic compounds from the photosynthesis in gramineae [42, 108]. Hence, the importance of the chemical composition of root, sphermosphere and rhizosphere, as inducers of colonization by X. autotrophycus in gramineae, is key for other EPGPB to be closely associated with its root, sphermosphere, rhizosphere system [60, 105, 109]; in part this also explains the nutritional requirement of X. autotrophicus for wheat as a distinctive characteristic of this species, which is not reported in X. autotrophicus this was verified when was inoculated in the soil without roots, this coupled with the competition and predation of the native soil microorganisms, antagonistic to the species of Xanthobacter, which prevented its persistence in that environment [20, 47]. In the literature it is reported that the positive response of T. aestivum to inoculation with X. autotrophicus and fed with NH4NO3 depends on fast they colonized exclusively the germination zone of the seed, as well as to invade inside the roots when they have developed [41, 109, 110]. This explains why, in the case of the test described, X. autotrophicus was detected during seed germination, in the period of root development, and even inside mature roots of wheat. This suggests that X. autotrophicus was not dependent on wheat’s sphermosphere/rhizosphere [17, 108, 109], it is reported that slowly used its energy reserve to prolong its persistence in unsterilized soil, a physiological characteristic in X. autotrophicus [111, 112]. These results support that T. aestivum were attractive for X. autotrophicus used according to the type of root growth observed with T. aestivum, compared to the appearance of the root system in the coronary part and by the density of secondary roots detected uninoculated wheat [37, 46, 47, 113, 114].
Related to phosphorus a key mineral for plant nutrition as phosphates normally applied to soil as fertilizer it is reported that concentration in average soils is about 0.05% (w/w) of which only 0.1% is available to plants [115]. There is evidence that the phosphate fertilizer applied as phosphate has a limited impact on plant nutrition, especially because, due to the solubilization constant (Ksp), of this phosphate anion is generally little available for plant roots [116]. It is calculated in the soil the concentration of phosphorus as phosphates is equal to or less than 0.02ppm, which drastically limits plant growth [117, 118]. In nature, the strategy that plants use for the absorption of the forms of phosphates necessary for plant metabolism are the solubilization actions of phosphates by genera and species of microorganisms that promote plant growth, such as mycorrhizae and bacteria that also mineralize organic compounds containing phosphates [119, 120]. In the last few years, the development of microbial inoculum containing phosphate-solubilizing microbes (PSM) gained attention of agriculturists [17].
Figure 3 shows the positive response of T. aestivum to X. autotrophicus fed at 50% of NH4NO3 and 100% phosphate fertilizer. Figure 3c shows that T. aestivum reached a greater number of leaves and a dense root system, as well as T. aestivum with X. autotrophicus fed with 100% nitrogen fertilizer and 50% phosphate fertilizer (Figure 3d) and T. aestivum with X. autotrophicus fed with 50% nitrogen and phosphate fertilizer (Figure 3e), compared to T. aestivum not inoculated irrigated with water (Figure 3a) and T. aestivum not inoculated fed with 100% nitrogen and phosphate fertilizer (Figure 3b). These facts indicates that X. autotrophicus transformed the organic compounds from photosynthesis of T. aestivum into root system to improve root absorption and optimize the reduced dose of nitrogen fertilizer without risk to plant health growth [17, 18, 38, 42, 43, 121, 122]. At the same time the synthesis of acid and mainly alkaline phosphatases improved the solubilization and absorption of soil phosphates and phosphate fertilizer apply [17, 123, 124] to enhance growth plant (data not showed). In Figure 1 it was evident that X. autotrophicus is an excellent option for the sustainable production of T. aestivum since it is not only capable of optimizing nitrogen fertilizer to avoid soil deterioration and environmental contamination due to nitrogen hyperfertilization [36, 54, 121, 125, 126]. While T. aestivum inoculated with X. autotrophicus simultaneously absorbs the immobilized phosphate from the soil and optimizes the effective application from the inside of its roots by avoiding competition with the native microorganisms [13, 40, 53] with a high prognosis of achieving healthy growth and profitable yield [43, 122]. In that sense Khalid et al. [127] reported that seed inoculation with 30 bacterial strains isolated from rhizospheric soils of wheat plants cultivated at different sites significantly increased length and weight of wheat roots and shoots. Linear positive correlation between in vitro auxin production by these bacteria and increases in the measured growth parameters was observed. Abd El-Azeem et al. [128] reported a highly significant positive linear correlation between the in vitro auxin production by the tested PGPR strains and each of grain yield, straw and total yield (grain plus straw) as well as the number of tillers of wheat plants. Auxin or indole acetic acid (IAA) production is considered a way in which X. autotrophicus promotes plant growth by stimulating enzymological reactions [125, 129]. IAA influences plant processes, such as initiation of cell division and promotes vascular differentiation [130, 131]. Besides its hormonal functions, IAA is involved in the stimulation of ethylene synthesis, which is produced, by plants and microorganisms [47]. Ethylene plays several active roles in plants including germination of root and shoot and the response of plants to stress [43]. There is an evidence that X. autotrophicus that solubilize phosphate in soil and promote its uptake by plants are referred as phosphate solubilizing bacteria (PSB) or phosphobacteria and are included within EPGPB [132]. Plant growth promoting rhizobacteria increase the efficiency of fertilizers while reducing nitrogen loss. Their counts in the rhizosphere comprise a considerable share of the rhizospheric microorganisms and vary depending on the soil location and type as well as the cultivated plants [133]. Inoculating the soil or seeds with PSB individually or in combination with other microorganisms, especially the nitrogen-fixing bacteria increased the availability of P, Fe, Mn, Zn and Cu for plants and consequently increased crop yield [114, 134, 135].
Figure 3.
Response of Triticum aestivum to Xanthobacter autotrophicus at different levels of nitrogen and phosphate fertilizer at seedling stage 30 days after sowing. (a) Absolute control: T. aestivum not inoculated irrigated only with water; (b) relative control: T. aestivum not inoculated fed at 100% nitrogen and phosphate fertilizer; (c) T. aestivum with X. autotrophicus fed with 50% of nitrogen fertilizer and 100% phosphate fertilizer; (d) T. aestivum with X. autotrophicus fed with 100% nitrogen fertilizer and 50% phosphate fertilizer; (e) T. aestivum with X. autotrophicus fed with 50% nitrogen and phosphate fertilizer.
Figure 4 shows the positive response of Z. mays to X. autotrophicus fed with 50% nitrogen fertilizer and 100% phosphate fertilizer (Figure 4c), had the highest number of leaves, plant height and the highest root density, as well as Z. mays with X. autotrophicus fed with 100% nitrogen fertilizer and 50% phosphate fertilizer (Figure 4d) and Z. mays with X. autotrophicus fed with 50% nitrogen and phosphate fertilizer (Figure 4e), compared to Z. mays not inoculated irrigated only with water (Figure 4a) and Z. mays not inoculated fed with 100% nitrogen and phosphate fertilizer (Figure 4b). Figure 2 shows the effect of X. autotrophicus on the healthy growth of Z. mays at different doses of nitrogen and phosphorous fertilizer, supporting that X. autotrophicus from the interior of the root system of Z. mays had the ability to convert compounds generated from photosynthesis in phytohormones for the optimization of the fertilizer reduced to 50%, simultaneously with an increase in the acid and alkaline phosphatase activity for the solubilization of the immobile phosphates of the soil and the optimization of the phosphate fertilizer also reduced 50% [17, 44, 45, 47, 106, 131] compared to the limited growth of Z. mays without inoculation with X. autotrophicus where the absence of this endophytic bacterium that promotes plant growth shows that Z. mays that none of these fertilizers is efficiently absorbed, causing loss of soil fertility and a possible environmental contamination [43].
Figure 4.
Response of Zea mays to Xanthobacter autotrophicus at different levels of nitrogen and phosphate fertilizer at seedling stage 15 days after sowing. (a) absolute control: Z. mays not inoculated irrigated with water; (b) relative control: Z. mays not inoculated fed with 100% nitrogen and phosphate fertilizer; (c) Z. mays with X. autotrophicus fed with 50% nitrogen fertilizer and 100% phosphate fertilizer; (d) Z. mays with X. autotrophicus fed with 100% nitrogen fertilizer and 50% phosphate fertilizer; (e) Z. mays with X. autotrophicus fed with 50% nitrogen and phosphate fertilizer.
In Figure 5, showed the response of O. sativa to X. autotrophicus by the root length and plant height of O. sativa at 50% nitrogen fertilizer as NH4NO3 and 100% phosphorous fertilizer as K2HPO4/KH2PO4 (Figure 5c), in comparation to O. sativa with the maximum dose of nitrogen and phosphorous fertilizer but without X. autotrophicus (Figure 5b), as well as O. sativa with X. autotrophicus fed with 50% nitrogen and phosphate fertilizer (Figure 5e). This support that X. autotrophicus h is able to transform organic compounds from photosynthesis into phytohormons like auxins to increase root soil exploration for optimizing uptake of nitrogen fertilizer reduced to 50% [18, 45, 46, 106]. There is evidence that to support that X. autotrophicus in wheat, as well as in, oats, corn, sorghum, and other types of plants the way do other genus and species of growth plant promoting bacteria. While inside the roots of O. sativa; X. autotrophicus synthesizes acid and alkaline phosphatases for the solubilization and absorption of insoluble phosphate from the soil, as well as optimizing the phosphate fertilizer applied to the soil at a reduced dose without affecting the healthy growth of O. sativa compared to the response of O. sativa without inoculating with X. autotrophicus fed with the recommended dose of nitrogen and phosphate fertilizer, which shows that without the help of X. autotrophicus, O. sativa has growth limitations, therefore it is advisable to apply it to the sowing of the seed [119, 120, 123, 124, 126]. While inside the roots of O. sativa; X. autotrophicus synthesizes acid and alkaline phosphatases for the solubilization and absorption of insoluble phosphate from the soil, as well as optimizing the phosphate fertilizer applied to the soil at a reduced dose without affecting the healthy growth of O. sativa compared to the response of O. sativa without inoculating with X. autotrophicus fed with the recommended dose of nitrogen and phosphate fertilizer, which shows that without the help of X. autotrophicus; O. sativa has growth limitations, therefore it is advisable to apply it to the sowing of the seed [46, 106, 136].
Figure 5.
Positive response of Oryza sativa to Xanthobacter autotrophicus at different levels of nitrogen and phosphate fertilizer at seedling stage 15 days after sowing. (a) Absolute control: O. sativa not inoculated irrigated with water; (b) relative control: O. sativa not inoculated fed with 100% nitrogen and phosphate fertilizer; (c) O. sativa with X. autotrophicus fed with 50% nitrogen fertilizer and 100% phosphate fertilizer; (d) O. sativa with X. autotrophicus fed with 100% nitrogen fertilizer and 50% phosphate fertilizer; (e) O. sativa with X. autotrophicus fed with 50% nitrogen and phosphate fertilizer.
In Figure 6, L. sativa inoculated with X. autotrophicus fed with 25% nitrogen and phosphate fertilizer (Figure 6e), as well as L. sativa with X. autotrophicus fed with 25% nitrogen fertilizer and 100% phosphate fertilizer (Figure 6d), had the highest number of leaves, plant height and the highest root density, compared with L. sativa not inoculated fed with 100% nitrogen and phosphate fertilizer (Figure 6b). It is reported that X. autotrophicus stimulated the proliferation of root hairs in wheat, as has been observed in other plants [17, 41, 44, 137, 138] and this increased the area of exploration of the root to capture the nitrogen and phosphate fertilizer [42], as reported in other works on X. autotrophycus inoculation: in corn [46, 106], in wheat and in rice [43, 139].
Figure 6.
Response of Lactuca sativa to Xanthobacter autotrophicus at different levels of nitrogen and phosphate fertilizer at flowering stage 120 days after sowing. (a) Absolute control: L. sativa not inoculated irrigated with water; (b) relative control: L. sativa not inoculated fed with 100% nitrogen and phosphate fertilizer; (c) L. sativa with X. autotrophicus fed with 100% nitrogen fertilizer and 25% phosphate fertilizer; (d) L. sativa withX. autotrophicus fed with 25% nitrogen fertilizer and 100% phosphate fertilizer; (e) L. sativa with X. autotrophicus fed with 25% nitrogen and phosphate fertilizer; (f) L. sativa with X. autotrophicus fed with 0% nitrogen and phosphate fertilizer.
Figure 6 shows the effect of X. autotrophicus on the growth of L. sativa at different doses of nitrogen and phosphate fertilizer, where it was evident that X. autotrophicus can optimize the reduced dose of both fertilizers, in relation to nitrogen fertilizer by means of a conversion of metabolites released during photosynthesis [10, 17, 138], that reach the root to maximize the absorption of NH4NO3 while X. autotrophicus from inside the roots generates acid and especially alkaline phosphatases to solubilize the immobile phosphate of the soil, as well as optimize phosphate applied during the growth of L. sativa [140], in this trial it was demonstrated that these were the main mechanisms of X. autotrophicus when both fertilizers were applied in variable doses or in similar concentration, but not when in the absence of both [18, 120, 123, 124].
The possible synthesis of phytohormons by X. autotrophicus was supported by the test shown in Figure 7, in which it is evidenced by inoculation of S. lycopersicum with X. autotrophicus fed with 25% nitrogen and phosphate fertilizer (Figure 7e), had the highest number of leaves, fruits, plant height and the highest root density, compared to S. lycopersicum not inoculated fed with 100% nitrogen and phosphate fertilizer (Figure 7b). The positive growth of S. lycopersicum was due to the fact that X. autotrophicus had a growth promoter effect, which was detected from the beginning of wheat germination from its seed, reported to be maintained in the early stages of wheat root development [20, 41, 50], as observed in this experiment and which was similar to what was observed in root system when X. autotrophicus it colonizes and influences the growth of roots of beans [45, 54]. In that sense Figure 7 shows the effect of X. autotrophicus on S. lycopersicum at different doses of nitrogen (NH4NO3) and phosphate (KH2PO4/K2HPO4) fertilizer, the growth of S. lycopersicum shows that the ability of X. autotrophicus to invade the interior of the radical system to transform compounds derived from photosynthesis into phytohormons improves the absorption and optimization of the reduced doses of NH4NO3 [13, 14, 15, 126] as well as of phosphorous fertilizer, and even when none of them were applied to the crop is reported that N demand was supplied by biological N2 fixation due to X. autotrophicus [18, 36, 52] it was also detected that it synthesized acid and alkaline phosphatase to solubilize the immobile of the soil, so that S. lycopersicum had a healthy growth with early formation of fruits [16, 17, 120, 135, 140] compared to S. lycopersicum without inoculating fed with the recommended doses both fertilizer.
Figure 7.
Response of Solanum lycopersicum to Xanthobacter autotrophicus at different levels of nitrogen and phosphate fertilizer at maturity stage 180 days after sowing. (a) Absolute control: S. lycopersicum not inoculated irrigated with water; (b) Relative control: S. lycopersicum not inoculated fed with 100% nitrogen and phosphate fertilizer; (c) S. lycopersicum with X. autotrophicus fed with 100% nitrogen fertilizer and 25% phosphate fertilizer; (d) S. lycopersicum with X. autotrophicus fed with 25% nitrogen fertilizer and 100% phosphate fertilizer; (e) S. lycopersicum with X. autotrophicus fed with 25% nitrogen and phosphate fertilizer; (f) S. lycopersicum with X. autotrophicus fed with 0% nitrogen and phosphate fertilizer.
Table 2 shows the acid and alkaline phosphatase activity of X. autotrophicus, measured indirectly by the amount of p-nitrophenol generated when measured in the stem and roots of S. lycopersicum (as it is a genus and endophytic growth plant promoting species) with nitrogen and phosphorous fertilizers at 25%, of the recommended dose, there it is observed that the values of the higher and lower acid phosphatase of the alkaline support that the healthy growth of the vegetable was due to the activity of the phosphatases synthesized by X. autotrophicus not only the interior of the stem and better in the root, also when this strain of X. autotrophicus recovered from the stem as well as from the root results suggest the importance of soil phosphorus availability in altering the interactions between leading to soil invasion by S. lycopersicum by X. autotrophicus. Overall, applying high amounts of available nutrients may reduce and increase the abundance plant-beneficial microbes and pathobiome in soil, respectively, which in return, could affect soil and plant health. This work greatly advances the mechanistic understanding why X. autotrophicus is a genus with high competitive capacity within the broad group of growth-promoting endophytes that synthesize acid and/or alkaline phosphatases in the absence of available phosphates and even when soluble phosphates fertilizer is applied to soil in agricultural production [141], that issue could be important for researchers working in the field of environmental microbiology, microbial ecology, plant-microbe interactions, soil health, and plant protection [16, 17, 18, 123, 142] in comparison with the activity of both phosphatases of S. lycopersicum without inoculation with X. autotrophicus, where the poor activity of both phosphatases explains that the growth of this vegetable was not as vigorous as observed in S. lycopersicum inoculated with X. autotrophicus [120, 136]. Similar results of a high acid and alkaline phosphatase activity of X. autotrophcius inside the roots: Beta vulgaris, Hordeum vulgare, Pinus leiophylla, T. aestivum, Sorhgum bicolor. Z. mays, grown in soil with insoluble phosphate problems [124, 135, 137, 143] or precipitation of the phosphate fertilizer at a lower dose than recommended (data no shown).
Activity of acid and alkaline phosphatases of Solanum lycopersicum at flowering stage 120 days after sowing at 25% of nitrogen and phosphate fertilizer with and without inoculating with Xanthobacter autotrophicus.
n = 3.
Values with different letter are stadistically distint according to ANOVA-Tukey (P < 0.05).
Figure 8 shows that fruit of S. lycopersicum with X. autotrophicus fed with 100% nitrogen fertilizer and 25% phosphate fertilizer had the largest size and red coloration (Figure 8) while S. lycopersicum not inoculated irrigated fed with 100% nitrogen and phosphate fertilizer had a smaller size, in addition to a green coloration which means that vegetative life cycle was shorter than the fruit from not inoculate S. lycopersicum (Figure 8a). These results demonstrate the importance of X. autotrophicus for healthy growing plants, with a reduced dose of nitrogen and phosphorous fertilizer [54, 120, 144, 145]. Figure 8 shows the effect of X. autotrophicus on the fruit of S. lycopersicum at a recommended dose of nitrogen fertilizer such as NH4NO3 with 25% of the phosphate fertilizer, in that sense X. autotrophicus is able to solubilize phosphate in soil and promote its uptake by plants are referred as phosphate solubilizing bacteria (PSB) or phosphobacteria and are included within PGPR [143]. Their counts in the rhizosphere comprise a considerable share of the rhizospheric microorganisms and vary depending on the soil location and type as well as the cultivated plants [133, 142, 146]. The results support that X. autotrophicus transformed organic compounds derived from photosynthesis in the inside the roots of S. lycopersicum in phytohormons for an efficient absorption of NH4NO3 while to optimize the phosphate fertilizer, X. autotrophicus by means of acid phosphatases, mainly alkaline phosphates solubilized the soil phosphates [123, 124, 142, 143, 145] and quickly absorbed the one applied consequently the fruit of the S. lycopersicum reached a larger size and ripened earlier in comparison with the size of the S. lycopersicum without inoculation fed with the recommended dose of both fertilizers [14, 16, 17, 38, 43, 50, 144].
Figure 8.
Fruit of Solanum lycopersicum with Xanthobacter autotrophicus at different levels of nitrogen and phosphate fertilizer at maturity stage 180 days after sowing. (a) Relative control: S. lycopersicum not inoculated fed with 100% nitrogen and phosphate fertilizer; (b) S. lycopersicum with X. autotrophicus fed with 100% nitrogen fertilizer and 25% phosphate fertilizer.
Figure 9 shows that A. thaliana with X. autotrophicus fed with 100% NH4NO3 (Figure 9d), as well as A. thaliana with X. autotrophicus fed with 50% NH4NO3, (Figure 9h) and A. thaliana with X. autotrophicus irrigated with only water (Figure 9l) had root growth inhibition, its suggested due over synthesis of phytohormons not depending of NH4NO3 concentration [20, 79, 99, 131, 147] compared to A. thaliana with B. vietnamiensis 2 fed with 100% NH4NO3 (Figure 9c), as well as A. thaliana not inoculated fed with 50% NH4NO3 (Figure 9e) and A. thaliana not inoculated irrigated with water (Figure 9i).
Figure 9.
Response of Arabidopsis thaliana to Burkholderia vietnamiensis and Xanthobacter autotrophicus on the germination of seed and first step of growth at seedlings stage at different dose of NH4NO3 under artificial culture media. (a) A. thaliana not inoculated fed with 100% NH4NO3; (b) A. thaliana with B. vietnamiensis 1 fed with 100% NH4NO3; (c) A. thaliana with B. vietnamiensis 2 fed with 100% NH4NO3; (d) A. thaliana with X. autotrophicus fed with 100% NH4NO3; (e) A. thaliana not inoculated fed with 50% NH4NO3; (f) A. thaliana with B. vietnamiensis 1 fed with 50% NH4NO3; (g) A. thaliana with B. vietnamiensis 2 fed with 50% NH4NO3; (h) A. thaliana with X. autotrophicus fed with 50% NH4NO3; (i) A. thaliana not inoculated irrigated with water; (j) A. thaliana with B. vietnamiensis 1 irrigated with only water; (k) A. thaliana with B. vietnamiensis 2 irrigated with water; (l) A. thaliana with X. autotrophicus irrigated with only water.
Figure 10 shows that A. thaliana with X. autotrophicus fed with 100% NH4NO3 (Figure 10d), as well as A. thaliana with X. autotrophicus fed with50% NH4NO3, (Figure 8h) and A. thaliana with X. autotrophicus irrigated with water (Figure 10l) had root growth inhibition, compared to A. thaliana with B. vietnamiensis 1 fed with 100% NH4NO3 (Figure 10b), as well as A. thaliana with B. vietnamiensis 1 fed with 50% NH4NO3 (Figure 10f) and A. thaliana with B. vietnamiensis 1 irrigated with water (Figure 10j). Figures 9 and 10 show the response of the seed and stem primordia and root of A. thalina inoculated with B. vietnamiensis compared to X. autotrophicus at doses 100, 50 and 0% of the nitrogen fertilizer as NH4NO3 where it was evident that while a positive effect of B. vietnamiensis strains on A. thaliana was dependent on the concentration of NH4NO3, [41, 110, 129, 148] X. autotrophicus inhibited seed germination and practically stem and root primordium, both effects were positive by B. vietnamiensis well-known plant beneficial bacteria for a domestic vegetal [149]. In opposite way X. autotrophicus can distinguish between a domestic plant and a weed planted in agricultural soil by stimulating the growth of the former and inhibiting the germination and growth of the latter [150]. A genetic capacity that few genera and species such as X. autotrophicus of growth-promoting endophytic bacteria possess and can be used to improve the growth of domestic plants and prevent the germination of weeds underline when they are dependent on the synthesis of phytohormons from compounds releasing of the seed and roots of A. thaliana [46, 47, 59, 79, 131, 147].
Figure 10.
Effect of Burkholderia vietnamiensis and Xanthobacter autotrophicus on the germination of seed and first step of growth of Arabidopsis thaliana seeds directly sown in inoculated in artificial culture media at different dose of nitrogen fertilizer as NH4NO3. (a) A. thaliana not inoculated fed with 100% NH4NO3; (b) A. thaliana with B. vietnamiensis 1 fed with 100% NH4NO3; (c) A. thaliana with B. vietnamiensis 2 fed with 100% NH4NO3; (d) A. thaliana with X. autotrophicus fed with 100% NH4NO3; (e) A. thaliana not inoculated fed with 50% NH4NO3; (f) A. thaliana with B. vietnamiensis 1 fed with 50% NH4NO3; (g) A. thaliana with B. vietnamiensis 2 fed with 50% NH4NO3; (h) A. thaliana with X. autotrophicus fed with 50% NH4NO3; (i) A. thaliana not inoculated irrigated with water; (j) A. thaliana with B. vietnamiensis 1 irrigated with water; (k) A. thaliana with B. vietnamiensis 2 irrigated with water; (l) A. thaliana with X. autotrophicus irrigated with water.
8. Conclusions
The plant growth promoting endophytic bacteria well known as X. autotrophicus is an exceptional genus and species of procaryote due to the ability it has to simultaneously fix CO2 and N2, it can exist in water, soil and in association with a wide variety of plant species, specifically because by invading the root tissue it influences positively in the absorbing both nitrogen and phosphorous regulated forms of fertilization by the synthesis of acid and alkaline phosphatases in soil with phosphate availability problems or where the application of the phosphate fertilizer precipitates. Whereas by converting seed exudates and derivates and photosynthesis inside the root’s plants in phytohormons have an interesting potential as a biofertilizer. As well as for the biological control of weeds that compete with the cultivation of domestic plants, it can contribute to sustainable agricultural production that reduces the effects of contamination by unregulated fertilization and application of chemical herbicides. Besides that X. autotrophicus is has been reported as useful biological tool for bioremediation of water and soil polluted by chemical agents. Easy to growth in simple culture media low cost to reproduce to industrial level, a friendly genus and bacterial species for humans, animals, plants and the environment.
Acknowledgments
The support of project 2.7 (2021-2022) of the Coordination of Scientific Research of the UMSNH, Morelia, Michoacan, Mexico is appreciated. As well as the project: “Field Test of a Living Biofertilizer for Crop Growth in Mexico” from Harvard University, Cambridge, Ma, USA with funding from the Rockefeller Foundation (2019–2022). To Jeaneth Caicedo Rengifo for her help working in this project. To Juan Luis Ignacio de la Cruz, MSc Blanca Celeste Saucedo Martinez and J Alberto Castro-Villaseñor for their technical support.
Conflict of interest
The authors declare no conflict of interest.
\n',keywords:"soil proprieties, cereals, vegetables and green nitrogen fertilizer, endophytic plant growth promoting bacteria, health",chapterPDFUrl:"https://cdn.intechopen.com/pdfs/80941.pdf",chapterXML:"https://mts.intechopen.com/source/xml/80941.xml",downloadPdfUrl:"/chapter/pdf-download/80941",previewPdfUrl:"/chapter/pdf-preview/80941",totalDownloads:35,totalViews:0,totalCrossrefCites:0,dateSubmitted:"October 7th 2021",dateReviewed:"December 17th 2021",datePrePublished:"March 23rd 2022",datePublished:"May 11th 2022",dateFinished:"March 23rd 2022",readingETA:"0",abstract:"The endophytic genus plant growth promoting bacteria (EPGPB) known as Xanthobacter autrotrophicus is one of the most interesting option to apply on the production of wheat (Triticum aestivum), and other domestic crops lettuce (Lactuca sativa), tomato (Solanum lycopersicum) rice (Oriza sativa) maize (Zea mays): under all types of agriculture systems: open field, protecting one or either organic sustainable type. The aims of this review is to analyze the qualities of X. autotrophicus as useful EPGPB for sustainable production of wheat and other crops regarding its capacity as able to fix molecular nitrogen (N2) as well as by transforming plant metabolic compounds in phytohormons, including phosphatase enzyme for solubilizing phosphate to solve different soil problems related with its fertility also some phytopathological like to stop of growing weed as Arabidopsis thaliana which are competing with health growth of domestic plants. Beside the potencial of X. autotrophicus for bioremediation of environmental polluted by chemicals.",reviewType:"peer-reviewed",bibtexUrl:"/chapter/bibtex/80941",risUrl:"/chapter/ris/80941",signatures:"Juan Manuel Sánchez-Yañez",book:{id:"9670",type:"book",title:"Current Trends in Wheat Research",subtitle:null,fullTitle:"Current Trends in Wheat Research",slug:"current-trends-in-wheat-research",publishedDate:"May 11th 2022",bookSignature:"Mahmood-ur-Rahman Ansari",coverURL:"https://cdn.intechopen.com/books/images_new/9670.jpg",licenceType:"CC BY 3.0",editedByType:"Edited by",isbn:"978-1-83968-594-1",printIsbn:"978-1-83968-593-4",pdfIsbn:"978-1-83968-595-8",isAvailableForWebshopOrdering:!0,editors:[{id:"185476",title:"Dr.",name:"Mahmood-ur-Rahman",middleName:null,surname:"Ansari",slug:"mahmood-ur-rahman-ansari",fullName:"Mahmood-ur-Rahman Ansari"}],productType:{id:"1",title:"Edited Volume",chapterContentType:"chapter",authoredCaption:"Edited by"}},authors:[{id:"329840",title:"Prof.",name:"Juan Manuel",middleName:null,surname:"Sanchez-Yañez",fullName:"Juan Manuel Sanchez-Yañez",slug:"juan-manuel-sanchez-yanez",email:"syanez@umich.mx",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",institution:null}],sections:[{id:"sec_1",title:"1. Introduction",level:"1"},{id:"sec_2",title:"2. Phylogeny and taxonomy of Xanthobacter spp",level:"1"},{id:"sec_3",title:"3. Taxonomy",level:"1"},{id:"sec_4",title:"4. Isolation cultivation and axenic culture",level:"1"},{id:"sec_4_2",title:"4.1 Methods of storage",level:"2"},{id:"sec_6",title:"5. Autotrophy and nitrogen fixation capability",level:"1"},{id:"sec_7",title:"6. Natural habitats",level:"1"},{id:"sec_7_2",title:"6.1 Ecological interactions with other domestic plants",level:"2"},{id:"sec_8_2",title:"6.2 Biofertilizer application of endophytic plant growth promoting bacteria in modern sustainable agriculture",level:"2"},{id:"sec_8_3",title:"6.2.1 Biofertilizer (X. autotrophicus) for bioremediation of environment polluted by chemical agents",level:"3"},{id:"sec_11",title:"7. Effect of Xanthobacter autotrophicus on the growth of Triticum aestivum and other domestic plants",level:"1"},{id:"sec_12",title:"8. 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Environmental Microbiology Laboratory, Research Institute in Biology and Chemistry, Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Mich, Mexico
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Guérin",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:{name:"Ghent University",institutionURL:null,country:{name:"Belgium"}}},{id:"119046",title:"MSc.",name:"Nico",surname:"Van Hecke",slug:"nico-van-hecke",fullName:"Nico Van Hecke",position:null,profilePictureURL:"//cdnintech.com/web/frontend/www/assets/author.svg",biography:null,institutionString:null,institution:{name:"Ghent University",institutionURL:null,country:{name:"Belgium"}}}]},generic:{page:{slug:"types-of-publications",title:"Types of publications",intro:"
IntechOpen publishes different types of publications
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EDITED VOLUME
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IntechOpen Edited Volumes are integrated collections of chapters about particular topics that present new areas of research or novel syntheses of existing research and, as such, represent perspectives from various authors.
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Edited Volumes can be comprised of different types of chapters:
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RESEARCH CHAPTER – A research chapter reports the results of original research thus contributing to the body of knowledge in a particular area of study.
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REVIEW CHAPTER – A review chapter analyzes or examines research previously published by other scientists, rather than reporting new findings thus summarizing the current state of understanding on a topic.
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CASE STUDY – A case study involves an in-depth, and detailed examination of a particular topic.
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PERSPECTIVE CHAPTER – A perspective chapter offers a new point of view on existing problems, fundamental concepts, or common opinions on a specific topic. Perspective chapters can propose or support new hypotheses, or discuss the significance of newly achieved innovations. Perspective chapters can focus on current advances and future directions on a topic and include both original data and personal opinion.
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INTRODUCTORY CHAPTER – An introductory chapter states the purpose and goals of the book. The introductory chapter is written by the Academic Editor.
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MONOGRAPHS
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Monographs is a self-contained work on a particular subject, or an aspect of it, written by one or more authors. Monographs usually have between 130 and 500 pages.
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TYPES OF MONOGRAPHS:
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Single or multiple author manuscript
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COMPACTS
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Compacts provide a mid-length publishing format that bridges the gap between journal articles, book chapters, and monographs, and cover content across all scientific disciplines.
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Compacts are the preferred publishing option for brief research reports on new topics, in-depth case studies, dissertations, or essays exploring new ideas, issues, or broader topics on the research subject. Compacts usually have between 50 and 130 pages.
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CONFERENCE PROCEEDINGS
\\n\\n
Collection of papers presented at conferences, workshops, symposiums, or scientific courses, published in book format
IntechOpen Edited Volumes are integrated collections of chapters about particular topics that present new areas of research or novel syntheses of existing research and, as such, represent perspectives from various authors.
\n\n
Edited Volumes can be comprised of different types of chapters:
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RESEARCH CHAPTER – A research chapter reports the results of original research thus contributing to the body of knowledge in a particular area of study.
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REVIEW CHAPTER – A review chapter analyzes or examines research previously published by other scientists, rather than reporting new findings thus summarizing the current state of understanding on a topic.
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CASE STUDY – A case study involves an in-depth, and detailed examination of a particular topic.
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PERSPECTIVE CHAPTER – A perspective chapter offers a new point of view on existing problems, fundamental concepts, or common opinions on a specific topic. Perspective chapters can propose or support new hypotheses, or discuss the significance of newly achieved innovations. Perspective chapters can focus on current advances and future directions on a topic and include both original data and personal opinion.
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INTRODUCTORY CHAPTER – An introductory chapter states the purpose and goals of the book. The introductory chapter is written by the Academic Editor.
\n\n
MONOGRAPHS
\n\n
Monographs is a self-contained work on a particular subject, or an aspect of it, written by one or more authors. Monographs usually have between 130 and 500 pages.
\n\n
TYPES OF MONOGRAPHS:
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Single or multiple author manuscript
\n\n
COMPACTS
\n\n
Compacts provide a mid-length publishing format that bridges the gap between journal articles, book chapters, and monographs, and cover content across all scientific disciplines.
\n\n
Compacts are the preferred publishing option for brief research reports on new topics, in-depth case studies, dissertations, or essays exploring new ideas, issues, or broader topics on the research subject. Compacts usually have between 50 and 130 pages.
\n\n
CONFERENCE PROCEEDINGS
\n\n
Collection of papers presented at conferences, workshops, symposiums, or scientific courses, published in book format
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