Reviewing Articles

In this page, I will summarize the articles of my interests and put relatively long highlights. It will be useful to check here before reading a long review article. One may also see my academic interests and perspectives clearly by investigating this place. [My comments will be in square brackets, the other parts were from the manuscript, mostly shortened and paraphrased]

1-] A review of selected microcontaminants and microorganisms in land runoff and tile drainage in treated sludge-amended soils, 2019 (review article)
2-] Biogeochemistry of soil organic matter in agroecosystems & environmental implications, 2019, (review article)
3-] Nanotechnology in remediation of water contaminated by poly- and perfluoroalkyl substances: A review, 2019 (review article)
4-] Pesticides in surface waters: from edge-of-field to global modelling, 2019 (review article)
5-] Application of the water-related spectral reflectance indices: A review, 2019 (review article)
A concise review of biochar application to agricultural soils to improve soil conditions and fight pollution, 2018, (review article)
7-] The role of satellite remote sensing in structured ecosystem risk assessments, 2018 (review article)
A review of coupled hydrologic and crop growth models, 2019 (review article)


03 February 2019 (my reviewing date)


Ghirardini, A., Verlicchi, P. (2019). A review of selected microcontaminants and microorganisms in land runoff and tile drainage in treated sludge-amended soils. Science of the Total Environment. 655 (2019), 939-957.


keywords: surface runoff, tile drainage, microcontaminants, bacteria, sludge-amended soil, rainfall intensity


The aim is reviewing the quality of surface runoff and tile drainage from sludge-amended soils. Review mainly discusses 16 studies from USA (6 studies 15 investigation), Canada (7 studies 11 investigation), Australia (1 study 4 investigation), Ireland (2 studies 8 investigation). Another narrowing down is 57 microcontaminants and 5 different bacteria species (E. coli, total coliform, fecal streptococcus, Clostridium perfringens). These selections came from the reviewed studies. Investigations mean actual chemical measurements, there are also m/o measurements as stated yet their number is very low, which will also be discussed later on.

After intense rainfalls and consequent surface runoff, and in places with tile drainage, sludge application was expected to be problematic. They also mentioned groundwater contamination risk very poorly, only from 4 Canadian studies. The literature was reported to be mostly concerned with macropollutants (suspended solids, organic substances, nutrients (N,P), or heavy metals). Soil also seems to be hostile for the newcomer bacteria (possible 2-4 month of life expectancy) so their growth and transport are expected to be on run-off water.

In legislation, the biosolid “reuse” was forbidden in Belgium, Romania, and Switzerland. In “many other” EU countries, Ontario-Canada, the USA, New South Wales Austria, [and I can also add Turkey here] sludge soil application is possible but there are thresholds regarding the receiving soil, the chemical composition of the sludge, and its application rate. Pharmaceuticals & Personal Care Products (PPCP) are left out to date on this legislation. For m/o, only a handful of states have some thresholds regarding Salmonella and E. coli. [Turkey does not have a threshold here, only a 99% reduction in sludge stabilization process for E. coli]. Also, because of these unregulated but harmful compounds, the benefit on the reuse of reclaimed water in irrigation might be hindered. [This reclaimed water irrigation is very popular in Mediterranean related studies, as climate change depletes the available freshwater for irrigation, among many other factors]. This paragraph also shows the relevance of the study for many parts of the world, where sludge might very well be applied for agricultural purposes.

Different parameters in studies:

(1) soil type, (2) municipal sludge type, (3) sludge application method, (4) sludge application rate, (5) water stream type, (6) rainfall frequency

were evaluated to uncover the impact of them over the PPCP and m/o concentration in tile drainage and surface runoff. Additionally, physicochemical properties of the PPCP were also considered. In reviewed papers, logKow of microcontaminants investigated ranges from -1.37 to 5.9. Sludge dry matter changes between <18% to 91.6%. Sludges were generally anaerobically digested and dewatered, some further processed with high T drying, gamma irradiation, centrifugal dewatering, or lime stabilization. Main sludge application (or land disposal) methods are land/surface spreading, tilling, one-pass aeration tilling, subsurface injections [with good illustrations in the manuscript]. It was also stated that some legislations also take into account the distance to waterways and groundwater table according to the plot size of sludge applied area.

Surface runoff experiments were in the order of a few m2 in plot size, whereas, tile drainage were generally >740 m2. Majority of the studies included a control plot without sludge application to check the difference. Most rain applications were artificial and except one 266 days interval study, their duration were shorter than 54 days. Real ones were all tile drainage investigations, lasted between 46 days to 365 days.

Different chemical compounds entered into surface runoff water in different times. Background concentrations were either

When compared with literature values of WW secondary effluents, and of surface water, the concentrations of these PPCP were lower in tile drainage and surface runoff samples. Also, no acute toxicological effect were expected from this release of compounds to the nature, as they will also be diluted and degraded. There are also a few bacteria data yet as [number of studies are low] and their units are different, comparison is impossible. [Unfortunately, no mention of bioconcentration/accumulation/magnification were considered].

The following paragraphs will summarize the factors on PPCP concentration in surface runoff and tile drainage.

 -Among them, influence of logKow was the first to be addressed. >4 means highly adsorbing and <2.5 states that the compound is mobile with water. No correlation was found, however, the variance among the characteristics of the studies in the scope already limits the possibility of finding a good correlation. The general expectance stated above as <2.5 and >4 found in pharmaceutical compounds, where all other factors were constant. There is also some impact of pKa values on the distribution of these chemicals in soil-water media. Another constant, octanol-water distribution coefficient was stated to be more accurate for these predictions, in which its logDow value can be calculated as below:

logDow=logKow+log (1/(1+〖10〗^(pH-pKa) )) Eq 1
logDow=logKow+log (1/(1+〖10〗^(pKa-pH) )) Eq 2
according to Schwarzenbach et al. (2003), eq 1 for acidic, 2 for basic compounds. >3 good sorption, <1 low sorption.

-In soil properties, interestingly, soil compaction, water content and T were found to be more relevant than soil texture when predicting leaching. Preferential flow in fissures, abandoned root places and worm burrows were also stated. More importantly, soil properties are not static, but changing continuously, and this was also observed in one of the cited study.

-Sludge treatment also has an impact on the outcome. If not dewatered, sludge applied to uncompacted soil behaves like a liquid and fills the pores, and consequently, establish a connection btw PPCP and soil microbes, further accelerating the degradation rate. In dewatered sludge application, on the other hand, aerobic microbial degradation is more or less prevented, this increases the lifetime of PPCP. However, if there is not any excess rainfall or irrigation water is present, transport of PPCP from dewatered sludge is also very less compared to that of liquid sludge. Slow, extended release of PPCP is expected from dewatered sludge. Interestingly, no clear correlation was found between sludge application rate and PPCP concentrations in tile drainage and surface runoff.

-Type of sludge application method has also its effect, in liquid sludge application through injection, surface runoff has lower concentrations of the microcontaminants, but some of the most persistent compounds may appear in future. The less persistent’s will degrade before reaching surface runoff water. In some studies, sludge application method did not seem to affect the transport of PPCP to tile drainage, especially related to the high number of macropore (such as worm burrow) flow. However, when these are broken with some method, the transport of PPCP will be reduced [as soil-PPCP sorption interactions will be increased].

 -Rain intensity did not directly affect the contaminant transport, but was a mild contributing factor among the other things discussed so far.

 Factors over m/o in runoff and tile drainage

 -Sludge type was not sufficiently investigated to make inferences. In terms of application method, direct injection caused higher bacteria concentrations. For different types of soils, only Atalay et al (2007)’s study were summarized, clay loam E. coli was found to be higher than that of sandy loam. However, their total coliform number did not differ significantly. Same situation also holds for rainfall effect.

One interesting conclusion reached in the review is that the PPCP in sludge is expected to be persistent in the environment as they have persisted through [harsh] conditions of WWTP. In addition to this, some hormones’ concentration in runoff may increase with successive rainfalls as they may have some metabolic pathways in bacteria, which also produces them.

As a good practice, especially disruption of macropores and lowering the T to postpone the decomposition of dewatered sludge was suggested. [To clarify, we can say that while many studies recently are proponents of the no-tillage, conservation tillage approaches in agriculture for many reasons, when applying sludge to soil the exact opposite was suggested, at least in this review. This has far more complications in terms of agricultural management].
Overall, the review generally accumulated the knowledge gained through the cited studies and was unable to make generalized comments, mostly due to the lack of data. However, the illustrations and data figures were very good at explaining the current situation in sludge application and subsequent risk in surface runoff and tile drainage. In figures, the compounds were ordered in their clusters according to their type; such as analgesics, antibiotics etc. However, given the stress on the review about octanol-water distribution coefficient, it would be good to see the compounds and concentrations in that order. Figure 6 and 7 has logKow correlation but at that time the compound classification and name were lost in the figure, in which many comments could be made according to the compounds' structure, on its fate, sorption, and concentration.

27 January 2019 (my reviewing date)




Ondrasek, G., Begić, H. B., Zovko, M., Filipović, L., Merino-Gergichevich, C., Savić, R., Rengel, Z. (2019). Biogeochemistry of soil organic matter in agroecosystems & environmental implications. Science of the Total Environment. 658 (2019), 1559-1573.



keywords: agroecosystem, soil organic matter, organic C, C emission, contaminants, trace metals


The focus of the article is metal mobility in different soils of Mediterranean region resulting from changes in SOM. Additionally, C cycling is also stressed beforehand, specifically pointing out the disproportionate rate of SOM decomposition and ways to add SOM to the soil. Besides, this is not only environmentally serious concern but also affects yields and then the economy (3.4 – 5.6 billion dollars /year from organic matter decline alone). One critical point is the export of agricultural litter and breaking of the carbon cycle, in which in natural areas this covers 50-75 of the SOM input in forests and wooded grasslands. Mediterranean climate is more dangerous on SOM depletion, especially with improper land management. One example is given from Croatia, especially after the construction of dams, hydro-electrical power plants, soil deposition profile changed, comprising only silt and sand. Another issue was “amelioration” of swampy areas, in which organic-rich sediment was manually taken and used in very intensive, 2-3 crop rotation/year, agriculture. Here aerobic respiration consumes SOM.


SOM depletion threats; soil subsidence, and consequently flooding risk since less soil will hold water, also seawater intrusion in coastal regions, salinization of land and water sources, the formation of acid-sulfate soils from normally flooded peats or other organic soils after their drainage, release of previously SOM adsorbed contaminants, co2 emission.


Non-living SOM includes >90 % high molecular weight organics, mostly humics, leastly polymerized exudates and inert black carbon. These SOM has more O containing functional groups than N and S, and they are affected by pH. Their specific surface area was also affected by pH changes.



Earth’s C pool is ~47000 Gt, 80 % is in oceans, terrestrial has 2860 Gt mostly in soils (1550 Gt), 750 Gt is inorganic, 560 Gt is plant biomass. ~760 tones are stored in the atmosphere. Remaining 5000 Gt or 11% is stored as carbonate sediments etc. The input to atm C pool 75-81 Gt C /year and its amount increases ~3.2-3.3 Gt C/year. There are also regional details over these material flows in the article.



Net primary production = Gross primary production (photosynthesis capture of CO2 by vascular plants) – their respiration. Global terrestrial NPP is generally measured between 50-58 Gt C/year lately. A similar amount is also predicted to be annual litter production of C. An interesting thing is the conversion from forest to pasture can increase soil C by 8%.



Root respiration can account for 10 to 90 % of total soil respiration, very high in arctic tundra ecosystems. Plant C exudates and rhizodeposits were used interchangeably in the article and in one study this comprised 30 % of total soil respiration. In total, rhizosphere respiration was accounted for 50% of total soil respiration, in addition to 50 % heterotrophic bulk soil respiration. In short, other than plant input, remaining soil organic matter is lost to the atmosphere by respiration continuously.



The rest of the article focuses on karstic soil structure, its high SOM, pyrite content and metals, and changes in them with changing environmental conditions [meteorological and artificial changes]. Wildfire and subsequent heavy storms can result in 50/50 SOM loss, by combustion and by leaching respectively, there is also the possibility of PAH generation.



Minerally sorbed SOM decomposition is slower, and SOM adsorbs on rough surfaces more. This organo-mineral fraction is significant on metal retention. The hydroxides of Fe and Mn is also considerable in metal retention, and even clay is relatively less important, it might preserve SOM. [In addition to this, different clays might adsorb different kinds of organic matter, kaolinite more polysaccharide, and smectite more aromatic in Feng et al., 2005. ]The effect of DOC on metal fate/transport is another focus, in which combined with pH, DOC is very important on metal fate, especially Cd featured. Zn is also similar but Cu was independent of pH effect. All these soils also have, albeit low, carbonate sorption. On the other hand, Ni speciation to carbonate mineral was much higher.








The article has two main focuses. One is SOM cycling, especially underlining C cycling, and the other is the OM effect on metal speciation in karstic environments. The SOM cycling part is very satisfying, with very clear illustrations. The metal part is somewhat lower in content but I think it is because of the narrower scope, the karstic environment, and Mediterranean climate and some trace metals. Overall, it is worth to read this article entirely in case one has an interest in terrestrial C dynamics and metal fate in karstic/Mediterranean environments.


5 February 2019 (my reviewing date)


Zhang, W., Zhang, D., Liang, Y. (2019). Nanotechnology in remediation of water contaminated by poly- and perfluoroalkyl substances: A review. Environmental Pollution. 247 (2019), 266-276.


keywords: PFASs, PFOA, nanotechnology, engineered nanomaterials, adsorption, photocatalysis


In the abstract, carbon nanotube modifications were highlighted for effective sorption. Among metal oxides, iron oxide-based nanoparticles were especially significant thanks to its magnetic properties, and consequently, its easier to recycle after adsorption. Additionally, TiO2, Ga2O3, In2O3 (best among them) based nano-photocatalyst were also considered from their effective UV combined degradation.

The manuscript, introduced the PFASs compounds, their use, spread, and toxicity/carcinogenicity, in short why we consider eliminating PFAS from the environment. Conventional methods simply don’t work for PFAS due to its extreme recalcitrance, and thermal stability, hydrophobic/oleophobic behavior. Here, nanomaterials are promising owing to their high surface area and high reactivity, so this review was prepared to compare different nanoparticle’s efficiency on treating PFAS contamination in water.

Physical adsorption is one method to remove PFAS. Electrostatic attraction, hydrophobic attraction, and self-aggregation as micelles are the routes to sorb and remove them. The interesting information is that hydrophobic-hydrophobic interactions between adsorbents and PFAS can even overcome electrostatic repulsion, and as a result, even negatively charged carbon nanotubes can effectively adsorb PFAS.

For carbon nanotube adsorption, increasing negatively charged functional groups like –OH, -COOH diminished the adsorption efficiency to the point of even lower than conventional sorbents, such as activated carbon. This was also found in another study with a correlation between increasing oxygen content and decreasing adsorption capacity, to a certain point. After that, more oxygen content on the surface of carbon nanotubes actually ameliorate the situation and results in better adsorption. Electrosorption is another enhancer method for carbon nanotube PFAS-PFOS sorption, which can the efficiency around 50-fold.

The second adsorbent is nanosized magnetic iron oxides. Their advantages are stabilization by either surface modification or added polymers, such as soluble starch. Only two studies were cited and one of them has capacity information, 62.5 mg/g. In that, the mechanism was found to be the inner sphere complexation of PFOA and Fe3O4 nanoparticles.

Photochemical reactions, is another method to deal with PFAS. Here, the reported studies took PFOA as a representative compound and found Ti, Ga, and In based oxides useful. In Ti-based nanomaterials, decomposition of PFOA and shorter PFCAs were investigated, and it was found that firstly decarboxylation occurs, then in the remaining perfluoroalkyl radical, two fluorides were lost to the solution and a carboxylic acid forms at the end again. These two reactions keep occurring one after another until complete mineralization to carbon dioxide and fluoride ions. The entire reaction pathway starts with the electron acceptance of hydroxyl radical or “hole” generated on TiO2, acting like a photovoltaic. This is not reported to be an effective pathway to degrade PFOA and similar compounds, [as hydroxyl radical reductive potential is smaller in magnitude than that of fluoride ion], so many other modifications on Ti-based oxides were done to improve this system. One method is oxalic acid addition. This results in the formation of carboxyl anion radicals and electrons with prolonged lifetime and finally resulted in 86.7% of PFOA decomposed in one study with this method. Another is TiO2 and multiple walled carbon nanotube (MWCNT). In one study, optimal conc. of this composite was 1.6 g/L, with 8 hours of 300 W, 365 nm irradiation nearly all PFOA was degraded. This advanced efficiency was attributed the electricity conduction and strong adsorptivity of MWCNT. The third one is Pb-modified TiO2. The sole enhancement of Pb doping is decreasing the recombination of electron and hole generated in Ti oxide. consequently, more hydroxyl radical was produced and more degradation was observed. [It was not discussed in the review, but after the decarboxylation or desulphurization (-SO4) rather than hydroxide radicals, hydroxide ions might very well displace –F by SN2 reactions. ]. Similar modifications on TiO2 can also be made by noble metals. The result was up to 12.5 times higher pseudo-first order rate constant. The noble metals in that study, stored photogenerated electrons and holes did not recombine with them, but react with PFOA, in especially Pd doped Ti oxide 100% degradation was observed, with 7 hours of UV radiation. A similar effect can also be seen in graphene composites.

Another metal oxide nanomaterial for this job is Ga2O3. In its mechanism, the only difference was an additional hydrolysis step on the terminal carbon with oxygen and fluoride. In one study, sheaf-like β galium oxides were very good in 254 nm with pure solutions, but when applied to the secondary effluent of municipal WW, the UV radiation was moved to 185 nm to prevent suppression by bicarbonate and organic matter, and the result was promising. Similar high efficiency was also seen in gallium oxide nanorods, and it was affected by pH, as it has an impact on the gallium oxide itself.

The third metal oxide was indium oxide nanomaterials. This metal has a slower hydroxyl radical generation, so the holes have more time to interact with other things, here PFOA. Its mechanism’s last step is also different, a combination of perfluoroalkyl radical with a hydroxyl or perhydroxyl radical, then its rapid HF loss and hydrolysis. [ I am not delving into detailed mechanism discussion as it was not discussed in the manuscript, either]. Different than others, PFOA adsorption can also take place by filling the oxygen vacancy on the surface of InO2 directly by chemisorbing there with PFOA’s one oxygen. One example of highly efficient indium oxide is nanoporous nanoparticles. Another study measured the impact of the shapes of the NPs and only found that the ones with higher specific surface area and oxygen vacancy will be more reactive towards PFOA. There is also graphene nanocomposite of InO2. In addition to that, some researches enwrapped InO2 by graphene, and when this is done partially the degradation was enhanced, both by having sufficient active site and an electron conduction layer, graphene. The last example of InO2 doping was CeO2. The role of cerium oxide here is similar to other modifications, it allowed better separation of electron and holes, but through its band gap. Additionally, the resultant composite’s stability was also found excellent.

The conclusion: [Conclusion’s first paragraph is almost a copy of the abstract]. The literature is limited with distilled water solutions of PFAS, there is a serious gap in PFAS removal in real cases, where there are also other compounds; such as natural organic matter. Besides, researchers generally used much higher concentrations of the contaminants than what is found in the environment, so the removal efficiencies might very well be overestimated. Additionally, studies did not consider the mix of PFAS, or even its degradation intermediates while working. This may not only be a significant gap but also the toxicity of the degradation by-products and other intermediates are unknown. Lastly, recoverable engineered nanomaterials were featured, also the immobilization of nanomaterials over a structure to prevent the loss of material and pollution.

[Overall, the mechanisms were more or less clearly demonstrated in figures, and not only the featured studies’ results were highlighted, but also their nanomaterial synthesis method were provided. The unclear points are why these nanomaterials were chosen among others, and what is the meaning of their presentation order (titanium, gallium, indium). The chemical mechanisms proposed for each metal oxide were taken for granted, not giving a place for their further in-depth discussion, albeit it is very critical on the prediction of their performance under different environmental conditions. Still, the tables were quite a good presentation of what has been done.]

16 February 2019 (my reviewing date)


Ippolito, A., Fait, G. (2019). Pesticides in surface waters: from edge-of-field to global modelling. Current oppinion in Environmental Sustainability. 36 (2019), 78-84.


keywords: [no keyword was found in the article]

The manuscript is related to the effect of the scale of the modeling on the results, in simple words. In its introduction, the narrowing down is precisely illustrated for the subject. Urban pesticide contamination was ruled out, the significance of the topic was also supported by sustainable development goals. Point source pesticide contamination was not considered since those came from unpredictable events, like inappropriate handling, spillage etc. so their modeling in the literature is rare. Good thing is that all these choices have their references to back their claim. All reviews in related topics with this manuscript were explained with one sentence, and in a paragraph, the lack of the literature and novelty (and requirement) of this review was stressed.

Scale of the assessment

Temporal variability of the pesticide concentration in the surface water was connected to intermittent spraying and precipitation (storm in the text) events. Combining this fact with, probably a result of easier access to data, recent larger scale pesticide fate models; there emerged a need to measure the effect of spatial scale of the model on the temporal resolution of the pesticide concentration.

Edge-of-the-field named scale is just a local, farm, agricultural ditch, small pond like little areas, with an emphasize on EU procedures requiring data in this scale. As a limitation, this does not take into account the landscape features, and hydrology of the water bodies are limited. Some examples for general use are PRZM, MACRO, providing runoff and drainage loads of pesticides, and these are input to TOXSWA. For the rice special condition of paddy fields, MEDRICE, Tier I Rice Model and RICEWQ can be given.

Catchment Scale

Ditches, streams and rivers’ pesticide concentrations are sought after. Hydrology of the catchment is essential in these models. SWAT and its hydrological response units (HRU) are quite popular. SPIDER and SoilPlus are other examples.

Here the landscape information gets easier and easier each day to obtain, yet the application of the pesticide and other related information are basically very difficult to get, albeit it is quite effective on the outcome of the models.

The advantages of catchment-scale models are that they illustrate the critical source areas and can be used to predict where to remediate to reduce the pesticide load most.

Regional Scale

These models are reported to be mostly static as otherwise highly specific temporal data of pesticide application is necessary. Hydrology may or may not be considered, there are both kinds of regional models.

Continental/global scale

Static maps are provided in these models. Lack of spatially explicit pesticide use data is a problem. Excluding pollution prevention approaches like banning chemicals or educating; the mitigation solutions for pesticide problem is local scale; e.g. vegetated buffer strips, hedgerows, no-spray areas, drift reducing nozzles.

Wrapping Up

Authors suggest that firstly catchment scale models should be conducted to uncover which factors are more significant, then these factors distribution should be globally modeled. [Then again selections will be done and catchment scale models will be constructed for assessing mitigation practices].

In the end, besides the suggested modeling approach and its utilization by regulatory agencies, hydrology and landscape properties should also be included in edge-of-the-field or catchment sized models as well. This is supposed to enhance the accuracy of the environmental risk assessment. The review is a bit poor than what its title suggests, and there is no infographics or little images to present the ideas, albeit it is easy to grasp from the text. Table 1 is quite summarizing and well-prepared. In the end, a good article to grasp the pesticide modeling for its surface water fate/transport.


9 May 2019 (my reviewing date)

Ma, S., Zhou, Y., Gowda, P. H., Dong, J., Zhang, G., Kakani, V. G., ... & Jiang, W. (2019). Application of the water-related spectral reflectance indices: A review. Ecological Indicators, 98, 68-79.

keywords: satellite remote sensing, drought, soil water content, surface water body, vegetation water content, wetland 

1. Introduction

This chapter summarizes the overall significance of water and its detection, as well as the current confusion on the indices being used for water analysis purpose. The problem is that people don’t really understand the meaning of the indices they use and time to time they even mismatch their definition with one another.

2. Water-related spectral reflectance indices

2.1 section is educative, mostly Figure 2 is referenced in which different land use types spectra are compared with each other. It is easy to figure out that especially differentiating between two different thing, dry grass or wet grass, for instance, there are always one or two wavebands to rely on, and many ratios of wavebands. Section 2.2 summarily gave information on how water related indices developed through time.

3. Application of water-related spectral reflectance indices

4 categories were reviewed, detecting open water body, vegetation water, soil water, wetland. NDWI and similar indices and their historical development were explained, along with NDPI and other indices. In vegetation, certain indices were found to perform better than NDVI under some, not all circumstances. In soil water detection, mostly the relationship of surface temperature and vegetation cover under different moisture conditions were assessed (with warm and cold edges triangle). The last unit was wetland detection, in whichit both includes water, soil and vegetation along many other complexities. The main problem, according to me, in this part is that albeit some thresholds are considered for these indices, method to calculate these and their impact on the outcome were not elaborated.

4. Terminology of water-related spectral reflectance indices in specific application areas

This section gave two concise tables of same name different indices and different name but actually same or reversed indices. Everything was clearly stated and the information is given chronologically.

5. A field experiment on mix of different ratios of soil, surface water, and vegetation

In this part, the authors used a spectroradiometer and chose a completely bare soil and densely grass region. Then while fixing the sensor on this area with resultant radius of 9 cm, slowly moved a water cylinder to this point until the ground was covered completely by this cylinder. Afterthat, the flooding and other soil-water mixing ratios were calculated with all indices.

6. Discussion and summary

This chapter is more or less one-sentence summary of what were all explained beforehand.

Wrapping up

This is a very interesting review in that all vegetation and water indices were put and elaborated with their respective indices, and compared with each other. Additionally, albeit quite simple, authors set up an experimental setup to directly compare the water/soil/vegetation mixing reflectance and the efficiency of indices and their combinations to detect water content. This is an unusual thing, something one simply does not expect from a review article. Overall, especially the tables were very good and informative, and the review is quite neat.

7 June 2019 (my reviewing date)

Shaaban, M., Zwieten, L. V., Bashir, S., Younas, A., Núñez-Delgado, A., Chhajro, M. A., Kubar, K. A., Ali, U., Rana, M. S., Mehmood, M. A., Hu, R. (2018). A concise review of biochar application to agricultural soils to improve soil conditions and fight pollution. Journal of Environmental Management, 228 (2018), 429-440.

 keywords :  biochar, soil fertility, microbial function, metal contaminants


 Structure, composition and characteristics of biochar
 Using biochar in plant production
 Biochar for the reduction of pollutants bioavailability
 Use of biochar to manipulate soil biological processes
 Future perspective and research needs

 Abstract is somewhat blurry in directing the readers for what to expect from the study. Still, it is clear that biochar is also a material of our real world, not suitable for every case and time and place. At the same time, it has significant impact on bioavailability reduction of contaminants, diminishing soil N loss, storing C in soil for longer times, regulating pH etc.

 1-      Introduction

The first two paragraphs introduce the concept of biochar completely from the literature, a good start yet not with a good style, resembling bullet points coming after one another instead of a coherent and fluid paragraph structure. The last paragraph explains the reason of undertaking the act of writing this review, “direct/indirect impacts of biochar on soil properties & biogeochemical processes to improve remediation, enhancing soil function and crop productivity.”

 2-      Structure, composition and characteristics of biochar

This section starts with the composition of biochar, how it was determined through raw material and production route conditions, then continues with comparing it loosely with other organic soil amendments. Table 1and 2 summarizes the composition and production parts, (albeit Table 2 comes before 1, it is numbered as such). Figure 1 to illustrate the “mechanistic outline” of biochar impacts on soil is somewhat too crude, such as water holding confounds hydraulic conductivity and other things together with soil structure, aggregation, and this makes it difficult to see the actualy effect of biochar on soil properties even if there are numerous research articles over this subject. Additionally, although not seen from the title, last paragraph of the section was allocated to unwanted possible impacts of biochar on soil, giving references mostly on surface area and water capacity.

3-      Using biochar in plant production

Figure 2 in this chapter is another way to put what was presented in Figure 1, and again seriously lacking soil hydraulic properties and relevant stuff. Even though this seems to be a general case for the manuscript, Table 3 is quite useful, in that type of raw material, application rate, crop, soil, and resultant yield increase was presented with corresponding references.

The subtitles for this part is the following:

3.1- Influence on soil acidity constraints

3.2- Cation exchange capacity and anion exchange capacity

3.3- Nitrogen and N transformations

3.4- Influence on P availability

3.5- Micronutrients availability

The largest part given to the 3.3 nitrogen. In 3.1, effect of soil pH on the mobility of toxic metals and other components and how biochar can lime this pH was explained. The one problem is with passing time the biochar’s liming effect declines. In 3.2, even if the title is CEC and AEC, only CEC was discussed, as biochar was seemed to be in negative charged state and with high CEC, as in the case of actual soil organic matter. [However, this may not be the case, with higher temperature pyrolysis, or different defunctionalization processes the structure on the whole might be made similar more to aromatic compounds and less to the molecules with polar functional groups. ] 3.3 section is devoted to N retaining property of biochars, for instance, nitrate is reported to be adsorbed by aliphatic ether, aromatic carbonyl and hydroxyl groups. Yet these adsorption are not the only thing biochars do, they also influence and increase nitrification which may change the outcome of nitrate uptake. Still, also reporting that the impact of biochar is soil specific, it generally increases crop growth and yield acc. to recent literature. Another paragraph on this section summarizes the situation of lowering gaseous N loss, a.k.a. nitrous oxide loss. Biochar is expected to enhance nitrous oxide to dinitrogen transformation so that it reduce the latter, albeit not concretely stated. In addition to that, some researchers stated that with ammonia oxidizing bacteria, in many cases biochar can actually enhance the nitrous oxide loss. Retaining humidity and nitrate more simply invites this result. In conclusion, it is a matter of optimization or trade-off, or simply one needs to supress nitrification. The next part investigates another nutrient, phosphorus and biochar’s impact on its availability. Biochar simply reduces the formation of metal chelates and consequent non-bioavailable precipitates, thus increasing phosphorus uptake by plants. Many studies related to Zea Mays L. (maize) indicated increased yield. The last part of this 3. section is related to micronutrients availability. Here the discussion mostly went on ash content of biochar, so it is predictable even before application which micronutrient and how much support biochar will provide to the plants. Yet last paragraph also summarizes the negative impacts of biochar application in certain studies, not for the case of micronutrient discussion but just general comments.

 4-      Biochar for the reduction of pollutants bioavailability

Here, Table 4 is a massive table for pesticide/herbicide sorption studies with biochar additions to soils. Rate of application, pyrolysis T, type of raw material, pesticide/herbicide and the extent of adsorption increase, if present desorption studies and corresponding reference. Table 5 does same for heavy metals. This is what people look for when searching a review article, so it is one of the significant, strong point of this review. In the text part for organic pollutants, 4.1. , biochar’s porosity’s importance was stated. Another significant point, reduction in the herbicide efficacy was also discussed. 4.2 was related to inorganic contaminants and concerned only with heavy metals, the Table 5 also shows only heavy metals albeit the text inclue some references with As.

 5-      Use of biochar to manipulate soil biological processes

Outline of this section is the following:

5.1- Biological dinitrogen fixation

5.2- Microbial activity

                        5.2.1 Bacteria

                        5.2.2 Fungi

                        5.2.3 Earthworm

5.1 states that the properties counted in previous parts make biochar suitable to support nodule formation, i.e. biological N fixation in legumes. Yet, literature is poor and did not thoroughly discuss adverse effects and reasons of possible nodule preventing mechanisms after biochar addition. In 5.2, biochars mediation of the soil environment, especially holding nutrients, labile OM, water and reducing acidity makes the environment more suitable for bacteria. Also, high C:N ratio coming from high lignin content of raw material is quite significant. There is also one issue of increased virus transportation after biochar application, albeit with blurry details and lack of sufficient research statement at the end. The next section is for fungi. Similar to the 5.1, biochar was reported to be mostly beneficial for fungi growth, but not totally, and literature is poor in the latter. The last part of the section is related to earthworm. Appearantly, while ingesting biochars, the gut of earthworms mineralize and excrete nutrients better and consequently increase soil nutrient status, as long as they stay there. So co-application of geophagous (soil ingesting) earthworm is suggested. Some studies also reported decline in earthworm biomass and abundance, more mortaility and genotoxicity as negative biochar impacts, hypothesized from increasing pH and PAH, heavy metal sorption.

The conclusion is a delicate paraphrase of the summary of the research. In general, the review’s bibliographic potential is fantastic. I mostly care about this part, but it would be a lot more useful if more overall insights on why different soils require different biochars etc. were present in the manuscript. Nevertheless, it is a must-read article for the ones scanning the biochar literature or willing to utilize them for agricultural purposes.


15 July 2019 (my reviewing date)
Murray, N. J., Keith, D. A., Bland, L. M., Ferrari, R., Lyons, M. B., Lucas, R., Pettorelli, N., Nicholson, E. (2018). The role of satellite remote sensing in structured ecosystem risk assessments. Science of the Total Environment. 619-620 (2018). 249-257.

 risk assessment, biodiversity monitoring, ecosystem status, earth observation, satellite remote sensing, ecological indicators

The article is about the use of satellite remote sensing images on ecosystem models, how to integrate them to these models and 1)
 predicting responses of the ecosystems through satellite remote sensing (17 study reviewed), and 2) monitoring ecosystems and feed risk assessment with satellite remote sensing (21 study reviewed). The facts that satellite remote sensing data analysis' requirement to work interdisciplinary and too many choices to handle in remote sensing data were also stressed. 

Chapter 2: Spatial distribution of ecosystems

Areal change of the ecosystems has significant effects on the health of it, as smaller ones are more vulnerable against threats. Remote sensing can efficiently generate time series maps yet this is a specialist task. It is especially difficult for developing countries to acquire and utilize required infrastructure and skills, yet Google Earth Engine and such romeve this and similar barriers by providing archives free for all. It is also important to utilize different analytical methods, and construct "virtual satellites", as well as even make use of other available data such as topographic maps and aerial photographs.

Chapter 3:
 Ecosystem processes and function

The first catch here is what to monitor is and will be different in different regions, and should carefully be selected, such also recommended by IUCN Red List of Ecosystems. Error introduction from this process can include result of variation in data processing streams, beginning and end point of the time series, remote sensing data biases, varying extent of change in the environment, and natural fluctuations. To select the variable of interests, Conceptual Models were suggested to be very suitable as they show the interrelationships between separate components of the environment. 

Chapter 4: Threatening processes

In this relatively short chapter, the potential of remote sensing data with its capability of illustrating location of threats as well as time series of it was presented. The general difficulties in the quantification of ecosystem threats are 1) lack of suitable data, 2) insufficient understanding of how ecosystem processes are affected by the threats, 3) subjective judgments about threats, and 4) cumulative / synergistic impacts of threats.

Chapter 5:
 Integrating remote sensing into ecosystem models
Two main examples for this integration are the following.

* Model parameterisation, initiation or validation by remote sensing data, eReefs model example, SST like data estimation from satellites.
* SimAmazonia, historical maps to assess deforestation

Nevertheless, the critical parts of this review, as what I actually expect from them, are the summary tables for reviewing the literature, here Table 1 and 2. In table 1, one can directly see the ecosystem of interest, such as coral reef, and what has been done using both remote sensing (such as sea surface temperature) and eosystem collapse identification (bleaching).
The second table is even more detailed, with ecosystem type, main pressures, collapse risk symptoms and potential remote sensing indicators as columns.

They also gave full references as another Table 1 and 2 in appendix part, which I have yet understood the reason, since right below there is References chapter already. Nevertheless, both Table 1 and 2 in main text are impressive enough to overlook this redundancy. The figures are also informative on the content but still shadowed under the Table's informative state. 


23 November 2019 (my reviewing date)

Siad, M. S., Iacobellis, V., Zdruli, P., Gioia, A., Stavi, I., Hoogenboom, G. (2019). A review of coupled hydrologic and crop growth models. Agricultural Water Management, 224 (2019), 105746.

 keywords :  coupling tools, crop models, hydrologic models, integrated modeling, modeling frameworks


 Introduction – which the authors introduce the necessity of coupling hydrologic and climate models and why the relevant people would like to have its results.

 Concepts and notions – in this part there is a separate sub-section for both hydrologic modeling and crop growth modeling. Then, how both type of modeling complements each other was briefly explained in section 2.3. 2.4 illustrates coupling procedure with 6 different ways. These are: 1 sequential coupling where both type of models are separately run; loose coupling where there is an input/output Exchange between these again separate engines; shared coupling with shared GUI or input/output database; embedded coupling in which one model completely contains the other; integrated modeling where these models are coded together in a way that only one resultant merged model is present; framework coupling where apart from the other 5 types, models are coupled with a third party tool. 2.5 gives information about open and closed source models. Section 2.6 is related to challenges of model coupling. “Interoperability” term is a keyword here; where it basically restricts only the coupling of models where they can work on spatially and temporally same scale and share information with each other successfully and satisfactorily.

 Overview of coupled hydrologic and crop growth models – This is the section where one wants to look at after seeing the title of the article, and related section is the land-scape view Table 1. There are example of coupled models from 2000 to 2017. The curious thing is there is no example of MODFLOW, farm process module, or even HYDRUS as a sole integrated model with embedded crop growth model (albeit there are coupled examples with HYDRUS and EPIC, DSSAT or PS123). It is also discussed that with better description of crop/vegetation Dynamics through coupling, energy, ET, carbondioxide, pollutant and water flux can be more accurately computed.

 General discussion and implications – This is the discussion/summary chapter. The issue of donwscaling or upscaling of the input data for scale equalization were revisited. The success of crop modeling integration also said to be dependent on the extent of cropping practice in the corresponding hydrologically modeled area, the more the better.

 Conclusions – After summing up, the authors concluded that current coupling mostly is interested in crop performance increase and environmental impact assessment. According to them, the hydrologic system of interest’s resilience to the agricultural activities should be considered more.


Üniversiteler Mah. Dumlupınar Blv. ODTÜ İnşaat Mühendisliği K4 - 119 / Çankaya, ANKARA
+905070252333 Whatsapp/Telegram