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Electron Transport Chains

An electron transport chain, or ETC,is composedof a group of protein complexes in and around a membrane that help energetically couple a series of exergonic/spontaneous red/ox reactions to the endergonic pumping of protons across the membrane to generate an electrochemical gradient. This electrochemical gradient creates a free energy potential that we call a proton motive force whose energetically "downhill"exergonic flow can laterbe coupledto a variety of cellular processes.

ETC overview

Step 1: Electrons enter the ETC from an electron donor, such as NADH or FADH2, whichare generatedduring a variety of catabolic reactions, including those associated glucose oxidation. Depending on the number and types of electron carriers of the ETC being used by an organism, electrons can enter at a variety of places in the electron transport chain. Entry of electrons at a specific "spot" in the ETC depends upon the respective reduction potentials of the electron donors and acceptors.


Step 2: After the first red/ox reaction, the initial electron donor will become oxidized and the electron acceptor will become reduced. The difference in red/oxpotential between the electron acceptor and donoris relatedto ΔG by the relationship ΔG = -nFΔE, wheren= the number of electrons transferred and F = Faraday's constant. The larger a positive ΔE, the more exergonic the red/ox reaction is.


Step 3:If sufficient energy is transferredduring an exergonic red/oxstep, the electron carrier may couple this negative change in free energy to the endergonic process of transporting a proton from one side of the membrane to the other.


Step 4: After usually multiple red/ox transfers,the electron is deliveredto a molecule known as the terminal electron acceptor. With humans, the terminal electron acceptor is oxygen. However, there are many, many, many otherpossibleelectron acceptors in nature; see below.

Note:possiblediscussion

Electrons entering the ETC do not have to come from NADH or FADH2. Many other compounds can serve as electron donors; the only requirements are (1) that there is an enzyme that can oxidize the electron donor and then reduce another compound, and (2) that the ∆E0' is positive (e.g., ΔG<0). Even a small amount of free energy transfers can add up. For example, there are bacteria that use H2 as an electron donor. This is not too difficult to believe because the half reaction 2H+ + 2e-/H2 has a reduction potential (E0') of -0.42 V. If these electronsare eventually deliveredto oxygen, then the ΔE0' of the reaction is 1.24 V, which corresponds to a large negative ΔG (-ΔG). Alternatively, there are some bacteria that can oxidize iron, Fe2+ at pH 7 to Fe3+ with a reduction potential (E0') of + 0.2 V. These bacteria use oxygen as their terminal electron acceptor, and, in this case, the ΔE0' of the reaction is approximately 0.62 V. This still produces a -ΔG. The bottom line is that, depending on the electron donor and acceptor that the organism uses, a little or a lot of energy canbe transferredand used by the cell per electrons donated to the electron transport chain.

What are the complexes of the ETC?

ETCs comprise a series (at least one) of membrane-associated red/ox proteins or (some are integral) protein complexes (complex =more thanone protein arranged in a quaternary structure) that move electrons from a donor source, such as NADH, to a final terminal electron acceptor, such as oxygen. This specific donor/terminal acceptor pair is the primary one used in human mitochondria. Each electron transfer in the ETC requires a reduced substrate as an electron donor and an oxidized substrate as the electron acceptor. In most cases, the electron acceptor is a member of the enzyme complex itself. Once the complexis reduced, the complex can serve as an electron donor for the next reaction.

How do ETC complexes transfer electrons?

As previously mentioned,the ETC is composedof a series of protein complexes that undergo a series of linked red/ox reactions. These complexes are in fact multi-protein enzyme complexes referred to as oxidoreductases orsimply,reductases. The one exception to this naming convention is the terminal complex in aerobic respiration that uses molecular oxygen as the terminal electron acceptor. That enzyme complexis referredto as an oxidase. Red/ox reactions in these complexesare typically carriedout by a non-protein moiety called a prosthetic group.The prosthetic groups are directly involvedin the red/ox reactions beingcatalyzedby their associated oxidoreductases.In general, theseprosthetic groups can be divided into two general types: those that carry both electrons and protons and those that only carry electrons.

Note

This use of prosthetic groups by members of ETC is true forall of theelectron carrierswith the exception ofquinones, which are a class of lipidsthat can directly be reduced or oxidized by theoxidoreductases. Both the Quinone(red) and the Quinone(ox) forms of these lipids are soluble within the membrane and can move from complex to complex to shuttle electrons.

The electron and proton carriers

  • Flavoproteins (Fp), these proteins contain an organic prosthetic group called a flavin, which is the actual moiety that undergoes the oxidation/reduction reaction. FADH2 is an example ofan Fp.
  • Quinones are a family of lipids, which means they are soluble within the membrane.
  • We also note thatwe consider NADH and NADPHelectron (2e-) and proton (2 H+) carriers.

Electron carriers

  • Cytochromes are proteins that contain a heme prosthetic group. The heme can carry a single electron.
  • Iron-Sulfur proteins contain a nonheme iron-sulfur cluster that can carry an electron. We often abbreviate the prosthetic group as Fe-S

Aerobic versus anaerobic respiration

We humans use oxygen as the terminal electron acceptor for the ETCs in our cells. This is also the case for many of the organisms we intentionally and frequently interact with (e.g. our classmates, pets, food animals, etc). We breathe in oxygen; Our cells take it up and transport it into the mitochondria, where it becomes the final acceptor of electrons from our electron transport chains. We call the process where oxygenisthe terminal electron acceptor aerobic respiration.

While we may use oxygen as the terminal electron acceptor for our respiratory chains, this is not the only mode of respiration on the planet. The more general processes of respiration evolved when oxygen was not a major component of the atmosphere. As a result, many organisms can use a variety of compounds, including nitrate (NO3-), nitrite (NO2-), even iron (Fe3+) as terminal electron acceptors. When oxygen is NOT the terminal electron acceptor, we refer the process to as anaerobic respiration. Therefore, respiration or oxidative phosphorylation does not require oxygen at all; It requires a compound with a high enough reduction potential to act as a terminal electron acceptor, accepting electrons from one complex within the ETC.

The ability of some organisms to vary their terminal electron acceptor provides metabolic flexibility and can ensure better survival if any given terminal acceptor is in limited supply. Think about this: in the absence of oxygen, we die; but other organisms can use a different terminal electron acceptor when conditions change to survive.

A generic example: A simple, two-complex ETC

The figure below depicts a generic electron transportchain,composed of two integral membrane complexes; Complex I(ox) and Complex II(ox). A reduced electron donor, designated DH (such as NADH or FADH2) reduces Complex I(ox), giving rise to the oxidized form D (such as NAD+ or FAD+). Simultaneously, a prosthetic group within ComplexI is now reduced(accepts the electrons). In this example, the red/ox reaction is exergonic and the free energy differenceis coupledby the enzymes in Complex I to the endergonic translocation of a proton from one side of the membrane to the other. The net result is that one surface of the membrane becomes more negatively charged, because of an excess of hydroxyl ions (OH-), and the other side becomes positively charged because of an increase in protons on the other side. Complex I(red) can now reduce a mobile electron carrier Q, which will then move through the membrane and transfer the electron(s) to the prosthetic group of Complex II(red). Electrons pass from Complex I to Q then from Q to Complex II via thermodynamically spontaneous red/ox reactions, regenerating Complex I(ox), which can repeat the previous process. Complex II(red) then reduces A, the terminal electron acceptor to regenerate Complex II(ox) and create the reduced form of the terminal electron acceptor, AH. In this specific example, Complex II can also translocate a proton during the process. If A is molecular oxygen, AH represents water and the process wouldbe consideredbeing a model of an aerobic ETC. If A is nitrate, NO3-, then AH represents NO2- (nitrite) and this would be an example of an anaerobic ETC.

Figure 1. Generic 2 complex electron transport chain. In the figure, DH is the electron donor (donor reduced), and D is the donor oxidized.Ais the oxidized terminal electron acceptor, and AH is the final product, the reduced form of the acceptor. AsDH is oxidizedto D, protonsaretranslocatedacross the membrane, leaving an excess of hydroxyl ions (negatively charged) on one side of the membrane and protons (positively charged) on the other side of the membrane. The same reaction occurs in Complex II asthe terminal electron acceptor is reducedto AH.

Attribution:Marc T. Facciotti (original work)

Exercise 1

Thought question

Based on the figure above, use an electron tower to figure out the difference in the electrical potential if (a) DH is NADH and A is O2, and (b) DH is NADH and A is NO3-. Which pairs of electron donor and terminal electron acceptor (a) or (b) "extract" the greatest amount of free energy?

Detailed look at aerobic respiration

The eukaryotic mitochondria have evolved a very efficient ETC. There are four complexes composed of proteins, labeled IthroughIV depicted in the figure below. The aggregation of these four complexes, together with associated mobile, accessory electron carriers,is calledan electron transport chain. This electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes.

Figure 2. The electron transport chain is a series of electron transporters embedded in the inner mitochondrial membrane that shuttles electrons from NADH and FADH2 to molecular oxygen.In the process, protonsare pumpedfrom the mitochondrial matrix to theintermembranespace, andoxygen is reducedto form water.

Complex I

To start, NADH delivers two electrons to the first protein complex. This complex, labeled I in Figure 2, includes flavin mononucleotide (FMN) and iron-sulfur (Fe-S)-containing proteins. FMN, which is derived from vitamin B2, also called riboflavin, is one of several prosthetic groups or cofactors in the electron transport chain. Prosthetic groups are organic or inorganic, nonpeptide molecules bound to a protein that facilitate its function; prosthetic groups include coenzymes, which are the prosthetic groups of enzymes. We also call the enzyme in Complex I NADH dehydrogenase. This protein complex contains 45 individual polypeptide chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space helping to generate and maintain a hydrogen ion gradient between the two compartments separated by the inner mitochondrial membrane.

Q and Complex II

Complex II directly receives FADH2, which does not pass through Complex I. The compound connecting the first and second complexes to the third is ubiquinone (Q). The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once reduced, (QH2), ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from Complex I and the electrons derived from FADH2 from Complex II, succinate dehydrogenase. Since these electrons bypass and thus do not energize the proton pump in the first complex, fewer ATP moleculesare madefrom the FADH2 electrons. As we will see in the following section, the number of ATP molecules ultimatelyobtainedis directly proportional to the number of protons pumped across the inner mitochondrial membrane.

Complex III

The third complex is composed of cytochrome b, another Fe-S protein, Rieske center (2Fe-2S center), and cytochrome c proteins; we also call this complex cytochrome oxidoreductase. Cytochrome proteins have a prosthetic group of heme. The heme molecule is like the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe2+ (reduced) and Fe3+ (oxidized). The heme molecules in the cytochromes have slightly different characteristics because of the effects of the different proteins binding them, giving slightly different characteristics to each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes (cytochrome c is the acceptor of electrons from Q; however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time).

Complex IV

The fourth complex is composedof cytochrome proteinsc,a,and a3. This complex contains two heme groups (one in each of the two Cytochromes,a,and a3) and three copper ions (a pair ofCuAand one CuB in Cytochrome a3). The cytochromes hold an oxygen molecule tightly between the iron and copper ions until it completely reduces the oxygen. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water (H2O). The removal of the hydrogen ions from the system contributes to the ion gradient used in the process ofchemiosmosis.

Chemiosmosis

In chemiosmosis, the free energy from the series of red/ox reactions just described is used to pump protons across the membrane. The uneven distribution of H+ ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the proton's positive charge and their aggregation on one side of the membrane.

If the membrane were open to diffusion by protons, the ions wouldtend todiffuse back across into the matrix, driven by their electrochemical gradient. Ions, however, cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, protons in theintermembranespace can only traverse the inner mitochondrial membrane through an integral membrane protein called ATP synthase (depicted below). This complex protein acts as a tiny generator, turned by transfer of energy mediated by protons moving down their electrochemical gradient. The movement of this molecular machine (enzyme) serves to lower the activation energy of reaction and couples the exergonic transfer of energy associated with the movement of protons down their electrochemical gradient to the endergonic addition of a phosphate to ADP, forming ATP.

Figure3. ATP synthase is acomplex,molecular machine that uses a proton (H+) gradient to form ATP from ADP and inorganic phosphate (Pi).

Credit:modificationof work by Klaus Hoffmeier

Note:possiblediscussion

Dinitrophenol (DNP) is a small chemical that serves to uncouple the flow of protons across the inner mitochondrial membrane to the ATP synthase, and thus the synthesis of ATP. DNP makes the membrane leaky to protons. People used it until 1938 as a weight-loss drug. What effect would you expect DNP to have on the difference in pH across both sides of the inner mitochondrial membrane? Why do you think this might be an effective weight-loss drug? Why might it be dangerous?

In healthy cells,chemiosmosis(depicted below) is used to generate 90 percent of the ATP made during aerobic glucose catabolism; it is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. Recall that the production of ATP using the process ofchemiosmosisin mitochondriais calledoxidative phosphorylation and that a similar process can occur in the membranes of bacterial and archaeal cells. The overall result of these reactions is the production of ATP from the energy of the electrons removed originally from a reduced organic molecule like glucose. In the aerobic example, these electrons ultimately reduce oxygen and create water.

Figure 4. In oxidative phosphorylation,the pH gradient formed by the electron transport chain is used by ATPsynthaseto form ATP in a Gram-bacteria.

Helpful link: How ATP is madefrom ATP synthase

Note:possiblediscussion

Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of theintermembranespace to increase or decrease? What effect would cyanide have on ATP synthesis?


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Fifty years of SBB: The most cited articles for each year

This Virtual Special Issue collates the 51 most cited research/review articles for each of the 50 years of the existence of Soil Biology & Biochemistry (1969-2019), according to the number of citations made on 31 December 2020, as recorded by Scopus. This census date – one year after the 50 th anniversary - was chosen since it allowed 12 months-worth of citations to papers published in 2019 to be accrued, and for this exercise to be completed within the first months of 2021, thus within reasonable time of the “Golden Anniversary” year of SBB. Over the first half-century of its existence, SBB published some 10,059 research papers, 162 review articles and 160 other pieces.

Research involving the (micro)biology and biochemistry of soils over this period includes the initial years of arguably the true development of the discipline, leading to the research boom arising in the 1990s and to the emergence of molecular techniques that supported an exponential increase in the number of papers published - and arguably a commensurate increase in the understanding of the biological basis of soil functioning.

  • Timeline of key topics covered by most-cited papers for each year in SBB 1969-2019, ranked according to frequency of coverage, then alphabetically. Yellow zones brace the overall range of years covered.

Topics which have received greatest coverage in the most cited papers are those devoted to methodology, microbial biomass and C dynamics, with those involving enzymes and N dynamics also being notably frequent. The methodology papers had their heyday 1969-1997, with none since then. Enzymology has the greatest longevity as a topic, with sporadic appearance from 1969-2017, and C dynamics a wide span from 1974-2016, with regular occurrences throughout this period. Singular instances of topics have been more frequent since 2014.

  • Wordcloud of all keywords used in titles of most-cited paper for each year in SBB 1969-2019. Size of word reflects frequency of use over this period.

Given the scope of the journal, it is unsurprising that ‘soil’ and ‘microbial’ are the dominant keywords. ‘Biomass’ reflects the dominant role that this concept has played in the history of the journal, whilst ‘enzyme’ is also frequent, as reflected in the topic timeline. Likewise for ‘method’ and ‘measure’, which are fundamental to effective study of soil systems. There is then a very wide range of less frequent terms, which reflect the diversity of the topics covered by the most-cited papers. Among these less frequent terms, it is remarkable that relatively little attention has been paid to meta-analysis studies, despite the fact that numerous such studies have been published, especially in the last decade and considering their quasi-review nature. It is also noteworthy that little attention has been paid to methods using genetic tools for the analysis of soil microbial communities, whose development has been exponential in the last two decades and which have been incorporated as routine research tools in many soil microbiology laboratories. This can be justified because many of these methods have been published preferentially in journals with a more applied focus on soil microbiology.

The ranking of the most cited articles in each of the 50 years of SBB history (List 1) does not always coincide with the list when ranked by number of citations regardless of year of publication (List 2), and although the same article appears in the same position on both lists occasionally (especially during the early years), this does not always occur. Nevertheless, the eight most cited articles throughout the history of the journal coincide with the articles most cited in the year of publication and ranked from 1 to 8 according to the number of citations. The most cited article in the 50-year history of Soil Biology & Biochemistry is the demonstrably seminal “An extraction method for measuring soil microbial biomass” by Vance, Brookes and Jenkinson (1987) which had been cited 7179 times on the census date and which, unsurprisingly, was also the most cited article in the corresponding year of publication (1987).

Only the top fifteen of the most cited articles every year had more than 1000 citations (range 1001-7179).

The number of citations made of the most cited articles in each year of publication is very variable, ranging between 7179 (Vance et al., 1987) to 44 (Kuzyakov and Razavi, 2019). Of course, the number of citations that an article received in the first two or three years after publication is generally very low, and high numbers are usually only reached after at least five years. However, there are some exceptions to this general rule such as the article by Bünemann et al., published in 2018, which in only two years has 332 citations (ranked 41), likely because this is a review article and this form of publication tends to be cited more frequently than research articles, in the short-term at least. That said, only twelve of the 50 articles included in this compilation are review articles. Fourteen of the 51 most cited papers in the year of publication are methodological papers, six of which are ranked within the top ten according to the number of citations (ranging from 1623 to 7176). Five of the six articles concern methods of measuring microbial biomass, published between the 1970s and 1990s (Vance et al., 1987 Brookes et al., 1982, 1985 Anderson and Domsch, 1978 Jenkinson and Powlson, 1976 and Wu et al., 1990). The other article involves the measurement of enzyme activity (phosphomonoesterase) and was published in the first year of the existence of the journal (Tabatabai and Bremner, 1969). Two of the other 4 articles within the top ten are review papers, one concerning how biochar application affects soil biota, published relatively recently (Lehmann et al., 2011) and one on the toxicity of methods of measuring microorganisms and soil microbial processes (Giller et al., 1998). The final article in the top ten (Kirschbaum, 1995) is not strictly a review paper, but closely resembles one, as the author used data from previously published papers to analyse the temperature sensitivity of organic matter decomposition processes and the implications for global climate.

Among the top 15 papers there are two other reviews. The first of these, published by Wrage et al. (2001) and ranked 11th, revises the knowledge at that time about nitrifier denitrification, aiming to “give an exact definition, spread awareness of its pathway and controlling factors and to identify areas of research needed to improve global N2O budgets”. The second review (ranked 12th) was published by Kögel-Knabner in 2002, and provides an overview of the amount of litter input, the proportion of various parts of plants and their below- and above-ground distribution, as well as the different proportion of plant tissues acting as parent material for the formation of soil organic matter. Particular emphasis is placed on the chemical composition of the organic matter parent materials, aiming to provide information to help identify the changes that occur during biodegradation of plant litter in soils.

In the aforementioned most cited article of those published in the 50-year history of SBB (Vance et al., 1987), the authors showed that the amount of C released after fumigation of soil with chloroform and direct extraction is related to microbial biomass C measured by the fumigation-incubation method as originally described by Jenkinson and Powlson (1976) and by the modified fumigation-incubation method for use in acid soils published by Vance et al., in SBB in 1987. Jenkinson and Powlson, (1976) was also the most cited article of those published in SBB in the year of publication (1819 citations). In addition, by examining the relationship between organic C extracted after fumigation and biomass N and ATP, Jenkinson and Powlson also showed that ATP and the C released by chloroform were derived from the same microbial biomass, indicating that the fumigation-extraction method was suitable for measuring soil microbial biomass. The method has since become the most commonly-used way of measuring this important soil component in laboratories worldwide.

Amongst the most cited articles in the year of publication, five others concerning the development or improvement of methods related to soil microbial biomass were all published between 1978 and 1990. During these years there was an increased interest in the role of soil microorganisms in organic matter decomposition and in nutrient cycling, in natural forest and grasslands as well as agricultural land. Methods of measuring P and N in microbial biomass (Brookes et al., 1982 1985), or in which some aspect of the microbial biomass measurement was modified or improved (Anderson and Domsch, 1978 Voroney and Paul, 1984 Wu et al., 1990), were rapidly adopted by laboratories worldwide, and therefore the number of citations also increased rapidly. Except for the studies by Anderson and Domsch and those by Voroney and Paul, carried out respectively in Germany (Institut für Bodenbiologie, Braunschweig), Canada (University of Saskatchewan) and the US (University of California Berkeley), all of the other studies were conducted at Rothamsted Experimental Station (UK). For example, David Jenkinson used 14 C-labelling to investigate plant decomposition and the findings led to several major developments, including the technique for measuring the quantity of carbon held in the cells of living microorganisms in soil. Treating soil microorganisms as a single entity (which Jenkinson referred to as the "soil microbial biomass"), rather than using classical microbiological techniques to identify and count the different species, was a revolutionary step and paved the way for a new wave of research on soil biological processes. First with David Powlson and then with Phil Brookes, David Jenkinson developed new concepts regarding the functioning and survival of soil microbes, and the above-mentioned most cited articles published in SBB report some of these studies. In addition to these articles, the most cited article published in SBB in 1997 (Beck et al., 1997) also concerns methods of determining microbial biomass. The latter was a comparative study of ten different versions of three methods of measuring the C associated with microbial biomass used in different institutions in Germany (fumigation-incubation, fumigation-extraction and substrate induced respiration). The authors found that the ten procedures used to determine the microbial biomass C content of the study soils yielded very similar results however, they also found that comparison of the data obtained by the different methods used in the different laboratories was hampered by various factors (e.g. soil-to-soil variation between the methods and by systematic effects on the biomass measurements that led to over- or under-estimation of values).

In addition to methods of determining the C, N and P associated with microbial biomass, the other methodological articles concern the determination of diverse enzyme activities, a topic that aroused great interest at the end of the 1970s. This interest was maintained until the 1990s, when new molecular techniques relegated the previous methods to second place. Three of these five articles on enzyme measurement were written by the research group led by Professor Tabatabai, at Iowa State University, USA. This group was very active for several years and developed many of the currently available assays for measuring enzyme activity. Most of these assays are based on colorimetric measurement of the p-nitrophenol released by the action of the corresponding enzyme. The first of these articles (Tabatabai and Bremner, 1969), which reports the use of p-nitrophenyl phosphate to measure phosphomonoesterase activity, was published in the first volume of SBB, and is ranked number 3 of the most cited articles published in the history of SBB. In the other two articles included in this compilation (Eivazi and Tabatabai, 1977 1988), the authors describe methods for determining phosphatases other than phosphomonoesterase (1977) and for determining glucosidases and galactosidases (1988). Another paper dedicated to methods of measuring enzyme activities is that by Ladd and Butler (1972), who described methods of determining proteases and dipeptidases in soil. Finally, amongst the methodological papers, rank 48 is an article that describes a rapid procedure for evaluating dehydrogenase activity in soils of low organic matter status (Klein et al., 1971). The methods of determining phosphatases, glucosidases and galactosidases and proteases were adopted in many enzymology laboratories worldwide, at least until the publication of methods that enable the simultaneous quantification of various enzymes in microplates and using fluorogenic substrates that release 4-methylumbelliferone (MUF) or 7-amino-4-methyl coumarin (7-AMC) (Freeman et al., 1995 Marx et al., 2001 – an SBB paper that is not in these ranked lists). Use of these later methods has increased progressively since they were first published.

As already indicated, the remaining articles cover a wide variety of topics reflecting the broad range of issues that have interested scientists working in the field of soil biology and soil biochemistry over the 50-year history of the journal. In general, however, these are topics that have not maintained a persistent level of interest over the years.

Finally, it is notable that the authors of nine of the most cited papers on the year of their publication included in this compilation have been invited to form part of the Soil Biology & Biochemistry Citation Classics series, edited by Richard Burns, and launched in 2004 for papers that “have made a difference” on the basis of the number of citations that the paper has received and assuming that this means that the findings reported in the paper have helped to initiate and interpret subsequent research. Sixteen Citation Classics have been published from 2004-2018 (Citation Classics I-XVI) and each was based on one or more SBB articles. These are marked with a CC abbreviation in the lists below.

The ten articles from this compilation included in the Citation Classics series are: Brookes et al. (1982, 1985) and Vance et al. (1987) in Citation Classics I (Measuring soil microbial biomass) Kirschbaum (1995) in Citation Classics IV (The temperature dependence of organic-matter decomposition—still a topic of debate) and V (Relationships between soil respiration and soil moisture) Giller et al. (1998) in Citation Classics VI (Heavy metals and soil microbes) Anderson and Domsch (1989) in Citation Classics VIII (Soil microbial biomass: The eco-physiological approach) Wu et al. (1990) in citation Classics IX (Measuring soil microbial biomass using an automated procedure) Frostegård et al. (1993) in Citation Classics X (Use and misuse of PLFA measurements in soils) Six et al. (2000) in Citation Classics XII (Aggregate-associated soil organic matter as an ecosystem property and a measurement tool) Kögel-Knabner (2002) in Citation Classics XIV (The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter: Fourteen years on) and Wrage et al. (2001) in Citation Classics XVI (The role of nitrifier denitrification in the production of nitrous oxide revisited).

Burns R.G. 2016. Soil Biology & Biochemistry Citation Classics I-XIII (2004-2015). Soil Biology & Biochemistry 100, 276-277.

Freeman C., Liska G., Ostle N.J., Jones S.E., Lock M.A. 1995. The use of fluorogenic substrates for measuring enzyme activity in peatlands. Plant and Soil 175, 147-152.

Marx M.-C., Woods M. Jarvis S.C. 2001. A microplate fluorimetric assay for the study of enzyme diversity in soils. Soil Biology & Biochemistry 33, 1633-1640.

List 1: Most cited articles for each year

[Census date 31 Dec 2020] CC denotes ‘Citation Classic’

Tabatabai, M.A., Bremner, J.M. 1969. Use of p-nitrophenyl phosphate for assay of soil phosphatase activity. Soil Biology & Biochemistry 1(4), pp. 301-307. https://doi.org/10.1016/0038-0717(69)90012-1 Cited: 2314.

Kaufman, D.D., Blake, J. 1970. Degradation of atrazine by soil fungi. Soil Biology and Biochemistry 2(2), pp. 73-80. https://doi.org/10.1016/0038-0717(70)90010-6 Cited: 107.

Klein, D.A., Loh, T.C., Goulding, R.L. 1971. A rapid procedure to evaluate the dehydrogenase activity of soils low in organic matter. Soil Biology & Biochemistry 3(4), pp. 385-387. https://doi.org/10.1016/0038-0717(71)90049-6 Cited: 156.

Ladd, J.N., Butler, J.H.A. 1972. Short-term assays of soil proteolytic enzyme activities using proteins and dipeptide derivatives as substrates. Soil Biology & Biochemistry 4(1), pp. 19-30. https://doi.org/10.1016/0038-0717(72)90038-7 Cited: 697.

Hardy, R.W.F., Burns, R.C., Holsten, R.D. 1973. Applications of the acetylene-ethylene assay for measurement of nitrogen fixation. Soil Biology & Biochemistry 5(1), pp. 47-81. https://doi.org/10.1016/0038-0717(73)90093-X Cited: 673.

Sørensen, L.H. 1974. Rate of decomposition of organic matter in soil as influenced by repeated air drying-rewetting and repeated additions of organic material. Soil Biology & Biochemistry 6(5), pp. 287-292. https://doi.org/10.1016/0038-0717(74)90032-7 Cited: 209.

Burford, J.R., Bremner, J.M. 1975. Relationships between the denitrification capacities of soils and total, water-soluble and readily decomposable soil organic matter. Soil Biology & Biochemistry 7(6), pp. 389-394. https://doi.org/10.1016/0038-0717(75)90055-3 Cited: 552.

Jenkinson, D.S., Powlson, D.S. 1976. The effects of biocidal treatments on metabolism in soil-V. A method for measuring soil biomass. Soil Biology & Biochemistry 8(3), pp. 209-213. https://doi.org/10.1016/0038-0717(76)90005-5 Cited: 1834.

Eivazi, F., Tabatabai, M.A. 1977. Phosphatases in soils. Soil Biology & Biochemistry 9(3), pp. 167-172. https://doi.org/10.1016/0038-0717(77)90070-0 Cited: 688.

Anderson, J.P.E., Domsch, K.H. 1978. A physiological method for the quantitative measurement of microbial biomass in soils. Soil Biology & Biochemistry 10(3), pp. 215-221. https://doi.org/10.1016/0038-0717(78)90099-8 Cited: 2274.

Smith, M.S., Tiedje, J.M. 1979. Phases of denitrification following oxygen depletion in soil. Soil Biology & Biochemistry 11(3), pp. 261-267. https://doi.org/10.1016/0038-0717(79)90071-3 Cited 504.

Lynch, J.M., Panting, L.M. 1980. Cultivation and the soil biomass. Soil Biology & Biochemistry 12(1), pp. 29-33. https://doi.org/10.1016/0038-0717(80)90099-1 Cited: 199.

Ladd, J.N., Oades, J.M., Amato, M. 1981. Microbial biomass formed from 14 C, 15 N-labelled plant material decomposing in soils in the field. Soil Biology & Biochemistry 13(2), pp. 119-126. https://doi.org/10.1016/0038-0717(81)90007-9 Cited: 178.

Brookes, P.C., Powlson, D.S., Jenkinson, D.S. 1982. Measurement of microbial biomass phosphorus in soil. Soil Biology & Biochemistry 14(4), pp. 319-329. https://doi.org/10.1016/0038-0717(82)90001-3 Cited: 887.

Orchard, V.A., Cook, F.J. 1983. Relationship between soil respiration and soil moisture. Soil Biology & Biochemistry 15(4), pp. 447-453. https://doi.org/10.1016/0038-0717(83)90010-X Cited: 559.

Voroney, R.P., Paul, E.A. 1984. Determination of kC and kN in situ for calibration of the chloroform fumigation-incubation method. Soil Biology & Biochemistry 16(1), pp. 9-14. https://doi.org/10.1016/0038-0717(84)90117-2 Cited: 420.

Brookes, P.C., Landman, A., Pruden, G., Jenkinson, D.S. 1985. Chloroform fumigation and the release of soil nitrogen: A rapid direct extraction method to measure microbial biomass nitrogen in soil. Soil Biology & Biochemistry 17(6), pp. 837-842. https://doi.org/10.1016/0038-0717(85)90144-0 Cited: 3296.

Keith, H., Oades, J.M., Martin, J.K. 1986. Input of carbon to soil from wheat plants. Soil Biology & Biochemistry 18(4), pp. 445-449. https://doi.org/10.1016/0038-0717(86)90051-9 Cited: 205.

Vance, E.D., Brookes, P.C., Jenkinson, D.S. 1987. An extraction method for measuring soil microbial biomass C. Soil Biology & Biochemistry 19(6), pp. 703-707. https://doi.org/10.1016/0038-0717(87)90052-6 Cited: 7179.

Eivazi, F., Tabatabai, M.A. 1988. Glucosidases and galactosidases in soils. Soil Biology & Biochemistry 20(5), pp. 601-606. https://doi.org/10.1016/0038-0717(88)90141-1 Cited: 713.

Anderson, T.-H., Domsch, K.H. 1989. Ratios of microbial biomass carbon to total organic carbon in arable soils. Soil Biology & Biochemistry 21(4), pp. 471-479. https://doi.org/10.1016/0038-0717(89)90117-X Cited: 962.

Wu, J., Joergensen, R.G., Pommerening, B., Chaussod, R., Brookes, P.C. 1990. Measurement of soil microbial biomass C by fumigation-extraction-an automated procedure. Soil Biology & Biochemistry 22(8), pp. 1167-1169. https://doi.org/10.1016/0038-0717(90)90046-3 Cited: 1634.

Palm, C.A., Sanchez, P.A. 1991. Nitrogen release from the leaves of some tropical legumes as affected by their lignin and polyphenolic contents. Soil Biology & Biochemistry 23(1), pp. 83-88. https://doi.org/10.1016/0038-0717(91)90166-H Cited: 496.

Tian, G., Kang, B.T., Brussaard, L. 1992. Biological effects of plant residues with contrasting chemical compositions under humid tropical conditions-Decomposition and nutrient release. Soil Biology & Biochemistry 24(10), pp. 1051-1060. https://doi.org/10.1016/0038-0717(92)90035-V Cited: 399.

Frostegård, Å., Bååth, E., Tunlio, A. 1993. Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis. Soil Biology & Biochemistry 25(6), pp. 723-730. https://doi.org/10.1016/0038-0717(93)90113-P Cited: 1021.

Zak, J.C., Willig, M.R., Moorhead, D.L., Wildman, H.G. 1994. Functional diversity of microbial communities: A quantitative approach. Soil Biology & Biochemistry 26(9), pp. 1101-1108. https://doi.org/10.1016/0038-0717(94)90131-7 Cited: 1001.

Kirschbaum, M.U.F. 1995. The temperature dependence of soil organic matter decomposition, and the effect of global warming on soil organic C storage. Soil Biology & Biochemistry 27(6), pp. 753-760. https://doi.org/10.1016/0038-0717(94)00242-S Cited: 1376.

Joergensen, R-G. 1996. The fumigation-extraction method to estimate soil microbial biomass: Calibration of the kEC value. 1996. Soil Biology & Biochemistry 28 (1): 25-31. https://doi.org/10.1016/0038-0717(95)00102-6 Cited: 599.

Beck, T., Joergensen, R.G., Kandeler, E., Makeschin, F., Nuss, E., Oberholzer, H.R., Scheu, S. 1997. An inter-laboratory comparison of ten different ways of measuring soil microbial biomass C. Soil Biology & Biochemistry 29(7), pp. 1023-1032. https://doi.org/10.1016/S0038-0717(97)00030-8 Cited: 329.

Giller, K.E., Witter, E., Mcgrath, S.P. 1998. Toxicity of heavy metals to microorganisms and microbial processes in agricultural soils: A review. Soil Biology & Biochemistry 30(10-11), pp. 1389-1414. https://doi.org/10.1016/S0038-0717(97)00270-8 Cited: 1403.

Bandick, A.K., Dick, R.P. 1999. Field management effects on soil enzyme activities. Soil Biology & Biochemistry 31(11), pp. 1471-1479. https://doi.org/10.1016/S0038-0717(99)00051-6 Cited: 801.

Six, J., Elliott, E.T., Paustian, K. 2000. Soil macroaggregate turnover and microaggregate formation: A mechanism for C sequestration under no-tillage agriculture. Soil Biology and Biochemistry32(14), pp. 2099-2103. https://doi.org/10.1016/S0038-0717(00)00179-6 Cited: 1540.

Wrage, N., Velthof, G.L., Van Beusichem, M.L., Oenema, O. 2001. Role of nitrifier denitrification in the production of nitrous oxide. Soil Biology & Biochemistry 33(12-13), pp. 1723-1732. https://doi.org/10.1016/S0038-0717(00)00179-6 Cited: 1180.

Kögel-Knabner, I. 2002. The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biology & Biochemistry 34(2), pp. 139-162. https://doi.org/10.1016/S0038-0717(01)00158-4 Cited: 1076.

Fierer, N., Schimel, J.P., Holden, P.A. 2003. Variations in microbial community composition through two soil depth profiles. Soil Biology & Biochemistry 35(1), pp. 167-176. https://doi.org/10.1016/S0038-0717(02)00251-1 Cited: 1007.

Schimel, J.P., Bilbrough, C., Welker, J.M. 2004. Increased snow depth affects microbial activity and nitrogen mineralization in two Arctic tundra communities. Soil Biology & Biochemistry 36(2), pp. 217-227. https://doi.org/10.1016/j.soilbio.2003.09.008 Cited: 434.

Belimov, A.A., Hontzeas, N., Safronova, V.I., Demchinskaya, S.V., Piluzza, G., Bullitta, S., Glick, B.R. 2005. Cadmium-tolerant plant growth-promoting bacteria associated with the roots of Indian mustard (Brassica juncea L. Czern.). Soil Biology & Biochemistry 37(2), pp. 241-250. https://doi.org/10.1016/j.soilbio.2004.07.033 Cited: 534.

Kuzyakov, Y. 2006. Sources of CO2 efflux from soil and review of partitioning methods. Soil Biology & Biochemistry 38(3), pp. 425-448. https://doi.org/10.1016/j.soilbio.2005.08.020 Cited: 744.

von Lützow, M., Kögel-Knabner, I., Ekschmitt, K., Flessa, H., Guggenberger, G., Matzner, E., Marschner, B. 2007. SOM fractionation methods: Relevance to functional pools and to stabilization mechanisms. Soil Biology & Biochemistry 39(9), pp. 2183-2207. https://doi.org/10.1016/j.soilbio.2007.03.007 Cited: 794.

Lauber, C.L., Strickland, M.S., Bradford, M.A., Fierer, N. 2008. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology & Biochemistry 40(9), pp. 2407-2415. https://doi.org/10.1016/j.soilbio.2008.05.021 Cited: 884.

Kuzyakov, Y., Subbotina, I., Chen, H., Bogomolova, I., Xu, X. 2009. Black carbon decomposition and incorporation into soil microbial biomass estimated by 14C labeling. Soil Biology & Biochemistry 41(2), pp. 210-219. https://doi.org/10.1016/j.soilbio.2008.10.016 Cited: 655.

Compant, S., Clément, C., Sessitsch, A. 2010. Plant growth-promoting bacteria in the rhizo- and endosphere of plants: Their role, colonization, mechanisms involved and prospects for utilization. Soil Biology & Biochemistry 42(5): 669-678. https://doi.org/10.1016/j.soilbio.2009.11.024 Cited: 956.

Lehmann, J., Rillig, M.C., Thies, J., Masiello, C.A., Hockaday, W.C., Crowley, D. 2011. Biochar effects on soil biota - A review. Soil Biology & Biochemistry 43(9), pp. 1812-1836. https://doi.org/10.1016/j.soilbio.2011.04.022 Cited: 2101.

Jones, D.L., Rousk, J., Edwards-Jones, G., DeLuca, T.H., Murphy, D.V. 2012. Biochar-mediated changes in soil quality and plant growth in a three year field trial. Soil Biology & Biochemistry 45, 113-124. https://doi.org/10.1016/j.soilbio.2011.10.012 Cited: 503.

Burns, R.G., DeForest, J.L., Marxsen, J., Sinsabaugh, R.L., Stromberger, M.E., Wallenstein, M.D., Weintraub, M.N., Zoppini, A. 2013. Soil enzymes in a changing environment: Current knowledge and future directions. Soil Biology & Biochemistry 58, pp. 216-234. https://doi.org/10.1016/j.soilbio.2012.11.009 Cited: 799.

Geisseler, D., Scow, K.M. 2014. Long-term effects of mineral fertilizers on soil microorganisms - A review. Soil Biology & Biochemistry 75, pp. 54-63. https://doi.org/10.1016/j.soilbio.2014.03.023 Cited: 433

Kuzyakov, Y., Blagodatskaya, E. 2015. Microbial hotspots and hot moments in soil: Concept & review. Soil Biology & Biochemistry 83, pp. 184-199. https://doi.org/10.1016/j.soilbio.2015.01.025 Cited: 505.

Jian, S., Li, J., Chen, J, Wang, G., Mayes, M.A., Dzantor, K.E., Hui, D., Luo, Y. 2016. Soil extracellular enzyme activities, soil carbon and nitrogen storage under nitrogen fertilization: A meta-analysis. Soil Biology & Biochemistry 101, pp. 32-43. https://doi.org/10.1016/j.soilbio.2016.07.003 Cited: 177.

Xu, Z., Yu, G., Zhang, X., He, N., Wang, Q., Wang, S., Wang, R., Zhao, N., Jia, Y., Wang, C. 2017. Soil enzyme activity and stoichiometry in forest ecosystems along the North-South Transect in eastern China (NSTEC). Soil Biology & Biochemistry 104, pp. 152-163. https://doi.org/10.1016/j.soilbio.2016.10.020 Cited: 93.

Bünemann, E.K., Bongiorno, G., Bai, Z., Creamer, R.E., De Deyn, G., de Goede, R., Fleskens, L., Geissen, V., Kuyper, T.W., Mäder, P., Pulleman, M., Sukkel, W., van Groenigen, J.W., Brussaard, L. 2018. Soil quality – A critical review. Soil Biology & Biochemistry 120, pp. 105-125. https://doi.org/10.1016/j.soilbio.2018.01.030 Cited: 332

Kuzyakov, Y., Razavi, B.S. 2019. Rhizosphere size and shape: Temporal dynamics and spatial stationarity. Soil Biology and Biochemistry 135, 343-360. https://doi.org/10.1016/j.soilbio.2019.05.011 Cited: 44.

List 2: Most cited articles for each year ranked by number of times cited


Soil Biology

Soil is a complex and dynamic habitat for soil organisms. Beneficial biological activity is heavily dependent on organic matter which provides a food supply for many organisms and this is influenced by land use, soil chemical composition and climate. The presence and ratios of mesofauna (animals 0.1 mm to 2 mm) can be good indicators of soil health. Mites and springtails are indicators of good biological activity. Mycorrhizal fungi help plants access water and nutrients by acting and an extension of their root systems. Soil aggregates, the presence of tiny white threads (hyphae), moisture and earthy smell can all be good indicators of mycorrhizal fungi. A healthy soil microbiome can improve nutrient uptake in plants, reduce susceptibility to pests and pathogens and improve soil fertility and structure.

What Inhibits Soil Biological Function?

1. Soil acidity
2. Poor soil organic matter management
3. Low groundcover
4. Tillage practices and
5. Cropping sequences.

Solutions

• Minimise erosion as soil organisms live mostly in the surface layers
• Maintain or increase the organic matter content of soil
• Use diverse rotations as they increase organic matter composition
• Don’t burn stubble and
• Choose crops and management practices that minimise plant pathogens.


Problem Statement

Due to the increasing threat that exotic pathogens and insects can have on the health of shade trees, it is essential to maximize genetic diversity within the nation’s urban forests. The graceful American elm that once dominated urban forests across the United States essentially disappeared from urban landscapes after the introduction of Dutch elm disease (DED) into North America. While DED-resistant elm cultivars have been planted in trials in various locations around the nation over the years, so often the trials lacked sufficient replication and/or cultivar performance data were never published. Scientific data on growth, form, and pest resistance for existing DED-resistant elm cultivars are essential in order to promote interest in planting these trees. The national trial of commercially available elm cultivars encompasses evaluation sites that represent a wide range of growing conditions and will be sufficiently replicated so that the data can be statistically analyzed.

  1. Determine the growth and horticultural performance of commercially available DED-resistant elm cultivars in various climate regimes in the United States.
  2. Determine the relative disease, insect, and abiotic stress tolerance of these cultivars.
  3. Promote the propagation and use of elms through local, regional, and national reporting of the trial results to wholesale tree propagators and growers, retail nursery and garden center operators, landscaper designers, arborists, and the general public.

Conventional Agricultural Production Systems and Soil Functions

Francisco J. Arriaga , . Birl Lowery , in Soil Health and Intensification of Agroecosytems , 2017

5.2.3 Conventional Agricultural Production Systems’ Impact on Soil Physical Properties

While good soil health is often described as being directly related to soil biology and its chemistry, especially abundance of organic matter, it should also be understood that ideal soil physical properties are also key to good soil health. Some of the key physical properties necessary for good soil health include low bulk density which in turn means high porosity (given that bulk density and porosity are inversely related/proportional), good infiltration and drainage, and rapid water movement under saturated and unsaturated conditions. It is generally a given that all these physical conditions are found in soil with an abundance of organic matter, but even soil with adequate organic matter can have poor physical properties or can be degraded to the point that its physical properties are not optimal. An example of this is when soil with good levels of organic matter becomes compacted, which leads to soil structure degradation ( Fig. 5.5 ), decreases in porosity, and water flow is restricted. Granted for this to happen to soils with adequate organic matter content, it is likely the result of bad soil management practices such as the increased use of heavy machinery and improper management (e.g., machine traffic and cultivating during wet soil conditions), but this is typically the case with CAPS. This is not to say that all other agricultural systems such as organic agriculture systems will be managed any better.

Figure 5.5 . Example of a soil that has been abused by compaction from heavy equipment during harvest of previous crop while soil was very wet. Note how the soil structure has been destroyed and subsequent tillage has pulled the B-horizon to the soil surface.

Courtesy of Richard P. Wolkowski, Personal Communication, Emeritus Research Scientist, University of Wisconsin-Madison.

The ratio of soil solids to soil pores, or void spaces, is key for accessing soil health because good or ideal soil condition is considered to have about 50% pores and 50% solids ( Fig. 5.6 ). For good soil health a large soil pore volume, or porosity, is desired. In order to assess soil porosity one must first understand soil bulk density. The mass of dry soil solids per unit volume of soil (volume of solids + voids) is a definition of soil bulk density. Since bulk density and porosity are inversely proportional, the smaller the value of a soil’s bulk density the greater will be its volume of pores. It should be noted that soil water and gas (air) reside in the pores and both are needed for proper plant function to occur. Soil bulk density is a finite value that can range between slightly less than 1000 and 2650 kg m −3 (the density of average soil particles) for an average mineral soil. Since organic matter has a much smaller density (800 kg m −3 ) when compared to mineral particles (i.e., quartz 2650 kg m −3 ), increases in soil organic matter result in a decrease in soil bulk density.

Figure 5.6 . The ratio of soil solids to soil pores, or void spaces, in an ideal soil is considered to be about 50% each. The solid phase of an ideal soil is comprised of minerals (

5%). The proportion of air and water that fills the soil pores (porosity) is dynamic, or always changing. An ideal soil with the characteristics described here would provide a good soil bulk density, which along with soil porosity are key for soil health and plant growth.

The total porosity of a soil is important, but the distribution of pore sizes is also key to good soil quality. That is a soil with a very high porosity (i.e., low bulk density) is not necessarily a good-quality soil if the total porosity is mainly composed of small pores. A soil with mainly small pores will have a high capacity to retain or hold water but will have a poor drainage capacity. Such conditions will often result in anaerobic soil environments that limit microbial activities. Thus an ideal soil with good soil health should have a good pore size distribution. It has been shown that the addition of organic matter to such soil will improve the soil physical condition including bulk density, pore size distribution, infiltration, and hydraulic conductivity because soil aggregation is enhanced ( Wei et al., 1985 ). These improvements will also likely promote good soil health.

Soil structure is defined as the combination and arrangement of primary (individual) soil particles into secondary structural units that form aggregates. The aggregation of primary soil particles (i.e., sand, silt, and clay) is accomplished by the necessary binding agents. Binding agents in the soil include certain chemicals such as oxides, clay minerals, and most of all soil organic matter ( Six et al., 1998 ). These aggregates are separated from adjoining aggregates by planes of weakness, creating larger and typically more continuous pores that improve water infiltration and redistribution within a soil profile. Soils with good structure will likely have small bulk density values and thus high porosity. Good structure also means large distribution of pores and other desirable physical properties. Management practices that increase soil organic matter are typically associated with improved soil aggregation.

Soil structure is significantly impacted by some conventional agricultural systems in that structure in these systems tends to be poor, which means greater bulk density and compaction. This all combines to make for poor drainage and water-logged conditions. This is obviously soil-specific as sandy soil is an exception since sands are subject to compaction, but even under compacted conditions sand will likely have sufficient drainage. In most cases a sandy soil will not have good structure below surface soil layers. By nature, sands tend to have single grains in the subsoil.

Conventional agricultural production systems often require more intensive tillage and greater inputs of external nutrients (especially N) as compared to systems which use cropping rotations and cover crops to control pest and weeds. This often leads to degradation of soil structure because of declines in soil organic matter ( Havlin et al., 1990 ). Consequently, it has been reported in several studies that there is a rapid decline in water-holding capacity and poor soil aeration associated with compaction, and reductions in soil organic matter, which in the long term results in yield reductions ( Doran, 2002 Liebig et al., 2004 ). Such reductions in soil structural aggregate stability and water-holding capacity will have further ramifications on the resiliency of vegetable and grain production systems when considering the potential effects of climate change, where many studies and models have predicted an increase in frequency of extreme rainfall events and droughts globally ( Pryor et al., 2014 ). Subsequently, many grain producers apply organic amendments to the soil, such as animal manures, sewage sludge, and household waste, to minimize the depletion of soil organic matter and improve soil structure and stability ( Six et al., 1999 Bationo et al., 2007 Fließbach et al., 2007 ).

Good drainage and water movement through the soil (hydraulic conductivity) is key to soil health. In addition to good drainage, soil water retention is also important to soil health. There must however be a good balance between water retention and soil air for maximum plant growth and a healthy mix of soil microorganisms ( Doran et al., 1996 Doran, 2002 ).

Soil compaction is a reduction in soil porosity often caused by human activities. Soil compaction is undesirable for agricultural plant production because it decreases infiltration and may physically restrict root growth ( Hilfiker and Lowery, 1988 Lowery and Schuler, 1991 ). It also causes aeration problems. Examples of the impact of compaction on soil properties can be borrowed from engineering applications, such as (1) increasing soil strength for reducing settling of roadbeds and foundations, and (2) decreasing hydraulic conductivity in earth-fill dams and other water-retaining structures by increasing soil bulk density. Engineers achieve these goals by removing soil with high organic matter (i.e., topsoil) and destroying soil aggregates via excavation, tillage, and compaction. In agricultural settings, tillage using moldboard plow forms a compacted “plow sole” at the bottom of the furrow if plow depth is not varied from year-to-year. Tillage pans are not limited to moldboard plowing as most other tillage implements form a subsurface compacted zone this includes disk-harrows, subsoilers, and disk-plows. Tillage also reduces a soil’s resilience against soil compaction in the soil surface, since soil aggregates are degraded and loose friable soil is left ( Lal, 1993 ). This reduction of soil aggregation in the long term will ultimately result in settling of smaller soil particles closer together, resulting in greater soil compaction. It has been shown that reduced and controlled traffic will reduce the amount of soil subjected to compaction in a given field area ( Batey, 2009 ). Additionally, management practices such as diverse cropping rotations and cover crops can reduce the effect of field traffic, and can also help reduce the use of pesticides and/or fertilizers ( Lal et al., 1994a Unger and Jones, 1998 ).


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It is now widely accepted that better management of the soil environment can provide substantial increases in yield and profitability. However, there is still debate over the best way to achieve 'good soil health'.

This has been compounded by research results that seem contradictory, especially when single-year trials are compared.

[Photo (left): DAFWA researcher Dave Gartner sprays pH-indicator solution in a soil pit to determine the pH status of subsoil at the Liebe Group long-term research site. pH status is an important factor in determining soil health.]

Because of this, since 2003 the Liebe Group at Buntine in WA has been trialling a range of soil management options at its long-term research site and at eight satellite sites. The long-term research site is focused on ameliorating biological constraints to yield, while the satellite sites are focused on overcoming local constraints.

Through its soil health project, the Liebe Group has benchmarked soil-quality indicators, identified key constraints to yield and established management practices. The project's aim is to increase yield by maintaining and improving soil health by addressing physical, chemical and biological constraints.

Biological soil health

Biological soil health is considered the most complex aspect of soil health, and is the aspect that requires longer-term monitoring to assess the effect of management.

The Liebe Group's biological soil-health trial comprises 16 treatments and is aimed at identifying different ways to increase the soil's biological fertility, overcome any constraints and increase soil water-holding capacity.

[Photo (left): Pithara grower Noel Mills and Liebe Group project coordinator Emma Glasfurd sample soil on Noel's property in May 2006 for the UWA, Land and Water Australia project, which is collaborating with the Liebe Group GRDC project.]

The treatments applied within the trial are listed in Table 1. Combinations of all treatments are also evaluated within the trial. All plots were sown to Wyalkatchem wheat in 2004 and 2005. The initial crop in 2003 was Belara lupins and the 2006 crop was seeded to Mandelup lupins.

In 2007, the site will be seeded to wheat following the lupin phase in 2006. The lupin phase allows weeds to be controlled and specific treatments such as brown manuring and organic matter to be applied for the subsequent wheat crop.

[Photo (left): Tilled and untilled plots within the soil biology trial at the Liebe Group long-term research site, pre-seeding in 2005. Tilled sites tended to have greater physical constraints to crop yield when compared with untilled sites.]

In 2004, a 22 per cent (600 kilogram per hectare) improvement in wheat yield was found in a crop sown after brown-manured lupins. In 2005, the treatment of burnt plots was introduced and the burnt stubble yielded 25 per cent more (560kg/ha) than full stubble retention. Results such as this make it difficult for farmers to economically justify full stubble retention, even though stubble retention has proved to be better for soil sustainability.

It is hoped 2007 will produce further comparisons between retained and burnt stubble to help determine which management option is more sustainable over the long term.

In the long-term biology trial in 2005, the yields reflected what many farmers encounter in the initial phases of converting to a full stubble-retention system as opposed to stubble burning.

Researchers Dr Frances Hoyle and Daniel Murphy consider that the lower yields obtained in the initial phases of converting to full stubble-retention systems may be associated with the initial microbial immobilisation of nitrogen associated with stubble decomposition. Where this occurs, yield penalty could be minimised if as much stubble as possible is allowed to decompose prior to seeding successive crops. Maximum stubble breakdown occurs when there is close stubble-soil contact, adequate nitrogen, sufficient moisture, optimal temperatures and oxygen is available.

The application of zeolite, humates, the decomposing agent and microbes had no significant effect on crop biomass and yield in either 2004 or 2005 (Figures 1 and 2). Grain protein levels were similar across all treatments at 11 to 12 per cent. Tilled treatments did tend to have lower protein contents compared with non-tilled treatments.

Biological soil health also includes the presence of fungi and bacteria, which can cause root disease. At one of the satellite sites it was discovered that the cause of poor lupin emergence was pleichaeta root rot disease, which occurs when spores that cause brown leaf spot are buried at depth. The history of green manuring at this site meant that lupin roots were growing into a disease pressure situation.

Physical soil health

Subsoil compaction by large machinery has been identified as limiting crop growth and yield in WA. Dr Paul Blackwell at the Department of Agriculture and Food, Western Australia (DAFWA), has found that yield improvements of up to 15 per cent are possible when subsoil compaction is improved. All eight satellite sites in the Liebe Group trial had subsoil compaction at yield-limiting levels.

The most common management strategy to overcome subsoil compaction is deep ripping followed by controlled-traffic farming. Penetrometer results show that deep-ripped soil allows plant roots to access more water and nutrients at greater soil depths.

Other advantages of controlled-traffic farming include:

  • reduced fuel, seed, fertiliser and spray costs
  • lower tractor power requirements
  • improved timeliness of operations
  • more accurate placement of inputs
  • reduced operator fatigue and
  • erosion and water-logging control.

Chemical soil health

Subsoil acidity was found at yield-limiting levels at seven of the eight sites sampled. A trial to ameliorate subsoil acidity involved deep placement of lime. At one of the satellite sites, lime was applied at varying depths below the surface at a rate of 2.5 tonnes per hectare. It is expected that this will increase pH by about 0.5 units within the soil profile, and effectively reduce the detrimental effects of an acid subsoil.

Soil health is rated by Liebe Group farmers as one of the top three production issues that will influence their farming over the next five years. The long-term research site hopes to continue to address this by developing a long-term soil health strategy.

Economic modelling will also be conducted with growers who are considering adopting a soil management strategy and/or technology to determine the costs and benefits for their enterprise. Management strategies to be researched will assess biological, physical and chemical components of the soil resource on varying soil types.


Watch the video: What is Trial De Novo? (August 2022).