Several microorganisms especially bacteria (Bacillus subtilis, Pseudomonas putida, and Enterobacter cloacae) have been successfully used for the reduction of Cr (VI) to the less toxic Cr (III) [77–80]. B. subtilis has also been reported to reduce nonmetallic elements. For instance, Garbisu et al. [81] recorded that B. subtilis reduced the selenite to the less toxic elemental Se. Further, B. cereus and B. thuringiensis have been shown to increase extraction of Cd and Zn from Cd-rich soil and soil polluted with effluent from metal industry [82]. It is assumed that the production of siderophore (Fe complexing molecules) by bacteria may have facilitated the extraction of these metals from the soil; this is because heavy metals have been reported to simulate the production of siderophore and this consequently affects their bioavailability [83]. For instance, siderophore production by Azotobacter vinelandii was increased in the presence of Zn (II) [84]. Hence, heavy metals influence the activities of siderophore-producing bacteria which in turn increases mobility and extraction of these metals in soil.
Bioremediation can also occur indirectly via bioprecipitation by sulphate reducing bacteria (Desulfovibrio desulfuricans) which converts sulphate to hydrogen sulphate which subsequently reacts with heavy metals such as Cd and Zn to form insoluble forms of these metal sulphides [85].
Most of the above microbe assisted remediation is carried out ex situ. However, a very important in situ microbe assisted remediation is the microbial reduction of soluble mercuric ions Hg (II) to volatile metallic mercury and Hg (0) carried out by mercury resistant bacteria [86]. The reduced Hg (0) can easily volatilize out of the environment and subsequently be diluted in the atmosphere [87].
Genetic engineering can be adopted in microbe assisted remediation of heavy metal polluted soils. For instance, Valls et al. [88] reported that genetically engineered Ralstonia eutropha can be used to sequester metals (such as Cd) in polluted soils. This is made possible by the introduction of metallothionein (cysteine rich metal binding protein) from mouse on the cell surface on this organism. Although the sequestered metals remain in the soil, they are made less bioavailable and hence less harmful. The controversies surrounding genetically modified organisms [89] and the fact that the heavy metal remains in the soil are major limitations to this approach to bioremediation.
Making the soil favourable for soil microbes is one strategy employed in bioremediation of polluted soils. This process known as biostimulation involves the addition of nutrients in the form of manure or other organic amendments which serve as C source for microorganisms present in the soil. The added nutrients increase the growth and activities of microorganisms involved in the remediation process and thus this increases the efficiency of bioremediation.
Although biostimulation is usually employed for the biodegradation of organic pollutants [90], it can equally be used for the remediation of heavy metal polluted soils. Since heavy metals cannot be biodegraded, biostimulation can indirectly enhance remediation of heavy metal polluted soil through alteration of soil pH. It is well known that the addition of organic materials reduces the pH of the soil [91]; this subsequently increases the solubility and hence bioavailability of heavy metals which can then be easily extracted from the soil [92].
Biochar is one organic material that is currently being exploited for its potential in the management of heavy metal polluted soils. Namgay et al. [93] recorded a reduction in the availability of heavy metals when the polluted soil was amended with biochar; this in turn reduced plant absorption of the metals. The ability of biochar to increase soil pH unlike most other organic amendments [94] may have increased sorption of these metals, thus reducing their bioavailability for plant uptake. It is important to note that, since the characteristics of biochar vary widely depending on its method of production and the feedstock used in its production, the effect different biochar amendments will have on the availability of heavy metals in soil will also differ. Further, more research is needed in order to understand the effect of biochar on soil microorganisms and how the interaction between biochar and soil microbes influences remediation of heavy metal polluted soils because such studies are rare in literature.