Sherlyn Tipayno

Effects of Metal and Metalloid Contamination on Microbial Diversity and Activity in Agricultural Soils

The continuous increase in the production of metals and their subsequent release into the environment has lead to increased concentration of these elements in agricultural soils. Because microbes are involved in almost every chemical transformations taking place in the soil, considerable attention has been given to assessing their responses to metal contaminants. Short-term and long-term exposures to toxic metals have been shown to reduce microbial diversity, biomass and activities in the soil. Several studies show that microbial parameters like basal respiration, metabolic quotient, and enzymatic activities, including those of oxidoreductases and those involved in the cycle of C, N, P and other elements, exhibit sensitivity to soil metal concentrations. These have been therefore, regarded as good indices for assessing the impact of metal contaminants to the soil. Metal contamination has also been extensively shown to decrease species diversity and cause shifts in microbial community structure. Biochemical and molecular techniques that are currently being employed to detect these changes are continuously challenged by several limiting factors, although showing some degree of sensitivity and efficiency. Variations and inconsistencies in the responses of bioindicators to metal stress in the soil can also be explained by differences in bioavailability of the metal to the microorganisms. This, in turn, is influenced by soil characteristics such as CEC, pH, soil particles and other factors. Therefore, aside from selecting the appropriate techniques to better understand microbial responses to metals, it is also important to understand the prevalent environmental conditions that interplay to bring about observed changes in any given soil parameter.

Actinobacteria isolation from metal contaminated soils for assessment of their metal resistance and plant growth promoting (PGP) characteristics

Heavy metals and metalloids removal can be considered as one of the most important world challenges because of their toxicity and direct impact on human health. Many processes have been introduced but biological processes of remediation seem to offer the most suitable solution in terms of efficiency and low cost. Actinobacteria constitute one of the major microbial populations in soil, and this can be attributed to their adaptive morphological structure as well as their exceptional metabolic power. Among microbes, actinobacteria are morphologic intermediate between fungi and bacteria. Studies on microbial diversities in metal contaminated lands have shown that actinobacteria may constitute a dominantly active microbiota in addition to α Proteobacteria. Furthermore, isolation studies have shown metal removal mechanisms which are reminiscent of notable multiresistant strains, such as Cupriavidus metallidurans. Apart from members of genus Streptomyces, which produce more than 90% of commercialized antibiotics, and the nitrogen fixing Frankia, little attention has been given to other members of this phylum. This is because of difficult culture condition requirements and maintenance. In this review, we focused on specific isolation of actinobacteria and their potential applications in metal bioremediation and plant growth promotion.

Psychrotolerance Mechanisms in Cold-Adapted Bacteria and their Perspectives as Plant Growth-Promoting Bacteria in Temperate Agriculture

Cold-adapted bacteria survive in extremely cold temperature conditions and exhibit various mechanisms of adaptation to sustain their regular metabolic functions. These adaptations include several physiological and metabolic changes that assist growth in a myriad of ways. Successfully sensing of the drop in temperature in these bacteria is followed by responses which include changes in the outer cell membrane to changes in the central nucleoid of the cell. Their survival is facilitated through many ways such as synthesis of cryoprotectants, cold acclimation proteins, cold shock proteins, RNA degradosomes, Antifreeze proteins and ice nucleators. Agricultural productivity in cereals and legumes under low temperature is influenced by several cold adopted bacteria including Pseudomonas, Acinetobacter, Burkholderia, Exiguobacterium, Pantoea, Rahnella, Rhodococcus and Serratia. They use plant growth promotion mechanisms including production of IAA, HCN, and ACC deaminase, phosphate solublization and biocontrol against plant pathogens such as Alternaria, Fusarium, Sclerotium, Rhizoctonia and Pythium.

Use of Terminal Restriction Length Polymorphism (T-RFLP) Analysis to Evaluate Uncultivable Microbial Community Structure of Soil

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

The bacterial community structure and functional profile in the heavy metal contaminated paddy soils, surrounding a nonferrous smelter in South Korea

Abstract The pollution of agricultural soils by the heavy metals affects the productivity of the land and has an impact on the quality of the surrounding ecosystems. This study investigated the bacterial community structure in the heavy metal contaminated sites along a smelter and a distantly located paddy field to elucidate the factors that are related to the alterations of the bacterial communities under the conditions of heavy metal pollution. Among the study sites, the bacterial communities in the soil did not show any significant differences in their richness and diversity. The soil bacterial communities at the three study sites were distinct from one another at each site, possessing a distinct set of bacterial phylotypes. Among the study sites, significant changes were observed in the abundances of the bacterial phyla and genera. The variations in the bacterial community structure were mostly related to the general soil properties at the phylum level, while at the finer taxonomic levels, the concentrations of arsenic (As) and lead (Pb) were the significant factors, affecting the community structure. The relative abundances of the genera Desulfatibacillum and Desulfovirga were negatively correlated to the concentrations of As, Pb, and cadmium (Cd) in the soil, while the genus Bacillus was positively correlated to the concentrations of As and Cd. According to the results of the prediction of bacterial community functions, the soil bacterial communities of the heavy metal polluted sites were characterized by the more abundant enzymes involved in DNA replication and repair, translation, transcription, and the nucleotide metabolism pathways, while the amino acid and lipid metabolism, as well as the biodegradation potential of xenobiotics, were reduced. Our results showed that the adaptation of the bacterial communities to the heavy metal contamination was predominantly attributed to the replacement process, while the changes in community richness were linked to the variations in the soil pH values.

Rhizobacteria: Restoration of Heavy Metal-Contaminated Soils

Heavy metal pollution has become one of the major culprits of environmental disasters. Their toxicity and damaging effects on soils and agricultural lands and direct impact on human health through soils and agricultural lands are considered a major world challenge. Many removal processes, such as mechanical and physicochemical ones have been introduced. However, because of their high cost, attention has been focused on biological solutions, which are less expensive and more efficient. Interestingly, some microorganisms have shown high potential to metal tolerance and removal. Cupriavidus metallidurans is certainly the most known example. The rhizosphere, an important interface between soil and plant, holds a diverse prokaryotic microflora population known as rhizobacteria. An important fraction of these microorganisms have been found to be involved in the removal of heavy metals through a panoply of mechanisms including release of chelating substances, microenvironment acidification, and promotion of redox potentials. The different mechanisms of resistance and interactions with metals have also been discussed. It has been also shown that rhizospheric bacteria may play beneficial roles in phytoremediation processes via facilitating bioavailability of heavy metals to plants such as maize and tomato, as well as for metal stress alleviation along rhizosphere of sensitive crops. In this chapter, we focused on the potentials of rhizobacteria for restoration of metal-affected soils and their role in improving metal uptake for phytoremediation processes. Because of the advantages of being less costly and environmental friendly, microbes are still the best tool for metal removal. But as living organisms, subject to death and decomposition through the geochemical cycles in the soil, their metal cleaning processes are never perfect and the removal may be tentative or not definitive. One of the foci now is on microbial bioengineering and genetic improvement of rhizobacteria and other soil microbial abilities for metal handling. Among the various microbial phyla in the rhizosphere, actinobacteria have drawn great interest due to their high biological compound production, which confer adaptation to a wide spectrum of ecological conditions, including metal contamination in soils. Their extremophilic traits and biological competitiveness in soil present them as possible efficient candidate for bioremediation. We included here their plant growth promotion capacity as well as their potentials for metal bioremediation.