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

Tipayno, Sherlyn C.,Chauhan, Puneet S.,Woo, Sung-Man,Hong, Bo-Hee,Park, Kee-Woong,Chung, Jong-Bae,Sa, Tong-Min Korean Society of Soil Science and Fertilizer 2011 한국토양비료학회지 Vol.44 No.1

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.

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

Sherlyn C. Tipayno,Puneet S. Chauhan,Sungman Woo,Bohee Hong,Keewoong Park,Jongbae Chung,Tongmin Sa 한국토양비료학회 2011 한국토양비료학회지 Vol.44 No.1

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.

Influence of Varying Degree of Salinity-Sodicity Stress on Enzyme Activities and Bacterial Populations of Coastal Soils of Yellow Sea, South Korea

( Siddikee Md. Ashaduzzaman ),( Sherlyn C. Tipayno ),( Ki Yoon Kim ),( Jong Bae Chung ),( Tong Min Sa ) 한국미생물 · 생명공학회 2011 Journal of microbiology and biotechnology Vol.21 No.4

To study the effects of salinity-sodicity on bacterial population and enzyme activities, soil samples were collected from the Bay of Yellow Sea, Incheon, South Korea. In the soils nearest to the coastline, pH, electrical conductivity (ECe), sodium adsorption ratio (SAR), and exchangeable sodium percentage (ESP) were greater than the criteria of salinesodic soil, and soils collected from sites 1.5-2 km away from the coastline were not substantially affected by the intrusion and spray of seawater. Halotolerant bacteria showed similar trends, whereas non-tolerant bacteria and enzymatic activities had opposite trends. Significant positive correlations were found between EC, exchangeable Na+, and pH with SAR and ESP. In contrast, ECe, SAR, ESP, and exchangeable Na+ exhibited significant negative correlations with bacterial populations and enzyme activities. The results of this study indicate that the soil chemical variables related with salinity-sodicity are significantly related with the sampling distance from the coastline and are the key stress factors, which greatly affect microbial and biochemical properties.

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

Puneet Singh Chauhan,Charlotte C. Shagol,Woojong Yim,Sherlyn C. Tipayno,Chang-Gi Kim,Tongmin Sa 한국토양비료학회 2011 한국토양비료학회지 Vol.44 No.1

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.

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

Chauhan, Puneet Singh,Shagol, Charlotte C.,Yim, Woo-Jong,Tipayno, Sherlyn C.,Kim, Chang-Gi,Sa, Tong-Min Korean Society of Soil Science and Fertilizer 2011 한국토양비료학회지 Vol.44 No.1

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.

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

Parthiban Subramanian,Manoharan Melvin Joe,임우종,홍보희,Sherlyn C. Tipayno,Venkatakrishnan Sivaraj Saravanan,유재홍,정종배,Tahera Sultana,사동민 한국토양비료학회 2011 한국토양비료학회지 Vol.44 No.4

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.

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

Subramanian, Parthiban,Joe, Manoharan Melvin,Yim, Woo-Jong,Hong, Bo-Hui,Tipayno, Sherlyn C.,Saravanan, Venkatakrishnan Sivaraj,Yoo, Jae-Hong,Chung, Jong-Bae,Sultana, Tahera,Sa, Tong-Min Korean Society of Soil Science and Fertilizer 2011 한국토양비료학회지 Vol.44 No.4

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.