Oguz Can Turgay

Soil Enzymes as Indication of Soil Quality

Soil, water and air are natural resources as well as pollution reservoirs. Soil quality can be changed by pollution, ecological perturbations and agricultural practices. Soil quality can be defined as, “the capacity of a specific kind of soil to function, within natural or managed ecosystem boundaries, to sustain plant and animal productivity, maintain or enhance water and air quality, and support human health and habitation”(Karlen et al. 1997). Preserving soil quality should be needed for sustaining of life and human nutrition. Soil enzymes are used as soil quality indicators for quick response of changes for environmental stress, pollution and agricultural practices much more sooner (1–2 year) than other soil properties (organic matter); easy to measure (relatively simple procedure), having relations with plant productivity, soil quality parameters (organic matter, soil physical properties, microbial activity, and microbial biomass), and biogeochemical cycle; and being integrative. This chapter mainly covers three distinct effects for changes in soils: (1) pollution (heavy metals, pesticides, industrial amendments or contaminants, hydrocarbons, acid precipitations, industrial air pollutants, sewage sludge, and waste usage), (2) ecological perturbations(land use, devegetation and revegetation, changing climatic conditions, and forest fires), and (3) agricultural practices (irrigation, fertilizers, amendments, different management and farming systems, crop rotation, and tillage).

Effects of Heavy Metals on Soil Enzyme Activities

The pollution of the soil with heavy metals is one of the worst legacies of our intensive agricultural–industrial activities, and it negatively affects various characteristics of the soil, including soil enzyme activities. Soil enzymes are natural molecules that catalyze soil microbial reactions and mainly originate from microorganisms and plants. Since enzyme activities play fundamental roles in soil chemical and biological reactions, their inhibition by heavy metals has received considerable attention and has been well documented by many researchers over the last few decades. The activities of soil enzymes have often been proposed as sensitive indicators of important microbial reactions involved in nutrient cycles and they respond to changes in the soil caused by natural or anthropogenic factors. In this regard, soil enzyme activities are often used to evaluate the impact of human activity on soil life. The purpose of this chapter is thus to emphasis some facts, hypotheses, and probabilities, as well as the results of research into the relationships between soil enzymes and heavy metals.

Seed biopriming with plant growth promoting rhizobacteria: a review.

Beneficial microbes are applied to the soil and plant tissues directly or through seed inoculation, whereas soil application is preferred when there is risk of inhibitors or antagonistic microbes on the plant tissues. Insufficient survival of the microorganisms, hindrance in application of fungicides to the seeds and exposure to heat and sunlight in subsequent seed storage in conventional inoculation methods force to explore appropriate and efficient bacterial application method. Seed priming, where seeds are hydrated to activate metabolism without actual germination followed by drying, increases the germination, stand establishment and stress tolerance in different crops. Seed priming with living bacterial inoculum is termed as biopriming that involves the application of plant growth promoting rhizobacteria. It increases speed and uniformity of germination; also ensures rapid, uniform and high establishment of crops; and hence improves harvest quality and yield. Seed biopriming allows the bacteria to enter/adhere the seeds and also acclimatization of bacteria in the prevalent conditions. This review focuses on methods used for biopriming, and also the role in improving crop productivity and stress tolerance along with prospects of this technology. The comparison of methods being followed is also reviewed proposing biopriming as a promising technique for application of beneficial microbes to the seeds.

Earthworm Interactions with Soil Enzymes

As one of the dominant members of soil fauna, earthworms fulfill significant tasks in the soil ecosystem by participating in the physico-chemical processes of the soil, such as organic matter cycles, nutrient transformations, and modifications in soil structure. These processes are also directed by the activities and amounts of the enzymes produced by soil microorganisms that inhabit a wide range of soil environments including intestine systems, excretions, casts, and burrow linings of the earthworms. Therefore, microbial activity and the enzymes produced are considered to be closely related with earthworm life in soil. The purpose of this chapter is to describe the interactions between soil enzymes and earthworms at different levels in soil.

Effects of Earthworms on the Availability and Removal of Heavy Metals in Soil

Earthworms originally evolved in aquatic ecosystems and began to colonize terrestrial ecosystems 600 million years ago. Over the past few decades, research into earthworms has revealed that they stimulate the physical, chemical, and biological properties of soil and hence enhance soil fertility. Recent works have revealed that earthworms are able to direct the fates of heavy metals by passing and accumulating toxic metals through and in their body tissues, and that this distinctive phenomenon is influenced by various factors.

Role of Plant Growth Promoting Bacteria and Fungi in Heavy Metal Detoxification

Heavy metals are found in nature and are the main component of a variety of enzymes, transcription factors, and other proteins. Excessive level of heavy metal is considered as a pollutant agent. Soil-heavy metals cannot be degraded biologically; they can only be transformed to organic complexes. Remediation techniques have high costs and low efficiency, whereas an alternative technique, phytoremediation has low cost and is environmentally friendly. To stimulate phytoremediation, fast-growing plants with high metal uptake and rapid and high biomass are required. Alternatively, soil microorganisms such as fungi and bacteria are used in heavy metal detoxification. This chapter reviews some recent advances in effect and significance of fungi and rhizobacteria in heavy metal detoxification.

Detoxification of Heavy Metals Using Earthworms

The number of different earthworm species living in a certain soil environment can be three or five and occasionally more than ten. Earthworms substantially enhance physical, chemical, and biological characteristics of soil through their feeding, casting, and burrowing activities. The factors affecting earthworm populations and activities in soil are climate, soil characteristics, plant vegetation, and biological relationships. The influences of earthworms on soil characteristics are mainly driven by their feeding, casting, and burrowing activities. Earthworms can affect either available or total metal concentrations in soil in that they have capability to accumulate heavy metals in their tissues and hence reduce their involvement in soil food chain. During their feeding activities, earthworms can change either available or total metal concentrations in soil in that they are capable to accumulate heavy metals in their tissues. The accumulation of heavy metals by earthworms is mainly associated with the factors such as type of mineral soil, organic matter content, and metal concentrations of their living environment and it should be kept in mind that earthworm–heavy metal relationships are mostly driven by soil characteristics and their ecological category.

Changes in soil ergosterol content, glomalin-related soil protein, and phospholipid fatty acid profile as affected by long-term organic and chemical fertilization practices in Mediterranean Turkey

The present study examines the effects of different fertilization treatments (chemical fertilization, farmyard manure, plant compost, and mycorrhiza-inoculated compost) on the soil fungi under a crop rotation of wheat (Triticum aestivum L.) and corn (Zea mays L.) in a long-term field experiment established in Mediterranean Turkey in 1996. Soil samples were collected in May, August, and October 2009. Soil pH, organic carbon, plant-available nitrogen and phosphorus, mycorrhizal colonization, and a series of biochemical markers (phospholipid and neutral lipid fatty acid [PLFA and NLFA] profiles, soil ergosterol content, and glomalin related soil protein [GRSP] as indicators of abundance of bacteria, saprotrophic, and arbuscular mycorrhizal [AM] fungi) were assessed. No significant difference was observed in soil organic C and plant available N in relation to long-term fertilization treatments, but plant available P in soil changed significantly in relation to the fertilization treatment used and the sampling season (between 11.5–33.8 mg · kg−1 in spring, 10.4–28.6 mg · kg−1 in summer, and 10.5–33.2 mg · kg−1 in autumn). Mycorrhizal colonization patterns were similar for both plants. However, mycorrhiza-inoculated compost treatment exhibited higher root colonization (77.3%) over control (16.3%), chemical fertilization (10.0%), farmyard manure (19.3%), and plant compost (20.0%). No statistically significant change was observed in ergosterol content. The effect of long-term organic treatments on soil PLFA structure was statistically prominent; whereas seasonality only affected bacterial PLFAs. Organic fertilization increased GRSP (mean annual ranging from 0.91 to 2.46 mg · g−1 total GRSP) but long-term annual mycorrhizal inoculation had no significant effect on the soil GRSP pool.

The Role of Plant Growth-Promoting Rhizosphere Bacteria in Toxic Metal Extraction by Brassica spp.

Brassicaceae are scattered all over the world, where they exclusively grow on serpentine rocks in Western Australia, New Zealand, South Africa, Japan, Philippines, Brazil, Portugal, Italy, Turkey, Cuba, eastern Canada, and western north America. Although serpentine rocks cover only less than 1% of the earth’s surface their worldwide distribution has recently attracted many researchers in exploring their distinctive potential for phytoremediation plant communities, mainly members of Brassicaceae plant family inhabiting on serpentine rocks of these countries. On the other hand, the majority of Brassicaceae plant family are slow-growing plants producing little biomass and their use for phytoextraction purposes may not be practical, especially when bioavailable metal concentration is high in the contaminated conditions. Therefore, recently emerging practices in the field of phytoremediation have pointed out various focuses such as the utility of high-biomass crops such as maize, peas, oats and Indian mustard and associated soil practices including application of synthetic chelators such as ethylenediaminetetraacetic acid and nitrilotriacetate and elemental sulphur to enhance metal uptake by these plants. These approaches may meet the conditions required for the phytoremediation. However, one of the most critical components of phytoextraction process is the bioavailability of heavy metals meaning the portion of the metals that is available for absorption into living organisms such as plants. It has been known that various plant growth-promoting rhizobacteria (PGPR) associated with plant roots may provide some beneficial effects on plant growth and nutrition through a series of well known mechanisms, namely, nitrogen fixation, production of phytohormones and siderophores, and transformation of nutrients once they are either applied to seeds or incorporated into the soil. Similarly, heavy metal mobility and availability can substantially be driven by PGPR populations through their release of chelating agents, acidification, and phosphate solubilization in rhizosphere. Miscellaneous PGPR were also shown to tolerate heavy metals in different ways including the mechanisms of exclusion, active removal, biosorption, precipitation, and extra- or intracellular bioaccumulation. Since these processes may affect the solubility and the bioavailability of heavy metals to the plant and hence modifying their toxic effects, interactions between hyperaccumulator plants such as Brassicaceae spp., and metal tolerant or resistant PGPR are considered to have an increasing biotechnological potential in the remediation of anthropogenically polluted soils. Present chapter/review considers the role of PGPR on soil-heavy metal-plant interactions and more specifically bioaccumulation of toxic metals by Brassicaceae plant family.

Molecular diversity of indigenous arbuscular mycorrhizal fungi in three different agricultural regions of Turkey

Abstract Little is known about the distribution of arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) in the Turkish arable soils. In this study, we investigated AM fungal phylotype composition in the roots of 13 different plant samples from one site each of the East Black Sea, Mediterranean, and Central Anatolian regions of Turkey. Fifty-seven distinguished operational taxonomic units at 97% nucleotide sequence identity were recorded among 424 partial sequences of the nuclear ribosomal large subunit (LSU) RNA genes determined. Most of the new sequences were clustered within 10 well-resolved phyloclades of the order Glomerales. About half of the newly determined sequences lacked similar sequences in the public databases. In particular, all sequences from Camellia sinensis collected in the East Black Sea region had only 83–97% sequence similarity to known AMF species. The findings suggest that novel and endemic AMF species may exist in Turkish agricultural soils. The AM fungal community composition in the East Black Sea region was relatively simple and completely differed from those in the other two regions, presumably due to the low soil pH and host specificity. The AM fungal community compositions of the Mediterranean and Central Anatolian samples were broadly similar; however, some sequences related to Rhizophagus were found only in the Mediterranean samples. This reflects the trend that more diverse AM fungal communities are established in the Mediterranean region than the Central Anatolian region.