1.3 Ecological assessment of floodplain characteristics
1.3.3 Microbial evaluation of water and soil samples
Microbial population in water and soil is often interpreted discretely depending on the nature and pathogenicity of microorganisms. Water and the soil system collectively contain useful as well as harmful microorganisms. Monitoring of water and soil samples from riverine floodplains provide an overview of the health hazards linked to harmful microorganisms in a region. Most of the useful microorganisms are isolated
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from their immediate environment for beneficiary uses like the thermophiles from hot springs (Inskeep et al., 2010), psychrophiles from cold regions (Cavicchioli et al., 2011), or in other words, extremophiles are screened for their enzymatic activities and utilized in several industrial purposes by the scientists (Cardoso et al.2011). The new era of metagenomics, i.e. isolating DNA directly from environmental samples and cloning the 16rDNA using vectors to obtain an organism with similar activities have widened the scientific domain of microbiological assessment.
Temperature profile and nutrient status in water determine growth of microorganisms that may change turbidity, odour and taste of waters. Presence of microorganisms significantly correlates to the DO in water and hence the fluctuating levels of BOD and COD. Plate count methods, use of selective media and Most Probable Number (MPN) estimation for coliform species are the basic methods of speculating presence of specific microorganisms or faecal coliforms in water. Standard methods of isolation of bacteria include extraction of bacteria from sample including a suitable media and enumeration of single colonies by plate culture method. Cells are lysed and DNA is purified for 16SrRNA sequencing to obtain the similarity of isolated strain to an already existing species. Most of the common pathogenic microorganisms reported in water samples from rivers, lakes, ponds and streams in India are Staphylococcus aureus (Kumar et al., 2013), Pseudomonas sp. (Kumar et al., 2013;
Sharma et al., 2013; Lyngdoh et al., 2012; Manivannan et al., 2013; Sati et al., 2011), Proteus vulgaris (Kumar et al., 2013), Clostridium tetani (Kumar et al., 2013), Alcaligenes faecalis (Kumar et al., 2013, Shigella sp. (Kumar et al., 2013; Manivannan et al., 2013), Salmonella sp. (Kumar et al., 2013; Manivannan et al. 2013), Micrococcus
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sp. (Kumar et al., 2013; Usharani et al., 2010), Enterobacter sp. (Sharma et al., 2013;
Manivannan et al., 2013), Aeromonas sp. (Sati et al., 2011) Enterococci sp. (Srivastava, 2012; Lyngdoh et al. 2012), Escherichia coli (Kumar et al., 2013; Sharma et al., 2013;
Chatterjee et al., 2010; Srivastava, 2012; Lyngdoh et al., 2012; Suneela et al. 2007;
Usharani et al., 2010), Bacillus sp. (Usharani et al., 2010), Klebsiella sp. (Lyngdoh et al. 2012; Manivannan et al., 2013; Sati et al., 2011), Staphylococcus sp. (Lyngdoh et al., 2012; Usharani et al., 2010), Vibrio sp. (Manivannan et al., 2013; Sati et al., 2011), Citrobacter sp. (Manivannan et al., 2013) and Streptococcus sp. (Chatterjee et al., 2010; Srivastava 2012; Manivannan et al., 2013; Usharani et al., 2010). Water in rivers, lakes, estuaries and wetlands are contaminated by three important sources: a) industrial effluents, b) household sewage and c) agricultural effluents. These wastes generated are rich in nutrient content generally observed with eutrophication events. However industrial and agricultural effluents indicate a lesser contribution as compared to household chores (EPA 2009).
In soil samples, presence of useful microorganisms however determines productivity connected to agricultural activities. Soil is a complex system comprising of several biochemical and physical processes under the influence of environmental factors in a particular ecosystem. Soil contains nutrients, chelates, microorganisms, air and moisture upholding the most important components of a terrestrial ecosystem (Bakshi et al., 2011). According to Hawsworth (2002), one billion bacteria are found in 1 gram of soil, fewer than 1 % have been discovered and named, and for fungi, out of 1.5 million species with only 5% have studied upon. Useful bacteria from soil
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rhizosphere are often isolated for their importance in significant enzyme activities and implementation in several industrial purposes.
Microbial evaluation for harmful bacterial species has been considered as vital investigation worldwide. Drinking water sources basically water from rivers, lakes, wetlands and streams have assessed for existence of coliform bacteria. Some of the important rivers and lakes studied for microbiological assessment in India are Kaushalya River (Aggarwal et al., 2012), Kallada River (Ashiq et al., 2012), Achal Taal, Lal Taal and Laal Diggi ponds in Aligarh (Ayub et al., 2011), Muttukadu Back Waters, East Coast of Tamil Nadu (Baheerathi, 2012), Koel River (Burh, 2011), Damodar River (Chatterjee et al., 2010), Datte – Da – Talab in Birpur, Jammu and Kashmir (Sharma et al., 2013), Vedvyas River and Koel River (Srivastava, 2012), Pamba River (Jalal et al., 2013), barmouths and lagoons in Chennai (Jayakumar et al., 2013), Bathu – da – Mandir and Beas River Dehra (Kumar et al., 2012), Umiam Lake (Lyngdoh et al., 2012), Ranganathapuram Lake, Chinthamani Lake, Vedapatti Lake, Pannimadai Lake, Vallan Lake (Manivannan et al., 2013), Indus River (Shafiq et al., 2011), Dal Lake (Saleem et al., 2011), Bhagirathi River and Alaknanda River (Sati et al., 2011), Manasbal Lake (Shafi et al., 2013), Udaipur Lakes (Sharma et al., 2008), Narmada River (Soni et al., 2013), Hussain Nagar Lake in Hyderabad (Suneela et al., 2007) and Noyyal River (Usharani et al., 2010). Apart from microbiological assessment in rivers and lakes, genotoxicity studies have been carried out as in Danube River (Kolarević et al., 2011). Yeasts species as Aureobasidium pullulans and Candida krusei have been isolated from Doce River Basin in Brazil (Medeiros et al., 2012). A detailed
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microbiological assessment of rivers and lakes all over the world is given in Table A 1.2, Appendix 1.
In case of soil microorganisms, methods of isolation are similar to isolation of bacteria from water samples. Use of selective media enables initial screening of the type of organisms and their pathogenicity. Soil microorganisms especially monitoring of bacteria, fungi and actinomycetes have been reported. Some of the microorganisms isolated from soils and sediments of rivers, lakes, salt marshes, etc. are bacteria as Pseudomonas sp. in Indus River, India (Praveen et al., 2011), Escherichia coli in Hussain Nagar Lake, Andhra Pradesh (Suneela et al., 2007), sulphur oxidizing bacteria as Micrococcus sp., Bacillus sp., Pseudomonas sp. and Klebsiella sp. from mangrove soil of Mahanadi River Delta (Behera et al., 2014), Corynebacterium sp., Bacillus sp., Enterobacter sp., Klebsiella sp., Staphylococcus sp., Micrococcus sp., Acinetobacter sp., Pseudomonas sp., Aeromonas sp., Salmonella sp., Streptococcus sp., Proteus sp.
and Erwinia sp. in Foma River, Nigeria (Agbabiaka et al. 2012), Escherichia coli in Awba Lake, Nigeria (Tijani et al., 2005), bacteria from the phyla Proteobacteria, Firmicutes, Planctomycetes, and Bacteroidetes in Pearl River Delta (Yang et al., 2013), diatoms as Achnanthes, Amphora, Cocconeis, Cymatopleura, Cymbella, Diatoma, Fragilaria, Gomphonema, Gyrosigma, Navicula, Nitzschia, Pinnularia, Rhoicosphenia (abbreviata) and Surirella in Rhine River (Yang et al., 2013), Actinobacteria from mangrove soils of Bhitarkanika in the estuarine region of Brahmani and Baitarani, Odhisa (Kishore, 2011), Actinobacteria, Thermomicrobia, Clostridium, Intrasporangium, Propionibacterium, Rubrobacter from Samoylov Island, Lena Delta, Siberia (Liebner et al., 2008), Proteobacteria in Mediterranean Temporary Rivers
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(Amalfitano et al., 2008), Proteobacteria, thermophilic species of Bacillus and Azotobacter in Inuvik on the on the East Channel of Mackenzie River (Boyd et al., 1990), Psychrotolerant species closely related to Pseudomonas and mesophilic Burkholderia cepacia in low temperature Arctic soils (Master et al., 1998) and Clostridium spores in Reno River Watershed, Italy (Ferronato et al., 2013).
Among these, bacterial species as Escherichia coli, Micrococcus, Bacillus, Pseudomonas (a few species), Salmonella, Streptococcus and Klebsiella have been clinically proven harmful to human beings imparting health related hazards and are frequently transmitted from soil to organisms through the food chain. Ecological assessment in sensitive areas likes permafrost in the polar ice caps in the Northern and Southern hemispheres have revealed a wide spectrum of economically useful bacteria.
These include methanogen from order Methanococcales and Methanomicrobiales form Canadian High Arctic (Allan et al., 2014), Methanomicrobiales from Siberian Arctic and Antarctica soils, bacteria belonging to the family Methanomicrobiaceae, Methanosarcinaceae and Methanosaetaceae from Laptev Sea coast, Siberian Arctic were reported (Ganzert et al., 2007). Other bacteria belonged to phyla Actinobacteria and Proteobacteria with a few species of Proteobacteria related to the order Rhizobiales (Alphaproteobacteria), more closely matching with Rhizobium, Mesorhizobium and Bradyrhizobium, some species belonged to Arthrobacter and Cryobacterium in Northeast Greenland (Ganzert et al., 2014) and β-Proteobacteria, species showed similarity with Iodobacter fluviatilis, Polaromonas vacuolata, Rhodoferax sp. in the cold environments of Southern Hemisphere Glaciers.
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Actinomycetes as species of Intrasporangium were reported in Samoylov Island, Lena Delta, Siberia (Liebner et al., 2008). Fungi as Curvularia, Aspergillus, Penicillium, Saccharomyces, Cladosporium, Geotrichum, Trichoderma, Mucor, Rhizopus, Fusarium and Mortierella were isolated in Foma River, Nigeria (Agbabiaka et al., 2012). Details of similar isolates recovered from soil and sediments at a global scale are detailed in Table 1.3, Appendix 1.