1.6.3.1 pH
Variations of water chemistry, such as pH, aluminium and humic acid concentrations play an important role in changing bacterial community composition (Yannarell and Triplett 2004). pH may play an indirect role by altering the chemical speciation of dissolved ions, increasing or decreasing their bioavailability and thus altering growth of taxa which require these as nutrients
22 or carbon sources (Yannarell and Triplett 2005). Fierer et al. (2007) found an interaction between the effects of dissolved organic carbon (DOC) and pH on bacterial community composition in steams and Deanross (1991) showed that pH modulated the effect of Zn on bacteria, with higher total bacterial numbers at low Zn concentration and high pH, and a shift towards more Zn tolerant organisms in high Zn environments.
pH is the environmental variable that has been found to have the greatest effect on freshwater bacterial communities, with greater effects than either temperature or residence time (Lindstrom et al. 2005). In 23 streams in the Hubbard Brook catchment in New Hampshire in America, communities were similar at sites with the same pH (Fierer et al. 2007). At low pH, Beier et al. (2008) found that Acidobacteria and Actinobacteria more common using temperature gradient gel electrophoresis (TGGE), while at higher pH, Proteobacteria are more common.
Kulichevskaya et al. (2011) assessed the bacterioplankton community abundance and diversity in some neutral lakes with different trophic status and pH using fluorescent in situ hybridization (FISH). They detected that in neutral lakes where pH = ~ 6.9, natural eutrophic lakes had the highest numbers and diversity of bacterioplankton compared with that in mesotrophic lakes which were highly dominated by phylum Actinobacteria. In acidic lakes with pH = ~ 5.5, the most common bacterial phylum was found to be Acidobacteria.
In different reservoirs in the Pearl River in China (Hong et al. 2010) and drinking water distribution systems in Milford (Carter et al. 2000) bacterial numbers were positively correlated with pH. However, in some headwater streams in North Carolina, no correlation observed between pH and bacterioplankton concentrations (Palumbo et al. 1987).
These results mirror those in soil, where more detailed studies have taken place. Both Rousk et al. (2010) and Bartram et al. (2013) found that pH values in the range 4 to 8 were positively correlated with abundance and diversity of soil bacteria using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing, with Acidobacteria dominating in acidic soils and Actinobacteria being more common in neutral and alkaline soils.
1.6.3.2 Trophic nutrient status and bacterial communities
One of the most important factors affecting bacterial activities is water trophic status, as organic matter provides carbon sources for microorganisms (Henriques et al. 2006; Zeng et al. 2011). Organic matter in aquatic environments may be allochthonous (provided by soil and terrestrial plants) and autochthonous (produced by algae and phytoplankton in water) (Fisher et al. 2000). Allochthonous organic carbon is often rather recalcitrant, such as humic materials and structural polysaccharides, while labile polysaccharides and proteins are major components of autochthonous DOM (Kirchman et al. 2004). In the Hudson River in New York, Kirchman et al. (2004) linked changes in the abundance and activity of the major groups of heterotrophic bacteria, such as Alphaproteobacteria and Betaproteobacteria to variations of composition and
23 concentration of DOM, using fluorescent in situ hybridization (FISH). High phosphatase activity was correlated with the abundance of Betaproteobacteria.
Spring runoff can carry terrestrial organic matter into freshwater, while during summer and autumn, phytoplankton and aquatic plants can produce autochthonous organic matter and support microbial growth and diversity (Fisher et al. 2000; Crump et al. 2003). Crump et al. (2003) found that in lake water, primary production by phytoplankton was much higher than secondary production by bacteria, which represented only 20% of primary production. Bacterial community diversity can be influenced by primary productivity (Kassen et al. 2000). Benlloch et al. (1995) observed a positive relationship between primary productivity and bacterial community diversity in two coastal lagoons, and others have reported a negative correlation in pristine aquatic sediments (Torsvik et al. 1998). In aquatic mesocosms, Horner- Devine et al. (2003) and Horner-Devine et al. (2004) observed that the relationship between primary productivity and the abundance of dominant bacterial taxa differed between major taxa, with Flavobacteria, Alpha and Beta-Proteobacteria, respectively showing positive, negative, and low correlations.
To understand the role and importance of heterotrophic bacteria in decomposing organic matter in water ecosystems, all aspects of bacterial dynamics, such as bacterial numbers and growth rate should be studied (Barillier and Garnier 1993). The quality of organic and inorganic sources as well as organic carbon is necessary to support and increase bacterial growth rates (Felip et al. 1996; Fazi et al. 2005). However, responses to these resources by individual bacterial communities are completely different (Ibekwe et al. 2012).
Many researchers investigated the correlation between bacterial community composition and diversity and different nutrients, for example, In two Canadian rivers (Meduxnekeag River and Dunbar River), Bell et al. (1982) found that ammonia was correlated positively with heterotrophic bacterial diversity. In alpine lakes and reservoirs in the Mediterranean region, Reche et al. (2009) found that bacterial production was positively related to dust inputs of particulate matter, with no correlation with bacterial diversity and composition. In aquatic mesocosms, Fisher et al. (2000) found that inorganic nitrogen and phosphorus plus carbon had a huge impact on bacterial production, while phosphorus and nitrogen alone had a huge impact on bacterial diversity. De Figueiredo et al. (2007) found that trophic status has substantial effects on bacterial diversity in some surface water ecosystems in Portugal using gradient gel electrophoresis (DGGE). Oligotrophic water bodies were dominant by Verrucomicrobia, while Bacteroidetes was the dominant group in mesotrophic and eutrophic waters.
Several studies have found a positive relationship between organic matter and bacterial growth in different environments, for example, different rivers and streams in Québec, France (Comte and del Giorgio 2009), Equatorial Pacific Ocean (Kirchman and Rich 1997), Seine River water, France (Barillier and Garnier 1993) and Warnow River, Germany (Warkentin et al. 2011). Shiah and Ducklow (1994) found that the number and growth rate of bacteria in Chesapeake Bay did not increase, although high concentrations of nutrients were present, and this was attributed to the low water temperature (below 7 ˚C) limiting their growth. However, Kirchman
24 and Rich (1997) stated that for bacteria to grow effectively in cold water at the same level in warm water, then high concentrations of substrates are needed.
Total bacterial numbers showed a positive relationship with different nutrients, for example, dissolved organic carbon (DOC) in the Ogilvie River in Canada and Swift River in New Hampshire (Albright et al. 1980), allochthonous organic matter in the Brda River in Germany (Małecka and Donderski 2006), Chlorophyll a in the River Hull, UK (Yamakanamardi and Goulder 1995), Chlorophyll a and organic matters in different aquatic environments (Schumann et al. 2003), Chlorophyll a in the Tarun River in Austria (Klammer et al. 2002), total organic carbon (TOC) in drinking water in Milford, US (Carter et al. 2000), TOC in different groundwaters in Sweden (Pedersen and Ekendahl 1990), total phosphorus (TP) in six lakes in Canada (Currie 1990) and TP in the Danube River (Velimirov et al. 2011).
1.6.3.3 Bacterial tolerance to chemical pollutants
Heavy metals at high concentrations represent a dangerous threat to ecosystem in rivers, and continuous exposure of microbial communities to metals may reduce their diversity and activity, and also change their structure (Vilchez et al. 2011). However, some organisms are able to develop to tolerate different concentration levels of heavy metals and may demonstrate a higher abundance than other organisms (Cebron et al. 2004). Microbial tolerance to heavy metals represents a very important feature of ecosystems, enabling them to continue their roles in some important processes, such as self-purification and nutrient cycling (Deanross and Mills 1989).
Several studies have investigated the tolerance of some bacterial taxa to heavy metals, such as cadmium, nickel and zinc in the Rémarde River in Paris (Fechner et al. 2011), nickel in the Saskatchewan River in Canada (Lawrence et al. 2004), zero-valent iron nanoparticles in a the River Thames (a natural river) in the UK (Barnes et al. 2010) and lead and copper in Maumee River, St. Mary's River and St. Joseph River in the US (Deanross and Mills 1989).
1.6.3.4 The role of bacterial communities in the bioremediation
Rivers highly loaded with sewage effluents can be inhabited by heterotrophic bacteria (Yamakanamardi and Goulder 1995), and some types of bacteria are able to decompose toxic materials, such as Malathion (pesticide) that is lethal to other organisms (Horner-Devine et al. 2004; Dang et al. 2010).
Several studies examined the role of some types of bacteria in the bioremediation of aquatic environments, for example, groundwater (Marzorati et al. 2006; D'Angelo and Nunez 2010; Vilchez et al. 2011), in the River Binlamdoune in Morocco (Essahale et al. 2010), in the
25 Kanzaki River in Japan (Araya et al. 2003) and in the Isle River Basin in France (Quemeneur et al. 2010).