4.3 Soil microbes
Microorganisms are the driving force for nutrient conversion and cycling, having the characteristics of large biomass, complex community composition, diverse metabolic functions, and complex interactive relationships (Bardgett & van der Putten, 2014). They can mediate important metabolic processes in the carbon and nitrogen cycles (Brussaard, de Ruiter & Brown, 2007). Climate change caused by greenhouse gas emissions has long been an important global issue. Therefore, biological mitigation of CO2 emissions has attracted the attention of many researchers (Mahinpey, Asghari & Mirjafari, 2011; Farrelly, Everard, Fagan & McDonnell, 2013). Aboveground plant parts provide organic carbon sources for roots and soil organisms, thus influencing strongly the underground system. In particular, rhizosphere secretions provide carbon sources and energy for the growth of microorganisms (Stephan Shockey, Moe & Dorn, 2002; van der Wielen, 2006; Selesi, Pattis, Schmid, Kandeler & Hartmann, 2007).
We found in our previous research that Jerusalem artichoke played a significant role in increasing soil microbial populations. We reported greater relative abundance of p_Proteobacteria, p_Bacteroidetes and p_Cyanobacteria in the bulk than rhizosphere soil, whereas p_Acidobacteria, p_Chloroflexi and p_Nitrospirae abundance was greater in the rhizosphere than bulk soil (Shao et al. 2019). Here, almost all autotrophic microorganisms and nitrogen-fixing microorganisms belonged to p_Proteobacteria, and its relative abundance in bulk soil was slightly lower than that in rhizosphere soil.
Among cbbL -containing autotrophic bacteria, the relative abundance of c_Ga mmaproteobacteria exceeded 65% in the bulk and rhizosphere soils, including the five dominant genera: g_Halorhodospira, g_Marichromatium, g_Thioalkalivibrio, g_Alkalilimnicola, and g_Ectothiorhodospira , all of which grow in oceans or high-salt environments where the pH is neutral to extremely alkaline (Sorokin, Muntyan, Panteleeva & Muyzer, 2012). There were also three dominant genera: g_Thiobacillus , g_Cupriavidus andg_Hydrogenophaga , all belonging to c_Betaproteobacteria .
Almost all of the unique cbbM -containing autotrophic bacteria in the rhizosphere soils belonged to c_Betaproteobacteria, c_Alphaproteobacteria and c_Actinobacteria , and the five dominant genera were g_Halothiobacillus, g_Sideroxydans, g_Rhodopseudomonas, g_Thiobacillus , and g_Sulfuritalea . The previous research data of our team demonstrated that the content of soil organic carbon (12.8 ± 0.79 g/kg) and total nitrogen of the Jerusalem artichoke planting area (0.96 ± 0.21 g/kg) in this experimental area were significantly higher than those of the bare control soil (5.6 ± 0.89 g C/kg and 0.40 ± 0.04 g N/kg) (Li et al., 2018). In the study presented here, the community diversity of cbbM -containing autotrophic bacteria and nitrogen-fixing bacteria containing nifH showed the order of rhizosphere soil > bulk soil, which indicated that Jerusalem artichoke could enhance soil fixation of carbon and nitrogen by changing the community composition of soil microorganisms.
Soil environments with low CO2 concentration are beneficial to the growth of autotrophic bacteria containing thecbbL gene, whereas the autotrophic bacteria with the cbbMgene are relatively abundant at low oxygen and high CO2concentrations (Videmsek et al., 2009), which was confirmed in the present study. Sideroxydans is a Fe-oxidizing bacterium.Thiobacillus and Sulfuritalea are ammonia-oxidizing bacteria, and both can also provide the available sulfate-sulfur plants can take up. In addition, Sulfuritalea also functions in the denitrification process. Some species of Hydrogenophaga also have anaerobic nitrate respiration and are denitrifiers (Vandamme & Coenye, 2004; Jazaeri, Akhgar, Sarcheshmehpour & Mohammad, 2016). Four dominant genera containing nifH were: g_Desulfuromonas, g_Geobacter, g_Geoalkalibacter, and g_Anaeromyxobacter, allbelonging to c_Deltaproteobacteria (Holmes, Nevin & Lovley, 2004; Zavarzina et al., 2006). Deltaproteobacteria exhibit considerable anaerobic physiological diversity, including sulfate reduction, iron reduction (g_Geobacter ), fermentation, and dehalogenation (Nevin, Holmes, Woodard, Covalla & Lovley, 2007). Moreover, rhizobia (g_Rhizobium, g_Bradyrhizobium, g_Sinorhizobium , and g_Azorhizobium) are symbiotic nitrogen-fixers, and responsible for the major share of global fixation of atmospheric nitrogen, and require low concentration of oxygen (Viprey, Rosenthal, Broughton & Perret, 2000; Lodwig et al., 2003). In the present study, the abundance of Gammaproteobacteria andDeltaproteobacteria at given soil salinity was higher in the bulk than rhizosphere soil. In contrast, the relative abundance ofBetaproteobacteria and Alphaproteobacteria was significantly higher in the rhizosphere than bulk soil, and the abundance was higher in low-salinity than high-salinity soils (Table 1). Most Betaproteobacteria are resistant to low pH and high temperature, and prefer low-oxygen conditions. BothBetaproteobacteria and Gammaproteobacteria include nitrogen-fixing rhizobia (Moulin, Munive, Dreyfus & Boivin-Masson, 2001; Shiraishi, Matsushita & Hougetsu, 2010; Klann, McHenry, Montelongo & Goffredi, 2016).
We also found other functional microorganisms such as aerobic methane oxidizing bacteria (g_Methylibium, g_Methylobacter, g_Methylobacterium, etc. ), desulfurization bacteria (g__Desulfarculus, g_Desulfatibacillum, g_Desulfitobacterium, etc. ), nitrifying bacteria (g_Nitrobacter, g_Nitrosospira, g_Nitrospira, etc. ), sulfur-oxidizing bacteria (g_Sulfuricurvum, g_Ectothiorhodospira, g_Halothiobacillus, etc. ), and photosynthetic bacteria (g_Rhodobacter, g_Rhodococcus, g_Rhodospirillum, etc. ). This indicated that some autotrophic and nitrogen-fixing microorganisms are not involved only in the carbon and nitrogen cycle, but also may participate in the biogeochemical cycles of other elements, thus playing a role in material cycling and energy flow in the micro-ecological environments in saline soils. Microbial communities with different functionalities jointly regulate and drive the various processes in the element cycling, and play an irreplaceable role in responding to global climate change and maintaining the function and stability of the ecosystems (Bardgett, Freeman & Ostle, 2008; Zhou et al. 2012; Madigan, Bender, Buckley, Sattley & Stahl, 2019).