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).