Hongzhao Yuan

Significant Role for Microbial Autotrophy in the Sequestration of Soil Carbon

ABSTRACT Soils were incubated for 80 days in a continuously labeled 14CO2 atmosphere to measure the amount of labeled C incorporated into the microbial biomass. Microbial assimilation of 14C differed between soils and accounted for 0.12% to 0.59% of soil organic carbon (SOC). Assuming a terrestrial area of 1.4 × 108 km2, this represents a potential global sequestration of 0.6 to 4.9 Pg C year−1. Estimated global C sequestration rates suggest a “missing sink” for carbon of between 2 and 3 Pg C year−1. To determine whether 14CO2 incorporation was mediated by autotrophic microorganisms, the diversity and abundance of CO2-fixing bacteria and algae were investigated using clone library sequencing, terminal restriction fragment length polymorphism (T-RFLP), and quantitative PCR (qPCR) of the ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) gene (cbbL). Phylogenetic analysis showed that the dominant cbbL-containing bacteria were Azospirillum lipoferum, Rhodopseudomonas palustris, Bradyrhizobium japonicum, Ralstonia eutropha, and cbbL-containing chromophytic algae of the genera Xanthophyta and Bacillariophyta. Multivariate analyses of T-RFLP profiles revealed significant differences in cbbL-containing microbial communities between soils. Differences in cbbL gene diversity were shown to be correlated with differences in SOC content. Bacterial and algal cbbL gene abundances were between 106 and 108 and 103 to 105 copies g−1 soil, respectively. Bacterial cbbL abundance was shown to be positively correlated with RubisCO activity (r = 0.853; P < 0.05), and both cbbL abundance and RubisCO activity were significantly related to the synthesis rates of [14C]SOC (r = 0.967 and 0.946, respectively; P < 0.01). These data offer new insights into the importance of microbial autotrophy in terrestrial C cycling.

Effect of land use on the abundance and diversity of autotrophic bacteria as measured by ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large subunit gene abundance in soils

Elucidating the biodiversity of CO2-assimilating bacterial communities under different land uses is critical for establishing an integrated view of the carbon sequestration in agricultural systems. We therefore determined the abundance and diversity of CO2 assimilating bacteria using terminal restriction fragment length polymorphism and quantitative PCR of the cbbL gene (which encodes ribulose-1,5-biphosphate carboxylase/oxygenase). These analyses used agricultural soils collected from a long-term experiment (Pantang Agroecosystem) in subtropical China. Soils under three typical land uses, i.e., rice–rice (RR), upland crop (UC), and paddy rice–upland crop rotation (PU), were selected. The abundance of bacterial cbbL (0.04 to 1.25 × 108 copies g−1 soil) and 16S rDNA genes (0.05–3.00 × 1010 copies g−1 soil) were determined in these soils. They generally followed the trend RR > PU > UC. The cbbL-containing bacterial communities were dominated by facultative autotrophic bacteria such as Mycobacterium sp., Rhodopseudomonas palustris, Bradyrhizobium japonicum, Ralstonia eutropha, and Alcaligenes eutrophus. Additionally, the cbbL-containing bacterial community composition in RR soil differed from that in upland crop and paddy rice–upland crop rotations soils. Soil organic matter was the most highly statistically significant factor which positively influenced the size of the cbbL-containing population. The RR management produced the greatest abundance and diversity of cbbL-containing bacteria. These results offer new insights into the importance of microbial autotrophic CO2 fixation in soil C cycling.

Cropping systems modulate the rate and magnitude of soil microbial autotrophic CO2 fixation in soil.

The effect of different cropping systems on CO2 fixation by soil microorganisms was studied by comparing soils from three exemplary cropping systems after 10 years of agricultural practice. Studied cropping systems included: continuous cropping of paddy rice (rice-rice), rotation of paddy rice and rapeseed (rice-rapeseed), and rotated cropping of rapeseed and corn (rapeseed-corn). Soils from different cropping systems were incubated with continuous 14C-CO2 labeling for 110 days. The CO2-fixing bacterial communities were investigated by analyzing the cbbL gene encoding ribulose-1,5-bisphosphate carboxylase oxygenase (RubisCO). Abundance, diversity and activity of cbbL-carrying bacteria were analyzed by quantitative PCR, cbbL clone libraries and enzyme assays. After 110 days incubation, substantial amounts of 14C-CO2 were incorporated into soil organic carbon (14C-SOC) and microbial biomass carbon (14C-MBC). Rice-rice rotated soil showed stronger incorporation rates when looking at 14C-SOC and 14C-MBC contents. These differences in incorporation rates were also reflected by determined RubisCO activities. 14C-MBC, cbbL gene abundances and RubisCO activity were found to correlate significantly with 14C-SOC, indicating cbbL-carrying bacteria to be key players for CO2 fixation in these soils. The analysis of clone libraries revealed distinct cbbL-carrying bacterial communities for the individual soils analyzed. Most of the identified operational taxonomic units (OTU) were related to Nitrobacter hamburgensis, Methylibium petroleiphilum, Rhodoblastus acidophilus, Bradyrhizobium, Cupriavidus metallidurans, Rubrivivax, Burkholderia, Stappia, and Thiobacillus thiophilus. OTUs related to Rubrivivax gelatinosus were specific for rice-rice soil. OTUs linked to Methylibium petroleiphilum were exclusively found in rice-rapeseed soil. Observed differences could be linked to differences in soil parameters such as SOC. We conclude that the long-term application of cropping systems alters underlying soil parameters, which in turn selects for distinct autotrophic communities.

Restricted mineralization of fresh organic materials incorporated into a subtropical paddy soil

BACKGROUND Microbial activities involved in the dynamics of organic matter determine the potential for organic carbon (C) accumulation in soil. To understand this for paddy soil, an incubation experiment (25 °C, 45% water-holding capacity) was established using (14)C-labelled glucose and rice straw (500 µg C g(-1) soil) as substrates; an adjacent upland soil was used for comparison. RESULTS The amount of microbial biomass in the paddy soil was approximately 6 times larger and its turnover rate was 1.5-3 times faster than in the upland soil. These proportions of (14)C-labelled glucose and rice straw mineralized in the paddy soil were about 3% smaller (P < 0.01) than those in the upland soil. Also, there was no significant priming effect of fresh substrate additions on the mineralization of native organic C in the paddy soil, while the priming effect was significant in the upland soil. CONCLUSION Although the paddy soil contains a large amount of microbial biomass, which is also very active, the mineralization of fresh substrates is significantly restricted in this soil, along with a small priming effect. This favours the accumulation of organic C in paddy soils.

Soil Carbon-Fixation Rates and Associated Bacterial Diversity and Abundance in Three Natural Ecosystems

CO2 assimilation by autotrophic microbes is an important process in soil carbon cycling, and our understanding of the community composition of autotrophs in natural soils and their role in carbon sequestration of these soils is still limited. Here, we investigated the autotrophic C incorporation in soils from three natural ecosystems, i.e., wetland (WL), grassland (GR), and forest (FO) based on the incorporation of labeled C into the microbial biomass. Microbial assimilation of 14C (14C-MBC) differed among the soils from three ecosystems, accounting for 14.2–20.2% of 14C-labeled soil organic carbon (14C-SOC). We observed a positive correlation between the cbbL (ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit gene) abundance, 14C-SOC level, and 14C-MBC concentration confirming the role of autotrophic bacteria in soil carbon sequestration. Distinct cbbL-bearing bacterial communities were present in each soil type; form IA and form IC RubisCO-bearing bacteria were most abundant in WL, followed by GR soils, with sequences from FO soils exclusively derived from the form IC clade. Phylogenetically, the diversity of CO2-fixing autotrophs and CO oxidizers differed significantly with soil type, whereas cbbL-bearing bacterial communities were similar when assessed using coxL. We demonstrate that local edaphic factors such as pH and salinity affect the C-fixation rate as well as cbbL and coxL gene abundance and diversity. Such insights into the effect of soil type on the autotrophic bacterial capacity and subsequent carbon cycling of natural ecosystems will provide information to enhance the sustainable management of these important natural ecosystems.

Effect of simulated tillage on microbial autotrophic CO2 fixation in paddy and upland soils.

Tillage is a common agricultural practice affecting soil structure and biogeochemistry. To evaluate how tillage affects soil microbial CO2 fixation, we incubated and continuously labelled samples from two paddy soils and two upland soils subjected to simulated conventional tillage (CT) and no-tillage (NT) treatments. Results showed that CO2 fixation (14C-SOC) in CT soils was significantly higher than in NT soils. We also observed a significant, soil type- and depth-dependent effect of tillage on the incorporation rates of labelled C to the labile carbon pool. Concentrations of labelled C in the carbon pool significantly decreased with soil depth, irrespective of tillage. Additionally, quantitative PCR assays revealed that for most soils, total bacteria and cbbL-carrying bacteria were less abundant in CT versus NT treatments, and tended to decrease in abundance with increasing depth. However, specific CO2 fixation activity was significantly higher in CT than in NT soils, suggesting that the abundance of cbbL-containing bacteria may not always reflect their functional activity. This study highlights the positive effect of tillage on soil microbial CO2 fixation, and the results can be readily applied to the development of sustainable agricultural management.

Influence of land use on bacterial and archaeal diversity and community structures in three natural ecosystems and one agricultural soil

Studying shifts in microbial communities under different land use can help in determining the impact of land use on microbial diversity. In this study, we analyzed four different land-use types to determine their bacterial and archaeal diversity and abundance. Three natural ecosystems, that is, wetland (WL), grassland (GL), and forest (FR) soils, and one agricultural soil, that is, tea plantation (TP) soil, were investigated to determine how land use shapes bacterial and archaeal diversity. For this purpose, molecular analyses, such as quantitative polymerase chain reaction (Q-PCR), 16S rRNA gene sequencing, and terminal restriction fragment length polymorphism (T-RFLP), were used. Soil physicochemical properties were determined, and statistical analyses were performed to identify the key factors affecting microbial diversity in these soils. Phylogenetic affiliations determined using the Ribosomal Database Project (RDP) database and T-RFLP revealed that the soils had differing bacterial diversity. WL soil was rich in only Proteobacteria, whereas GR soil was rich in Proteobacteria, followed by Actinobacteria. FR soil had higher abundance of Chloroflexi species than these soils. TP soil was rich in Actinobacteria, followed by Chloroflexi, Acidobacteria, Proteobacteria, and Firmicutes. The archaeal diversity of GL and FR soils was similar in that most of their sequences were closely related to Nitrososphaerales (Thaumarchaeota phylum). In contrast, WL soil, followed by TP soil, had greater archaeal diversity than other soils. Eight different archaeal classes were found in WL soil, and Pacearchaeota class was the richest one. The abundance of bacterial and archaeal 16S rRNA gene copies in WL and GL soils was significantly higher than that in FR and TP soils. Redundancy analysis showed that bacterial diversity was influenced by abiotic factors, e.g., total organic carbon and pH, whereas total nitrogen, pH, and cation exchange capacity (CEC) significantly affected archaeal community composition. Pearson correlation analysis showed that bacterial and archaeal 16S rRNA gene abundance had the highest correlation with clay content (r > 0.905, P < 0.01), followed by total-P, CEC, pH, and silt (%). These results will lead to more comprehensive understanding of how land use affects microbial distribution.

Microbial assimilation of atmospheric CO2 into soil organic matter revealed by the incubation of paddy soils under 14C-CO2 atmosphere

ABSTRACT Similar to higher plants, microbial autotrophs possess photosynthetic systems that enable them to fix CO2. To measure the activity of microbial autotrophs in assimilating atmospheric CO2, five paddy soils were incubated with 14C-labeled CO2 for 45 days to determine the amount of 14C-labeled organic C being synthesized. The results showed that a significant amount of 14C-labeled CO2 incorporated into microbial biomass was soil specific, accounting for 0.37%–1.18% of soil organic carbon (14C-labeled organic C range: 81.6–156.9 mg C kg−1 of the soil after 45 days). Consequently, high amounts of C-labeled organic C were synthesized (the synthesis rates ranged from 86 to 166 mg C m−2 d−1). The amount of atmospheric 14CO2 incorporated into microbial biomass (14C-labeled microbial biomass) was significantly correlated with organic C components (14C-labeled organic C) in the soil (r = 0.80, p < 0.0001). Our results indicate that the microbial assimilation of atmospheric CO2 is an important process for the sequestration and cycling of terrestrial C. Our results showed that microbial assimilation of atmospheric CO2 has been underestimated by researchers globally, and that it should be accounted for in global terrestrial carbon cycle models.