Multiple spatial scales of bacterial and fungal structural and functional traits affect carbon mineralization.

Studying the functional heterogeneity of soil microorganisms at different spatial scales and linking it to soil carbon mineralization is crucial for predicting the response of soil carbon stability to environmental changes and human disturbance. Here, a total of 429 soil samples were collected from typical paddy fields in China, and the bacterial and fungal communities as well as functional genes related to carbon mineralization in the soil were analysed using MiSeq sequencing and GeoChip gene microarray technology. We postulate that CO2 emissions resulting from bacterial and fungal carbon mineralization are contingent upon their respective carbon consumption strategies, which rely on the regulation of interactions between biodiversity and functional genes. Our results showed that the spatial turnover of the fungal community was 2-4 times that of the bacterial community from hundreds of meters to thousands of kilometres. The effect of spatial scale exerted a greater impact on the composition rather than the functional characteristics of the microbial community. Furthermore, based on the establishment of functional networks at different spatial scales, we observed that both bacteria and fungi within the top 10 taxa associated with carbon mineralization exhibited a prevalence of generalist species at the regional scale. This study emphasizes the significance of spatial scaling patterns in soil bacterial and fungal carbon degradation functions, deepening our understanding of how the relationship between microbial decomposers and soil heterogeneity impacts carbon mineralization and subsequent greenhouse gas emissions.

[Functional Genomics Analysis of Nitrogen and Phosphorus Transformation in Maize Rhizosphere Microorganisms].

Fertilizer reduction and efficiency improvement is an important basis for ensuring the safety of the agricultural ecological environment. Microorganisms are the key driving force for regulating the soil nitrogen and phosphorus cycle. Studying the nitrogen and phosphorus transformation function of rhizosphere microorganisms can provide a microbiological regulation approach for further improving the use efficiency of soil nitrogen and phosphorus. Based on the field micro-plot experiments of three typical farmland soils(phaeozem, cambisol, and acrisol), metagenomic sequencing technology was used to study the differences in functional genes and regulatory factors of maize rhizosphere microorganisms during soil nitrogen and phosphorus transformation. The results showed that the functional diversity of maize rhizosphere microorganisms was affected by soil type. The functional diversity of rhizosphere microorganisms in phaeozem and cambisol was mainly affected by water content and nutrient content, and that in acrisol was affected by total phosphorus(TP) and available phosphorus(AP). For soil nitrogen transformation, the gene abundance of related enzymes in the pathway of nitrogen transformation was the highest in the urease gene(ureC) and glucose dehydrogenase gene(gdh), which were 7.25×10-5-12.88×10-5 and 4.47×10-5-7.49×10-5, respectively. The total abundance of assimilatory nitrate reduction functional genes in acrisol was higher than that in phaeozem and cambisol, and the total abundance of functional genes related to other processes was the highest in cambisol. The abundance of functional genes encoding enzymes related to nitrogen metabolism was mainly driven by soil bacterial richness, total potassium(TK), and TP. For soil phosphorus transformation, the number of alkaline phosphatase genes(phoD) catalyzing organic phosphorus mineralization was 1093, and the number of acid phosphatase genes(PHO) was 42. The abundance of phoD was two orders of magnitude higher than that of PHO. In addition, fertilization had no significant effect on the abundance of phoD and PHO in the same soil type. Random forest analysis showed that the abundances of phoD and PHO were significantly affected by soil moisture, organic matter(OM), and total nitrogen(TN), but AP content had the greatest impact on PHO abundance. These results clarified the nitrogen and phosphorus transformation characteristics of maize rhizosphere microorganisms at the functional genomic level and enriched the molecular biological mechanism of the microbial nitrogen and phosphorus transformation function.

Soil pH Filters the Association Patterns of Aluminum-Tolerant Microorganisms in Rice Paddies.

Soil microbes are considered the second genome of plants. Understanding the distribution and network of aluminum (Al)-tolerant microorganisms is helpful to alleviate Al toxicity to plants in acidic soils. Here, we examined soluble Al3+ and bacterial communities carrying Al resistance genes in paddy soils with a soil pH range of 3.6 to 8.7. In the acidic soil with pH <5.1, the content of Al3+ increased significantly. There were abundant and diverse Al-tolerant microorganisms in acidic soils, including Clostridium, Bacillus, Paenibacillus, Desulfitobacterium, and Desulfosporosinus, etc. Moreover, compared with neutral and alkaline soils, the network structure of Al-tolerant microorganisms was more complex. The potential roles of major Al-tolerant microbial taxa on each other in the ecological network were identified by a directed network along 0.01 pH steps. The influential taxa in the network had a broader niche and contained more antioxidant functional genes to resist Al stress, indicating their survival advantage over the sensitive taxa. Our study is the first to explore the distribution of Al-tolerant microorganisms in continental paddies and reveal their potential associations mediated by pH, which provides a basis for further utilization of microbial resources in acidic agricultural soils. IMPORTANCE Aluminum (Al) toxicity is the primary limiting factor of crop production in acidic soils with pH <5.0. Numerous studies have focused on the mechanism of Al toxicity and tolerance in plants; however, the effects of Al toxicity on soil microorganisms and their tolerance remain less studied. This study investigated the distribution and association patterns of Al-tolerant microorganisms across continental paddy fields with a soil pH range of 3.6 to 8.7. The results showed that soil pH filters exchangeable Al3+ content, diversity, and potential associations of Al-tolerant microbial community. The influential taxa in community network play an important role in Al tolerance and have potential applications in mitigating Al toxicity and promoting crop growth in acidic soils.

Microbial metabolism and necromass mediated fertilization effect on soil organic carbon after long-term community incubation in different climates.

Understanding the effects of changing climate and long-term human activities on soil organic carbon (SOC) and the mediating roles of microorganisms is critical to maintain soil C stability in agricultural ecosystem. Here, we took samples from a long-term soil transplantation experiment, in which large transects of Mollisol soil in a cold temperate region were translocated to warm temperate and mid-subtropical regions to simulate different climate conditions, with a fertilization treatment on top. This study aimed to understand fertilization effect on SOC and the role of soil microorganisms featured after long-term community incubation in warm climates. After 12 years of soil transplantation, fertilization led to less reduction of SOC, in which aromatic C increased and the consumption of O-alkyl C and carbonyl C decreased. Soil live microbes were analyzed using propidium monoazide to remove DNAs from dead cells, and their network modulization explained 60.4% of variations in soil labile C. Single-cell Raman spectroscopy combined with D2O isotope labeling indicated a higher metabolic activity of live microbes to use easily degradable C after soil transplantation. Compared with non-fertilization, there was a significant decrease in soil α- and ß-glucosidase and delay on microbial growth with fertilization in warmer climate. Moreover, fertilization significantly increased microbial necromass as indicated by amino sugar content, and its contribution to soil resistant C reached 22.3%. This study evidentially highlights the substantial contribution of soil microbial metabolism and necromass to refractory C of SOC with addition of nutrients in the long-term.

Coexistence patterns of soil methanogens are closely tied to methane generation and community assembly in rice paddies.

BACKGROUND: Soil methanogens participate in complex interactions, which determine the community structures and functions. Studies continue to seek the coexistence patterns of soil methanogens, influencing factors and the contribution to methane (CH4) production, which are regulated primarily by species interactions, and the functional significance of these interactions. Here, methane emissions were measured in rice paddies across the Asian continent, and the complex interactions involved in coexistence patterns of methanogenic archaeal communities were represented as pairwise links in co-occurrence networks. RESULTS: The network topological properties, which were positively correlated with mean annual temperature, were the most important predictor of CH4 emissions among all the biotic and abiotic factors. The methanogenic groups involved in commonly co-occurring links among the 39 local networks contributed most to CH4 emission (53.3%), much higher than the contribution of methanogenic groups with endemic links (36.8%). The potential keystone taxa, belonging to Methanobacterium, Methanocella, Methanothrix, and Methanosarcina, possessed high linkages with the methane generation functional genes mcrA, fwdB, mtbA, and mtbC. Moreover, the commonly coexisting taxa showed a very different assembly pattern, with ~ 30% determinism and ~ 70% stochasticity. In contrast, a higher proportion of stochasticity (93~99%) characterized the assembly of endemically coexisting taxa. CONCLUSIONS: These results suggest that the coexistence patterns of microbes are closely tied to their functional significance, and the potential importance of common coexistence further imply that complex networks of interactions may contribute more than species diversity to soil functions. Video abstract.

[Interactions of Fungi Community and Relationship with the Carbon Structure in Arable Mollisols with Gradient Organic Matter Content].

Fungi play an important role in the accumulation and transformation of soil organic matter (SOM) and nutrient cycling. To investigate the relationship between the fungal community and soil organic carbon functional groups under gradient SOM contents in arable mollisols, arable mollisols with 2%-9% SOM content were collected in Northeast China. Solid-state 13C-NMR technology was used to explore the differences in the functional group structure of SOM, and ITS high-throughput sequencing was used to investigate the fungal community structure. The potential interactions between different taxonomic groups of soil fungal community and their associations with organic carbon molecular structures were compared by constructing molecular ecological networks under low SOM (2%-5%) and high SOM (7%-9%) conditions. The 13C-NMR results indicated an increase in the relative abundance of Alkyl C (25.8% to 35.9%). The decrease in Alkyl C/O-Alkyl C indicated a smaller degree of decomposition in high SOM soils. Sordariomycetes and Mortierellomycotina dominated the fungal community and their relative abundance increased with the SOM gradient (P<0.05) from 14.33% to 28.17% and from 7.32% to 23.14%, respectively. The network analysis showed simpler ecological topological properties of the fungal community in low SOM soils, with lower numbers of nodes, edges, and average clustering coefficients than those in high SOM soils. A closer relationship between fungi and organic carbon functional groups, especially LOC, was observed in low SOM soils. The random forest model showed that LOC had the largest amount for fungal interactions in low SOM soils (10%), followed by recalcitrant organic carbon (ROC). In comparison, LOC contributed less to the variations in fungal interactions in high SOM soils (7.4%). With globally increasing soil carbon loss, the limition of the carbon resources, especially the reduction of LOC, may reduce the stability and ecological functions of soil fungal communities.