Abstract:【Objective】 With global climate change and overgrazing, shrub encroachment is extensively occurring in global grasslands. However, relatively little is known about how the structure of bacterial communities shifts with shrub encroachment. Thus, considering the aboveground plant community, soil carbon chemical composition, soil bacterial community structure and network beneath the canopies of three typical shrub species (Potentilla fruticosa, Spiraea alpina, and Caragana microphylla) as well as in adjacent grassland (as a control), the effects of shrub encroachment on the structure of soil bacterial communities and soil carbon pools were explored.【Method】 16S rRNA gene sequencing was used to investigate the bacterial communities and co-occurrence features among bacterial taxa while Fourier transform infrared spectroscopy (FTIR) was conducted to assess the soil organic carbon (SOC) chemical composition.【Result】 Shrub encroached grasslands (Potentilla fruticosa and Caragana microphylla) showed significant changes in aboveground plant community composition (P < 0.01) while the aboveground plant community diversity and richness remained constant (P > 0.05). The biomass of the three shrub plots was significantly higher than that of grassland (P < 0.05) whereas underground biomass showed no significant difference (P > 0.05). Shrub encroachment had no significant effects on SOC and total nitrogen (TN) contents, but weakened the differences of SOC contents between top- and subsoils, as shown by significantly higher SOC contents in the topsoil of the grassland than in its subsoil (P < 0.05), with no such trend in the three shrub plots.The SOC chemical composition in both top- and subsoils of the three shrublands and grassland was dominated by aromatics(except for deep soil in Caragana microphylla plots), with no significant difference in aromatic content between shrub and grassland plots (P > 0.05). However, the Caragana microphylla plots exhibited a surface-aggregated distribution of aromatics (P < 0.05). Random forest model analysis revealed that the distribution of Acidobacteria and Actinobacteria was the most important predictor of shrub encroachment in top and subsoils (P < 0.01). According to Non-metric multidimensional scaling (NMDS) analysis, the bacterial community composition of alpine grassland was significantly altered by shrub encroachment. Moreover, plant community composition and SOC chemical compositions were the main explanatory factors affecting bacteria community composition in both depths. Functional prediction analysis identified four biological metabolic pathways, including cellular processes, environmental information processing, metabolism, and genetic information processing, with metabolism being enriched in shrub plots (P < 0.05). Based on topological parameters of total links, complexity, and natural connectivity, the results showed that the soil bacterial network of shrublands was more complicated and stabilized than that in grasslands, and mutualism or commensalism may play an important role in establishing the bacterial community structure. 【Conclusion】 In summary, the results of this study suggest that shrub encroachment had an important regulatory effect on soil bacterial community structure and soil carbon pool. The results enrich the literature on soil microbial community in alpine grassland and provide a theoretical basis for the effect of soil carbon source and sink in alpine grassland.

Abstract:【Objective】 Land reclamation is a significantly important way to restore soil productivity in high groundwater mining areas. However, most of the reclaimed soil always shows poor functions, such as lower fertility and biodiversity, while the in-depth understanding of microbiological mechanisms underlying the formation and restoration of multifunctional reclaimed soil is still deficient. 【Method】 Four reclamation plots including 9 years, 12 years, 15 years, and 18 years of reclamation, and 1 control plot from the Dongtan mining area in Zoucheng City, Shandong Province, were selected as the research objects. A total of 75 surface soil samples were collected, and 18 soil physical, chemical, and biological indicators such as organic carbon were measured to explore the interaction between soil microbial communities and soil multifunctionality, as well as the microbiological mechanisms of multifunctionality variation. Moreover, based on the molecular ecological network methods, supplemented by statistical analysis methods, several microbial networks were constructed to investigate the interaction between microbial community diversity, network structure, and soil multifunctionality. 【Result】 The results showed that: (1) Land reclamation activities and the normal vegetation rotation of the cultivated land have significantly improved soil multifunctionality, with soil multifunctionality almost reaching the undisturbed control level after 18 years of reclamation. Moreover, among the soil properties, soil organic carbon, pH, available phosphorous, and most enzyme activities were important influencing factors for multifunctionality. (2) With the increasing reclamation years, soil microbial diversity significantly increased, while the richness performance of bacteria and fungi was different. The increasing trend of bacteria was not significant after 12 years of reclamation whereas fungi increased significantly until 18 years of reclamation. However, the abundance of bacteria and fungi reached normal farmland levels after 15 years and 18 years of reclamation, respectively. (3) The analysis results of the microbial co-occurrence network showed that the nodes, edges, average degree, average path length, network density, clustering coefficient, and betweenness centrality in the bacterial community co-occurrence network significantly increased with the increase of reclamation time. Moreover, the topological properties of bacterial and fungal subnetworks such as edge, degree, and network density were significantly positively correlated with soil multifunctional properties. The diversity of microbial communities showed a positive impact on the network complexity, enhancing the association between species and thereby enhancing their versatility. Both the complexities of bacterial and fungal community networks presented significant correlations with soil multifunctionality. The impact of bacterial network complexity on soil multifunctionality was not affected by other indicators, whereas the correlation between fungal network complexity and soil multifunctionality was influenced by bacterial richness, soil microbial diversity, and fungal richness. The structural equation model results indicated that microbial diversity can directly and positively regulate soil multifunctionality, or indirectly manipulate soil multifunctionality by positively influencing the network complexity of bacteria and fungi. 【Conclusion】 This study has revealed the driving mechanism of multifunctional restoration of reclaimed soil in the eastern plain mining area, which would provide important guidance for the deeper understanding of the development and functional succession of reclaimed soil microbiota, as well as soil quality management and protection.

Abstract:【Objective】The combined application of crop straw with chemical fertilizers and chicken manure can change soil microbial community structure and the interaction between microorganisms. However, whether there is a correlation between these changes and wheat yield remains unclear.【Method】A 7-year field experiment was used as the research platform, and this included five management strategies: (1) N0S0: no fertilizer or crop straw returning, (2) N0S: crop straw returning, (3) NS0: traditional chemical fertilization, (4) NS: crop straw returning with chemical fertilizer, and (5) NSM: crop straw returning with chemical fertilizer and the nitrogen was substituted 20% by chicken manure. The effects of different management strategies on microbial community composition in bacterial-fungal co-occurrence networks and the correlation between key microorganisms and wheat yield were studied.【Result】The results showed that compared with N0S0 treatment, the grain yield of wheat under NS0, NS and NSM treatments increased by 539.20%, 611.56% and 676.56%, respectively, while there was no significant change under N0S treatment. The bacterial and fungal community compositions were divided into three significantly different groups: N0S0 and N0S, NS0, and NS and NSM, respectively, indicating that the microbial community composition was significantly different with or without chemical fertilizer application. Under both chemical fertilizer applications, there was a significant difference in whether organic materials were applied. Ranked from high to low importance, we found that available phosphorus, electrical conductivity, microbial biomass nitrogen, soil organic carbon, readily oxidizable organic carbon, and particulate organic carbon were the main soil physicochemical properties that caused the changes in bacterial community composition under different treatments. Also, electrical conductivity, microbial biomass nitrogen, readily oxidizable organic carbon, particulate organic carbon, available phosphorus, and soil organic carbon were the main soil physicochemical properties that caused the changes in fungal community composition under different treatments. In the bacterial-fungal co-occurrence network, two key modules (module 1 and module 4) were significantly correlated with wheat yield changes. NS+NSM treatments increased the relative abundance of beneficial microorganisms in module 4, including Nocardioides, Cellulomonas, Pir4_lineage, Chrysosporium,Acaulium, and Schizothecium, which were positively correlated with wheat yield. These beneficial microorganisms could degrade cellulose and lignin, promote nutrient conversion and recycling, or inhibit the growth of the potential pathogen. NS+NSM treatments also significantly reduced the relative abundance of plant pathogenic fungi in module 1, including Stachybotrys,Achroiostachys, and Fusicolla, which were negatively correlated with wheat yield and were detrimental to soil health and crop growth.【Conclusion】Therefore, crop straw returning with chemical fertilizer and crop straw returning with chemical fertilizer and chicken manure were beneficial to the increase of key beneficial microorganisms and the decrease of pathogenic fungi. The function and the relative abundance of key microorganisms had effects on wheat yield.

Abstract:【Objective】 Fungal decomposition plays a key role as the primary driving force of the nutrient cycling and energy flow in the soil. However, the response characteristics of fungal communities to different types of straw carbon inputs and the key environmental factors at the aggregate scale are not yet clear.【Method】 In this study, corn straw was used as the experimental, and three treatments were set according to the equal carbon content of straw returning: regular crushed straw (RS), decomposed straw (DS) and straw biochar (BC). A control group without straw application (CK) was also set up. The study aimed to investigate the effects of different carbon types from straws on the diversity, composition, and distribution of fungi in soil macroaggregates (>0.25 mm) and microaggregates (<0.25 mm), as well as the interactions within fungal communities. Furthermore, key environmental factors influencing the variation of soil fungal communities were explored.【Result】 The results of a 2-year field experiment indicate that RS treatment significantly reduced fungal α diversity (P<0.05) in microaggregates (<0.25 mm) and macroaggregates (>0.25 mm). The top three dominant phyla in each treatment were Ascomycota, Mortierellomycota, and Basidiomycota, while the top three dominant genera were Plectosphaerella, Chaetomium, and Mortierella. Compared to different aggregate size fractions, the treatment with straw carbon significantly induced differentiation in fungal community structure (P<0.01), with notably distinct fungal community structure observed in the RS treatment compared to the other treatments. Also, analysis of fungal co-occurrence network showed that BC treatment increased the number of nodes (10.08%) and modularity (5.55%) while DS treatment increased the number of nodes (11.17%), the number of edges (32.57%) and the average degree of nodes (19.27%) included in the co-occurrence network, and all of which improved the structural stability of the fungal network of soil aggregates. The Mantel test analysis found that ammonium nitrogen (AN) and pH were the key environmental factors affecting the fungal community structure of soil aggregates, with the fungal community in the RS treatment being the most influenced by soil environmental factors. The prediction analysis of fungal community function showed that the input of straw carbon could reduce the relative abundance of pathogenic fungi and reduce the occurrence of soil-borne diseases in farmland. 【Conclusion】 Our results reveal that in the short term, different soil aggregates of fungi are more susceptible to the influence of straw carbon types, leading to differentiation. The addition of decomposed straw and straw biochar can increase soil AN content, thereby increasing the complexity of the fungal network, thus, promoting fungal community stability. Therefore, for practical applications, it is advisable to consider appropriately increasing the input of decomposed straw or straw biochar to promote the stability of soil ecological functions.

Abstract:【Objective】 The black soil region of Northeast China is an important commodity grain production base in China. However, intense soil erosion has led to a decline in soil health and ecological functions in the region. 【Method】 The microbial diversity of soils at different slope positions and their relationship with the co-occurrence network was analyzed using slope farmland soils from typical black soil areas, and the effects of erosion-deposition on soil microbial communities were investigated in combination with soil physicochemical properties. 【Result】 The results showed that: (ⅰ)Soil erosion significantly reduced microbial α-diversity while deposition increased it. Soil organic carbon (SOC) and mean weight diameter (MWD) had a significant positive correlation with microbial diversity. (ⅱ)Erosion-deposition did not change the major dominant groups at the phylum or family levels of bacterial and fungal. However, at the phylum and family level, changes in the relative abundance of the main dominant groups at the fungal were more pronounced than in the case of bacteria. (ⅲ)The results of redundancy analyses indicated that erosion-deposition, by altering SOC, total phosphorus (TP), MWD, etc., led to different trends in the relative abundance of species significantly affected by them. (ⅳ)Soil erosion significantly reduced the complexity of the bacterial co-occurrence network, whose node and edge respectively decreased from 540 and 572 (top of slope) to 488 and 520 (lower slope) and increased to 546 and 602 (foot of slope). Also, soil erosion significantly increased the number of clustering coefficients, the number of which increased from 0.38 (top of the slope) to 0.41 (lower slope). Meanwhile, erosion-deposition significantly changed the number of nodes of the fungal network, the number of which decreased from 223 (foot of slope) to 187 (lower slope) and increased to 201 (foot of slope). In addition, the bacterial network stability showed a decreasing trend with increasing erosion intensity while the fungal network stability showed a decreasing and then increasing trend.【Conclusion】 This study revealed the changes and driving factors of soil microbial diversity and community structure under erosion-depositions and provided a theoretical basis for further understanding of the interaction between soil physicochemical properties and microbes in slope farmland of typical black soil area.

Abstract:【Objective】The mechanism of the inconsistent effects of straw application on crop yield is still unclear, and the main reason may be related to the insufficient understanding of the effects of straw application on soil microbial community composition and its abundance changes on crop yield.【Method】A pot experiment to study the growth of wheat was carried out using red and yellow-cinnamon soils. Three levels of straw application were set for each soil, namely 0, 10 and 30 g·kg-1 soil(S0, S10, S30). Based on bacterial-fungal co-occurrence networks, the Path analysis model was used to evaluate the contribution of microbial ecological clusters, enzyme activities and chemical properties to wheat yield. 【Result】The results showed that although the content of available nutrients, soluble organic carbon, microbial biomass carbon and enzyme activities(amylase, invertase, polyphenol oxidase, urease, acid phosphatase, dehydrogenase) increased significantly in both soils, the wheat yield increased with the increase in straw dosage in the red soil but decreased in yellow-cinnamon soil. Compared with S0, S10 and S30treatments increased wheat grain yield and above-ground biomass by 33%-44% and by 73%-85% in the red soil; and decreased wheat grain yield and above-ground biomass by 22%-25% and by 55% in the yellow-cinnamon soil, respectively. The abundance of two key ecological clusters within the bacterial-fungal co-occurrence network, enzyme activities and soil chemical properties had positive effects on wheat yield in red soil while the abundance of two key ecological clusters had a larger positive effect on wheat yield in yellow-cinnamon soil. The straw application significantly increased the abundance of Aspergillus, a key microorganism positively correlated with wheat yield in red soil, while significantly decreased the abundance of Bacillus, Burkholderia, and Basidiobolus, which were positively correlated with wheat yield in yellow-cinnamon soil.【Conclusion】The combined effects of straw application, an increase in key microbial abundance, enzyme activities, and improvement of soil chemical properties was responsible for improving wheat yield in the red soil. In the yellow-cinnamon soil, the decrease in wheat yield was mainly related to lower key microbial abundance, whose effect was superior to the potential positive effects of improved soil chemical properties and enzyme activities. These results suggest that the change in the abundance of key microorganisms has an important influence on the variation of crop yield after straw returning.

Abstract:【Objective】Great differences exist in the utilization of carbon and nutrients between habitat generalists and specialists, which play unique roles in the cycle of soil energy and nutrients. At present, the research on farmland microorganisms mainly focuses on the whole bacteria, fungi, archaea or other functional communities, and the understanding of habitat generalists and specialists in farmland ecosystems is still lacking. Therefore, this study was designed to explore the community structure, assembly mechanism and possible functions of habitat generalists and specialists in typical paddy soils in eastern and southwestern China. 【Method】Sixteen surface soil samples (0~20 cm) were collected from the eastern area (Jiangsu, Anhui, Shanghai) and southwestern area (Guizhou and Yunnan) of China according to the data of the second soil survey, and their physico-chemical properties and next generation high-throughput sequencing were analyzed. 【Result】The results showed that 3.28% of all OTUs were classified as habitat generalists while 9.07% as habitat specialists. There were significant differences in species composition between habitat generalists and specialists. At the level of phylum, the proportions of habitat specialists in Chloroflexi, Actinobacteria, Nitrospirae, Firmicutes and Planctomycetes were higher than those of habitat generalists. The analysis of the community assembly process based on the β diversity null model showed that habitat generalists and specialists were dominated by deterministic process. Compared with habitat specialists, habitat generalists were more affected by the stochastic process. The environmental factors driving the community structure variation of habitat generalists and specialists were different. pH, mean annual precipitation, clay content and total nitrogen were the main factors driving the community structure variation of habitat generalists, while the community structure variation of habitat specialists was dominated by pH and clay content. By analyzing the co-occurrence network and robustness of habitat generalists and specialists, it was found that the habitat specialists’ network had more connections, more complexed structure and stronger robustness. The functional prediction by FAPROTAX showed that biological nitrogen fixation mainly existed in habitat generalists. 【Conclusion】Information derived from the community structure, environmental driving factors, assembly process, co-occurrence network characteristics and related functions of nitrogen metabolism of habitat generalists and specialists, provides a theoretical basis for the evolution and regulation of bacterial communities in paddy fields.

Abstract:【Objective】The combined application of woody peat and straw has the potential to rapidly increase soil organic matter (SOM) and crop yield. However, how the application proportion of woody peat and straw affects crop yield and its microbiological mechanism remains unclear. 【Method】A field experiment was designed, based on the application of straw and activator (RJ). Then, a was comparative analysis of the effects of the ratio of woody peat and straw at 2: 1 (RJM1), 3: 1 (RJM2), and 4: 1 (RJM3) on soil physicochemical properties, bacterial community composition and rice yield was carried out, and compared with the control (CK) without any organic matter. At the same time, based on co-occurrence networks, the path analysis model was used to elucidate the potential relationship between specific bacterial flora and crop yield under different treatments. 【Result】The results showed that the rice yield of RJM1, RJM2, and RJM3 was similar, and their average yield was 16.09% and 31.46% higher than that of RJ and CK, respectively. The soil physicochemical properties of the five treatments were divided into three different groups (P < 0.01). The first group was RJM2+RJM3, which was characterized by remarkably increased pH, SOM, dissolved organic carbon (DOC), available phosphorus (AP) and available potassium (AK) contents. The second group was RJ+RJM1, which was characterized by significantly increased nitrate-nitrogen (NO3--N) and dissolved organic nitrogen (DON). The third group was CK. The average content of SOM, DOC, and AP in RJM2+RJM3 was 29.69%, 22.65%, and 23.95% higher than those of RJM1, respectively, which indicates that RJM2+RJM3 has the potential of rapidly increasing the content of soil organic matter. The bacterial community composition between RJM2 and RJM3 was similar, and was mainly influenced by soil pH, SOM and DOC, while they were significantly different from RJM1. Module 1 of key ecological clusters within the bacterial co-occurrence network had a direct and significant positive effect on rice yield, in which soil physicochemical properties indirectly affected crop yield by directly and significantly affecting module 1 properties. The improvement of yield was mainly affected by the relative abundance and community composition of module 1, while module 2 and module 3 had no significant effect on rice yield. RJM2+RJM3 significantly increased the abundance of Gaiellaceae unidentified, Nocardioidaceae unidentified, Terracoccus, Comamonadaceae unidentified, WD2101 unidentified, and Sphingobacteriales unidentified, which were positively correlated with rice yield. Also, RJM1 significantly increased the abundance of the other five species mentioned above, except Sphingobacteriales unidentified, which indicates that RJM2+RJM3 could stimulate more dominant species that were positively correlated with crop yield than RJM1. Meanwhile, the sustainability of increasing rice yield in RJM1 was lower than RJM2+RJM3 because the SOM content of RJM1 was not significantly different from that of CK and RJ. 【Conclusion】Combining the above results with economic benefits, RJM2, the application ratio of woody peat to straw 3: 1, is recommended as an appropriate ratio that can rapidly improve SOM and crop yield at the same time.

Abstract:Soil microbial biogeography is a discipline that aims to study the spatial distribution pattern of soil microbial community and their changes across time, and is research frontiers in the fields of soil biology and microbial ecology. In recent years, despite the tremendous progress in the study of soil microbial biogeography, there are still many difficulties and challenges. This mini-review will briefly review the development of soil microbial biogeography and emphatically introduce the recent progresses of soil microbial biogeography in forest, grassland and farmland ecosystems in China. This mini-review further elaborates the current international frontiers of soil microbial biogeography, including the spatial distribution of microbial communities and their driving mechanisms, community assembly processes and co-occurrence network, the relationship between microbial geographic distribution and ecosystem functions, and the prediction of microbial community under global change scenarios. Finally, this mini-review outlooks the future developments in the study of soil microbial biogeography, and emphasizes the importance of clear microbial species definitions, temporal dynamics of microbial communities, multiomics approaches and synthetic biology, and the prediction modelling with high accuracy in the study of soil microbial biogeography.

Abstract:【Objective】Soil microbes are an indispensable active component of soil ecosystems. The research on soil microbes is closely linked to current international hotspot issues such as global change, agricultural production, soil environmental protection, etc. The research in soil microbiology is very fruitful, and of great significance for quantitative analysis of soil microbiology literature and data. The use of traditional literature analysis methods to handle large volumes of relevant literature and information and to track development of the research fields has come across a number of difficulties. This paper was oriented to find out latest research hotspots and development trends in the field of soil microorganisms at home and abroad.【Method】Bibliometric analysis of the soil microbial literature contained in the Science Citation Index Expanded (SCI-EXPANDE) database of 1990-2018 in the Web of Science was carried out by country, research institute, source journal, citation, main research content and hot spot of attention, with the aid of visual analysis software, like VOSviewer and CiteSpace. A diagram of cooperations between countries or between research institutions was drawn with the aid of VOSviewer, and keyword co-occurrence network atlases by time period and by country were with CiteSpace. 【Result】Results show that in this research field, the number of documents in China is growing rapidly, but the total citation is still low; the USA ranks first in number of documents and total citation frequency. The Chinese Academy of Sciences, an important research institution in China, its on the top of the lists of number of documents and total citation frequency in the country, but is still quite low in per-paper citation frequency. The Applied and Environmental Microbiology, Soil Biology & Biochemistry are the main journal sources. Though the journal “Soil Science Society of America Journal” is quite low in influence and in volume of publications, it is high or in the forefront in total citation frequency. The keyword co-occurrence network in China formed quite late, but it develops rapidly, showing a trend of convergence with foreign researches in hotspot. The study object has evolved from a single species to a complex microflora, and the research direction has turned more attention to microbial community composition and diversity. Keywords in the soil microbiology research papers in China are increasing in number and in linkage, forming cross-cutting research hotspots. Soil microbiology researches both at home and abroad focus mainly on the following aspects: soil microbes participating in soil organic matter decomposition, carbon and nitrogen recycling as nutrient; biodegradation of heavy metal or organic pollutants matter and bioremediation of heavy metal or organic compound polluted soils; mechanisms of soil microbial communities responding to global environmental change in structure; and mechanisms of rhizosphere microbes, soil and plants interacting with each other. 【Conclusion】Researchers all over the world in this field have made great progresses in the field of soil microbial community structure, function and diversity. Through co-occurrence analysis of keywords by time periods in China and abroad, this paper has brought to light hotspots and trend of the research on soil microbiology, which may be of some reference value for understanding the context of the overall researches in the field of soil microbe and provide certain theoretical guidance to researchers who have just begun their exploration in the field.