A comparison of microbial composition under three tree ecosystems using the stochastic process and network complexity approaches

Assembly Characteristics and Influencing Factors of the Soil Microbial Community in the Typical Forest of Funiu Mountain

Assessing the relationship between litter characteristics and soil microbial community traits across different forest types can enhance our understanding of the synergistic interactions among litter, soil, and microorganisms. This study focused on three representative forest types in the Funiu Mountains-Larix gmelinii (LG), Quercus aliena var. acutiserrata (QA), and Quercus aliena var. acutiserrata + Pinus armandii (QAPA). The findings indicated no significant differences in Chao1 among the three forests; however, the Shannon index exhibited an initial increase followed by a decline. NMDS and ANOSIM analyses revealed significant structural differences across these forest types. Network topological metrics (nodes, edges, average degree, and average path distance) for bacterial taxa were higher in LG and QA compared with QAPA. Additionally, LG and QA demonstrated significantly greater average niche breadth than QAPA. The results from the null models (the proportion occupied by dispersal limitation is 62.2%, 82.2%, and 64.4% in LG, QA, and QAPA), modified stochasticity ratio (LG: 0.708, QA: 0.664, and QAPA: 0.801), and neutral community models (LG: R2 = 0.665, QA: R2 = 0.630, and QAPA: R2 = 0.665) suggested that stochastic processes predominantly govern the assembly of soil bacterial communities. Random forest analysis alongside Mantel tests highlighted LTP (litter total phosphorus), STN (soil total nitrogen), MCP (carbon-to-phosphorus ratio of microbial biomass), and SCN (soil carbon-to-nitrogen ratio) as critical factors affecting bacterial niche width; conversely LCN (litter carbon-to-nitrogen ratio), RCP (ratio of dissolved carbon to phosphorus), MCP, and SCN emerged as key determinants influencing community assembly processes. Furthermore, the PLS-SEM results underscored how both litter characteristics along with soil properties-and their associated alpha diversity-impact variations in niche breadth while also shaping community assembly dynamics overall. This research provides vital insights into understanding synergistic relationships between litter quality, soil characteristics, and microbial community across diverse forest ecosystems.

Response of soil fungal-community structure and function to land conversion to agriculture in desert grassland

Land conversion to agriculture is an important factor affecting soil ecological processes in the desert grasslands of northern China. However, soil fungal-community structure and function in response to Land conversion remain unclear. In this study, desert grassland, artificial shrubland, and land conversion were investigated in the western part of the Mu Us Sandland (Yanchi, Ningxia; Dingbian, Shaanxi). We found that land conversion significantly increased soil total carbon, nitrogen, and phosphorus, and available phosphorous and potassium contents. In the early stage of conversion to agricultural (April), soil fungal operational taxonomic units and abundance-based coverage estimator were lower than those of dessert grasslands and shrubland plots and had significant correlations with pH, electric conductivity, and available phosphorus and potassium. The dominant phyla strongly correlated with soil physicochemical properties. Concomitantly, the relative abundance of Glomeromycota was significantly lower, and the complexity of the network in the land conversion plots was lower than that in the shrubland plots. In the late stage of land conversion (September), soil fungal operational taxonomic units and abundance-based coverage estimator were lower in the conversion plots than in the desert grassland plots, with more complex network relationships compared to the desert grassland or shrubland plots. Symbiotrophic groups, a functional group of desert grassland soil fungi, can be used as a predictor of environmental change; in addition, land conversion decreases the relative abundance of arbuscular mycorrhizal functional groups. Our study highlights the response of soil fungal communities and functions to human disturbances in desert grasslands. Considering the potential of land conversion to agriculture to influence soil secondary salinization, there is a need for continued observation of soil ecological health over the time continuum of land conversion to agriculture.

Natural Foraging Selection and Gut Microecology of Two Subterranean Rodents from the Eurasian Steppe in China

As the most abundant group of mammals, rodents possess a very rich ecotype, which makes them ideal for studying the relationship between diet and host gut microecology. Zokors are specialized herbivorous rodents adapted to living underground. Unlike more generalized herbivorous rodents, they feed on the underground parts of grassland plants. There are two species of the genus Myospalax in the Eurasian steppes in China: one is Myospalax psilurus, which inhabits meadow grasslands and forest edge areas, and the other is M. aspalax, which inhabits typical grassland areas. How are the dietary choices of the two species adapted to long-term subterranean life, and what is the relationship of this diet with gut microbes? Are there unique indicator genera for their gut microbial communities? Relevant factors, such as the ability of both species to degrade cellulose, are not yet clear. In this study, we analyzed the gut bacterial communities and diet compositions of two species of zokors using 16S amplicon technology combined with macro-barcoding technology. We found that the diversity of gut microbial bacterial communities in M. psilurus was significantly higher than that in M. aspalax, and that the two species of zokors possessed different gut bacterial indicator genera. Differences in the feeding habits of the two species of zokors stem from food composition rather than diversity. Based on the results of Mantel analyses, the gut bacterial community of M. aspalax showed a significant positive correlation with the creeping-rooted type food, and there was a complementary relationship between the axis root-type-food- and the rhizome-type-food-dominated (containing bulb types and tuberous root types) food groups. Functional prediction based on KEGG found that M. psilurus possessed a stronger degradation ability in the same cellulose degradation pathway. Neutral modeling results show that the gut flora of the M. psilurus has a wider ecological niche compared to that of the M. aspalax. This provides a new perspective for understanding how rodents living underground in grassland areas respond to changes in food conditions.

Response of Phyllosphere and Rhizosphere Microbial Communities to Salt Stress of Tamarix chinensis

As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na+ and K+ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na+ and K+ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na+, the bacteria-fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na+. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.

Kalidium cuspidatum colonization changes the structure and function of salt crust microbial communities

The changes of soil moisture, salinity, and nutrients by halophyte colonization in high-salinity environment profoundly affect the assembly and structure of microbial communities. However, salt marshes in arid region have received little attention. This study was conducted in Lianhuachi Lake, a typical inland salt marsh wetland in China, to determine the physicochemical characteristics of salt crusts in [Kalidium cuspidatum (Ung.-Sternb.) Grub.] colonization areas and bulk soil, respectively, and to analyze the microbial community structure of salt crusts by high-throughput sequencing. Kalidium cuspidatum colonization significantly decreased total salinity, soil water content, and water-soluble ions of salt crusts and increased total carbon, total nitrogen, and total phosphorus content. At the same time, changes in physicochemical properties caused by Kalidium cuspidatum colonization affect the ecological processes of bacterial, fungal, and archaeal community assemblies in salt crusts. In addition, cross-kingdom network analysis showed that Kalidium cuspidatum colonization increased the complexity and stability of microbial networks in salt crust soils. Functional projections further showed that bacterial diversity had a potential driving effect on the nitrogen cycle function of salt crust. Our study further demonstrated the different ecological strategies of microorganisms for halophyte colonization in extreme environments and contributed to the understanding of restoration and management of salt marsh wetlands in arid region.

Dynamics of Microbial Community Structure, Function and Assembly Mechanism with Increasing Stand Age of Slash Pine (Pinus elliottii) Plantations in Houtian Sandy Area, South China

Establishing slash pine plantations is the primary method for restoring sandification land in the Houtian area of South China. However, the microbial variation pattern with increasing stand age remains unclear. In this study, we investigated microbial community structure and function in bare sandy land and four stand age gradients, exploring ecological processes that determine their assembly. We did not observe a significant increase in the absolute abundance of bacteria or fungi with stand age. Bacterial communities were dominated by Chloroflexi, Actinobacteria, Proteobacteria, and Acidobacteria; the relative abundance of Chloroflexi significantly declined while Proteobacteria and Acidobacteria significantly increased with stand age. Fungal communities showed succession at the genus level, with Pisolithus most abundant in soils of younger stands (1- and 6-year-old). Turnover of fungal communities was primarily driven by stochastic processes; both deterministic and stochastic processes influenced the assembly of bacterial communities, with the relative importance of stochastic processes gradually increasing with stand age. Bacterial and fungal communities showed the strongest correlation with the diameter at breast height, followed by soil available phosphorus and water content. Notably, there was a significant increase in the relative abundance of functional groups involved in nitrogen fixation and uptake as stand age increased. Overall, this study highlights the important effects of slash pine stand age on microbial communities in sandy lands and suggests attention to the nitrogen and phosphorus requirements of slash pine plantations in the later stages of sandy management.

Response of soil bacteria on habitat-specialization and abundance gradient to different afforestation types

Studies involving response of subgroups of soil microorganisms to forest change, especially comparative studies on habitat-specialization and abundance gradient were still lack. In this study, we analyzed the response of soil bacterial diversity and structure to afforestation types and its relationship to environment of Fanggan ecological restoration area under the classification of subgroups by habitat-specialization and abundance gradient based on abundance ratio respectively. The results were: (1) On the habitat-specialization gradient, the variation of OTUs species number and abundance was consistent and positively correlated with habitat-specialization; on the abundance gradient, the variation was opposite and OTUs species number was negatively correlated with abundance gradient; (2) The distribution frequency of each subgroup on both gradients was the highest in broad-leaved forests, but the abundance was the opposite. The distribution frequency of the same stand showed no difference among habitat-specialization subgroups, but the abundant subgroup in broad-leaved forests was the highest among the abundance subgroups; (3) α-diversity was positively correlated with habitat-specialization but negatively with abundance, with the highest mostly in broad-leaved and mixed forests; (4) Community structure among stands on habitat-specialization gradient showed no significant difference, but that of rare subgroup between broad-leaved forests and other stands significantly differed. Plant diversity and vegetation composition correlated stronger with community structure than spatial distance and soil physicochemical properties on both gradients. Our results provided a new perspective for revealing the effects of afforestation types on soil bacteria from the comparison of habitat specialization and abundance gradient.

Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil

Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.

Deciphering biochar compost co-application impact on microbial communities mediating carbon and nitrogen transformation across different stages of corn development

Under current climatic conditions, developing eco-friendly and climate-smart fertilizers has become increasingly important.The co-application of biochar and compost on agricultural soils has received considerable attention recently.Unfortunately, little is known about its effects on specific microbial taxa involved in carbon and nitrogen transformation in the soil.Herein, we report the efficacy of applying biochar-based amendments on soil physicochemical indices, enzymatic activity, functional genes, bacterial community, and their network patterns in corn rhizosphere at seedling (SS), flowering (FS), and maturity (MS) stages.The applied treatments were: compost alone (COM), biochar alone (BIOC), composted biochar (CMB), fortified compost (CMWB), and the control (no fertilizer (CNTRL).The non-metric multidimensional scaling (NMDS) indicated total nitrogen (TN), pH, NO₃^--N, urease, protease, and microbial biomass C (MBC) as the dominant environmental factors driving soil bacteria in this study.The dominant N mediating genes belonged to nitrate reductase (narG) and nitronate monooxygenase (amo), while beta-galactosidase, catalase, and alpha-amylase were the dominant genes observed relating to C cycling.Interestingly, the abundance of these genes was higher in COM, CMWB, and CMB compared with the CNTRL and BIOC treatments.The bacteria network properties of CWMB and CMB indicated robust niche overlap associated with high cross-feeding between bacterial communities compared to other treatments.Path and stepwise regression analyses revealed norank_Reyranellaceae and Sphingopyxis in CMWB as the major bacterial genera and the major predictive indices mediating soil organic C (SOC), NH₄⁺-N, NO₃^--N, and TN transformation.Overall, biochar with compost amendments improved soil nutrient conditions, regulated the composition of the bacterial community, and benefited C/N cycling in the soil ecosystem.

Fungal diversities and community assembly processes show different biogeographical patterns in forest and grassland soil ecosystems

Soil fungal community has been largely explored by comparing their natural diversity. However, there is a relatively small body of literature concerned with fungal community assembly processes and their co-occurrence network correlations carried out across large spatial-temporal scales with complex environmental gradients in natural ecosystems and different habitats in China. Thus, soil fungal community assembly processes were assessed to predict changes in soil function in 98 different forest and grassland sites from the Sichuan, Hubei, and Hebei Provinces of China using high-throughput sequencing of nuclear ribosomal internal transcribed spacer 2 (ITS-2). The 10 most abundant fungal phyla results showed that Ascomycota was the most abundant phylum in forests from Sichuan province (64.42%) and grassland habitats from Hebei province (53.46%). Moreover, core fungal taxa (487 OTUs) represented 0.35% of total fungal OTUs. We observed higher fungal Shannon diversity and richness (the Chao1 index) from diverse mixed forests of the Sichuan and Hubei Provinces than the mono-cultured forest and grassland habitats in Hebei Province. Although fungal alpha and beta diversities exhibited different biogeographical patterns, the fungal assembly pattern was mostly driven by dispersal limitation than selection in different habitats. Fungal co-occurrence analyses showed that the network was more intense at Saihanba National Forest Park (SNFP, Hebei). In contrast, the co-occurrence network was more complex at boundaries between forests and grasslands at SNFP. Additionally, the highest number of positive (co-presence or co-operative) correlations of fungal genera were inferred from grassland habitat, which led fungal communities to form commensalism relationships compared to forest areas with having higher negative correlations (mutual exclusion or competitive). The generalized additive model (GAM) analysis showed that the association of fungal Shannon diversity and richness indices with geographical coordinates did not follow a general pattern; instead, the fluctuation of these indices was restricted to local geographical coordinates at each sampling location. These results indicated the existence of a site effect on the diversity of fungal communities across our sampling sites. Our observation suggested that higher fungal diversity and richness of fungal taxa in a particular habitat are not necessarily associated with more complex networks.