Yeast and Lactic Acid Bacteria Dominate the Core Microbiome of Fermented ‘Hairy’ Tofu (Mao Tofu)

Microbial communities are closely related to the overall health and quality of soil, but studies on microbial ecology in apple pear orchard soils are limited. In the current study, 28 soil samples were collected from three apple pear orchards, and the composition and structure of fungal and bacterial communities were investigated by high-throughput sequencing. The molecular ecological network showed that the keystone taxa of bacterial communities were Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Nitrospirae, and Chloroflexi, and the keystone taxon of fungal communities was Ascomycota. Mantel tests showed that soil texture and pH were important factors shaping soil bacterial and fungal communities, and soil water soluble organic carbon (WSOC) and nitrate nitrogen (NO3−-N) were also closely related to soil bacterial communities. Canonical correspondence analysis (CCA) and variation partition analysis (VPA) revealed that geographic distance, soil texture, pH, and other soil properties could explain 10.55%, 13.5%, and 19.03% of the overall variation in bacterial communities, and 11.61%, 13.03%, and 20.26% of the overall variation in fungal communities, respectively. The keystone taxa of bacterial and fungal communities in apple pear orchard soils and their strong correlation with soil properties could provide useful clues toward sustainable management of orchards.

Diverse compost products influence soil bacterial and fungal community diversity in a potato crop production system

Compost processing is assumed to be related to the microbial communities present. However, methods that will evaluate these relationships are not well understood. In this study, terminal restriction fragment length polymorphism (T-RFLP) analysis was used to evaluate the diversity of PCR-amplified bacterial 16S and fungal 18S rDNA communities from manure composts at different stages of composting (initial [day 0], thermophilic [day 24], and mature [day 104]). Results showed that the bacterial and fungal community profiles changed over the composting process, with bacterial communities showing a higher diversity compared with the fungal communities. During the thermophilic stage (day 24), the diversity of the bacterial communities increased, while the fungal communities decreased. As the compost reached maturity (day 104), a reverse pattern was observed between the diversity of bacterial and fungal communities. That is, the 18S rDNA T-RFLP-based diversity indices increased, while the 16S rDNA T-RFLP-based diversity decreased. Differences in temperature profiles at different stages of composting impacted the chemical properties and the diversity of the microbial communities. The day 104 compost (mature) had lower water, organic matter and C contents and higher C and OM loss compared with the day 0 (initial) and day 24 (thermophilic) composts, which affected the diversity of the microbial communities. The results presented here demonstrated that distinctive community patterns from manure composts could be rapidly generated using T-RFLP analysis. The succession of peaks in combination of increasing and decreasing peak heights at different stage of composting indicates the high potential of T-RFLP technique to monitor the dynamics of microbial communities, and their variation qualitatively and quantitatively.

<p indent="0mm">Microorganisms are the most active components of soil and are very sensitive to external disturbances, so they are often used as an important indicator for evaluating the function and health of soil ecosystems. Many studies have investigated the effects of grazing on soil microorganisms, however, how the grazing effects on soil microbes vary among different grassland types and the underlying mechanism are still largely unexplored. In this study, we selected four different types of grasslands in northern China, i.e., meadow steppe, typical steppe, desert steppe and alpine meadow and compared the variation of heavy-grazing effects on soil microbial community composition and diversity and explored the potential drivers of soil microbial community composition and diversity in each grassland type. The results showed that within the same grassland type, the effects of heavy grazing on the α diversity of soil bacterial and fungal communities were not significant compared with those of the control. Similarly, we found that the β diversity of soil bacterial and fungal communities from the heavy-grazing plots was not significantly different from those from the control plots. However, we found that the α diversity and β diversity of soil fungal and bacterial communities varied significantly among the four grassland types. The ASV richness and Shannon diversity of soil bacterial community in meadow steppe was consistently higher than those of the other three grassland types. In contrast, alpine meadow generally had the highest fungal α-diversity. The fungal ASV richness in alpine meadow was significantly higher than that of meadow steppe and desert steppe and the fungal Shannon diversity in alpine meadow was significantly higher than that of typical steppe. The bacterial and fungal community structures of typical steppe and meadow steppe were similar, and differed significantly from those of desert steppe and alpine meadow. The random forest results showed that the key drivers of soil bacterial and fungal α-diversity and β-diversity differed among the different grassland types. Soil organic carbon, C:N ratio, available phosphorus, nitrate nitrogen and plant belowground biomass were the most important predictors driving the α diversity of soil bacterial communities. Soil available nitrogen, total nitrogen, available phosphorus, pH and plant aboveground biomass were the most important predictors driving the α diversity of soil fungal communities. Soil organic carbon, plant belowground biomass and total nitrogen were the most important predictors driving the β diversity of soil bacterial communities. Soil organic carbon and available nitrogen were the most important predictors driving the β diversity of soil fungal communities. This study compared the difference of heavy grazing on soil microbial community diversity in different grassland types, revealed the key drivers of soil microbial diversity in different types of grasslands, and provided a theoretical basis for the management of natural grasslands as well as the restoration of degraded grasslands.

The application of biogas slurry and chemical fertilizer in paddy fields can be a practical method to reduce the environmental risk and utilize the nutrients of biogas slurry. The responses of bacterial and fungal communities to the application of biogas slurry and chemical fertilizer are important reflections of the quality of the ecological environment. In this study, based on a 3-year field experiment with different ratios of biogas slurry and chemical fertilizer (applying the same pure nitrogen amount), the Illumina MiSeq platform was used to investigate the bacterial and fungal community diversity and composition in paddy soil. Our results revealed that compared with the observations under regular chemical fertilization, on the basis of stable paddy yield, the application of biogas slurry combined with chemical fertilizer significantly enhanced the soil nutrient availability and bacterial community diversity and reduced the fungal community diversity. Dissolved organic carbon (DOC), DOC/SOC (soil organic carbon), available nitrogen (AN) and available phosphorus (AP) were positively correlated with the bacterial community diversity, but no soil property was significantly associated with the fungal community. The bacterial community was primarily driven by the application of biogas slurry combined with chemical fertilizer (40.78%), while the fungal community was almost equally affected by the addition of pure biogas slurry, chemical fertilizer and biogas slurry combined with chemical fertilizer (25.65–28.72%). Biogas slurry combined with chemical fertilizer significantly enriched Proteobacteria, Acidobacteria, Planctomycetes, Rokubacteria, and Ascomycota and depleted Chloroflexi, Bacteroidetes, Crenarchaeota, Basidiomycota, and Glomeromycota. The observation of the alteration of some bacteria- and fungus-specific taxa provides insights for the proper application of biogas slurry combined with chemical fertilizer, which has the potential to promote crop growth and inhibit pathogens.

This study aimed to explore the effects of different disturbances on the fungal communities in the sediments of the Jialing River in order to provide scientific basis for the protection of the river ecosystem. The fungal community in the sediments of the main stream of the Jialing River was taken as the research object, and high-throughput sequencing and bioinformatics techniques were used to analyze the differences in the composition and function of fungal communities in river sediment of different types of disturbance （project disturbance, tributary disturbance, sand mining disturbance, and reclamation disturbance） and non-disturbance sections. The results showed that： ① The reclamation and project disturbances significantly inhibited the diversity and richness of fungal communities （P<0.05）. The tributary disturbance increased the richness of fungal communities, whereas the impact of sand mining disturbance on sediment fungal communities was not significant. ② The diversity and composition of fungal communities tended to be similar at the different sampling sites in the section with low input of exogenous substances （non-disturbance and sand mining disturbance）, whereas there were obvious differences in the diversity of fungal communities at the different sampling sites of high input of external substances （tributary disturbance, project disturbance, and reclamation disturbance） sections. ③ Ascomycota, Rozellomycota, and Basidiomycota were the main dominant fungal phyla in the sediments of the Jialing River. The relative abundance of Rozellomycota was the highest in the sand mining interference section, and the relative abundance of Basidiomycota was the highest in the tributary interference section. Project disturbance significantly increased the relative abundance of saprotrophs, animal pathogens, plant pathogens, and dung saprotrophs, whereas other disturbances inhibited the relative abundance of fungal parasitic fungi, plant pathogens, and plant saprophytes. In conclusion, human disturbance has caused changes in fungal diversity, community structure, and function in the sediment of the Jialing River, and xenobiotic input was a key factor contributing to this phenomenon. The results can provide a reference for predicting and evaluating the ecological quality of river sediments.

To obtain the difference of the fungal and bacterial community diversity between wild Cordyceps sinensis, artificial C. sinensis and their habitat soil, Illmina Hiseq high-throughput sequencing technology was applied. The results show that Proteobacteria was the dominant bacterial phylum in C. sinensis, Actinobacteria was the dominant bacterial phylum in soil microhabitat, Ophiocordyceps sinensis was the predominant dominant fungus of C. sinensis. The α diversity analysis showed that the fungal diversity of stroma was lower than other parts, and the fungal diversity of wild C. sinensis was lower than that of artificial C. sinensis. The β diversity analysis showed that the fungal and bacterial community diversity of soil microhabitat samples was significantly different from that of C. sinensis. The fungal community diversity was less different between wild and artificial C. sinensis, especially in sclerotia. LEfSe analysis showed a lot of species diversity between wild and artificial C. sinensis. Those different species between wild C. sinensis, artificial C. sinensis and their habitat soil provide ideas for further research on breed and components of C. sinensis.

The composition, physical and chemical properties, sources, and temporal and spatial changes in airborne particulate matter have been extensively investigated in previous studies. However, less is known about bioaerosols, which are mainly composed of bacteria and fungi and constitute up to 25% of the total airborne particulate matter. In this study, we used inductively coupled plasma mass spectrometry and ion chromatography to determine the concentrations of trace elements and water-soluble ions in atmospheric particulates, respectively. These analyses were combined with high-throughput sequencing methods and real-time quantitative polymerase chain reaction to analyze the microbial compositions in PM1.0, PM2.5, and PM10 samples, which were collected from July to September in Hefei City. The results showed that there were no significant differences in the bacterial community diversity across the three size fractions (analysis of variance (ANOVA), P>0.05). The bacterial and fungal community diversities on sunny days were lower than those on rainy days, and the bacterial community diversity in all samples was significantly higher than the fungal community diversity (ANOVA, P<0.01). The predominant bacterial phyla were Proteobacteria (46.19%), Firmicutes (33.42%), Bacteroidetes (10.99%), Cyanobacteria (3.33%), and Actinobacteria (2.11%). Ascomycota (73.23%), Basidiomycota (5.78%), Mortierellomycota (3.41%), and Mucoromycota (0.10%) were the dominant fungal phyla. Our results indicated that soils, plant leaves, and animal feces were the dominant sources of airborne bacterial communities in Hefei City, and the main sources of the fungal communities were plant leaves and soils. The bacterial community was mainly affected by K, Pb, Al, Fe, Mg, Ca, Na+, NO2-, and wind speed, and the main influencing factors of the fungal community were V, Mn, Sr, NO2-, NO3-, Na+, Cl-, the air quality index, and PM10. In addition, nine specific bacteria and fungi that are linked to human health risks were identified, including Acinetobacter, Streptococcus, Enterobacter, Pseudomonas, Delftia, Serratia, Trichoderma, Alternaria, and Aspergillus, which can lead to a wide range of diseases in humans and other organisms. The research results are helpful for revealing the various characteristics of airborne microbial communities, their influencing factors, and their impacts on human health, and are an important reference for subsequent research and the formulation of government policies.

Shrub encroachment (SE) is a phenomenon in which grasses and herbaceous vegetation are replaced by woody shrubs. Many previous studies have highlighted the effects of SE on soil respiration rates and nutrient storage, but little is known about impacts on soil microbiota. While previous work considered shrubs to be non-species specific or as a single intervening species, we selected an Ampelodemsos mauritanicus grassland and six coexisting shrubs (i.e. Pistacia lentiscus L., Juniperus phoenicea L., Myrtus communis L., Rosmarinus officinalis L., Olea europaea L., and Euphorbia dendroides L.) to investigate the effects of their encroachment on soil microbiota. We used high-throughput sequencing, coupled with soil chemical analyses and litter using 13C CPMAS NMR spectroscopy. Results showed a strong influence of shrub species on bacterial and fungal community diversity, species richness and overall community composition in the soil. Litter chemistry was dominated by O-alkyl-C, with the highest content in Ampelodesmos and E. dendroides, but richer of aromatic C in P. lentiscus and R. officinalis. Bacterial diversity was highest under J. phoenicea and E. dendroides, while lowest under R. officinalis and grassland. Conversely, fungal diversity was highest under O. europaea and E. dendroides, while lowest under M. communis and grassland. Moreover, soil C and N contents were highest under O. europaea, P. lentiscus and M. communis compared to the other shrub species. In addition, grassland and R. officinalis had the highest Fe content. Structural equation model (SEM) analysis ascertained that the shifts of bacterial and fungal community composition and diversity were closely related with the changes of litter and soil chemical properties. Our results suggest that the individual effect of each shrub on the grassland matrix depends mainly on the chemical properties of the shrub litter, which alters the chemical profile of the soil and, in cascade, shapes the associated microbiota.

Plant diversity and soil properties regulate the microbial community of monsoon evergreen broad-leaved forest under different intensities of woodland use

Cunninghamia lanceolata is an important species in plantations and is widely planted in sub-tropical regions of China because of its fast-growing and productive characteristics. However, the monoculture planting is carried out in the pursuit of economic value. This planting mode has led to problems such as the exhaustion of soil fertility, decrease in vegetation diversity, and decrease in woodland productivity. In order to restore soil fertility and increase timber production, the introduction of broad-leaved tree species to plantations is an effective transformation model. Understanding how forest age changes and stand structure differences drive the composition and diversity of soil microbial communities is helpful in understanding the trend of soil–microbial changes in plantations and evaluating the effects of the introduction of broad-leaved tree species in soil–plant–microbial ecosystems in plantations. Therefore, the purpose of our study is to investigate the effects of forest age and pure forest conversion on C. lanceolata–P. bournei-mixed forest soil microbial community structure and diversity by detecting soil nutrients, enzyme activities, and soil microbial 16S and ITS rRNA gene sequencing. According to the findings, the diversity and abundance of bacterial communities in C. lanceolata plantations of different ages increased first and then decreased with the increase in forest age, and the max value was in the near-mature forest stage. The fungal abundance decreased gradually with stand age, with the lowest fungal diversity at the near-mature stand stage. During the whole growth process, the bacterial community was more limited by soil pH, nitrogen, and phosphorus. After introducing P. bournei into a Chinese fir plantation, the abundance and diversity of the bacterial community did not improve, and the abundance of the fungal community did not increase. However, soil nutrients, pH, and fungal community diversity were significantly improved. The results of these studies indicate that the introduction of broad-leaved tree species not only increased soil nutrient content, but also had a significant effect on the increase in the diversity of soil fungal communities, making the microbial communities of mixed forests more diverse.

The bacterial, acidobacterial, and fungal communities in wetlands can undergo perturbations by various human activities, such as disturbances caused by cultivation and during the process of system restoration. In this study, we investigated the relationships between the composition of the soil bacterial, acidobacterial, and fungal communities and the transformation of wetlands by human activities in the Sanjiang Plain. Soil microbial communities were assessed in wetland soils collected from pristine marsh, neighboring cropland (wetland turned into arable land), and land that had been reforested with Larix gmelinii. The alpha-diversities of bacteria, Acidobacteria, and fungi were affected by land-use change and were highest in the arable land and lowest in the wetland soils. The soil microbial community structures were also altered with changing land-use. Canonical correlation analyses showed that beta-diversity was significantly affected by soil pH, available phosphorus, soil nitrogen, and total organic carbon. Overall, our results showed that the agricultural cultivation of wetlands changes the available soil carbon, nitrogen, and phosphorus pools, thereby influencing the bacterial, acidobacterial, and fungal diversity and community structure. Once the soil microbial community has been altered by human activity, it might be difficult to restore it to its original state. These findings highlight the importance of effectively maintaining the diversity of soil bacterial, Acidobacterial, and fungal communities despite land use change in order to sustain a microbial community diversity and ecosystem function.

Soil microbes are of great significance to driving the biogeochemical cycles and are affected by multiple factors, including urbanization. However, the response of soil microbes to urbanization remains unclear. Therefore, we designed an urban-to-rural gradient experiment to investigate the response of soil microbial composition and diversity to urbanization. Here, we used a high-throughput sequencing method to analyze the biotic and abiotic effects on soil microbial composition and diversity along the urban-to-rural gradient. Our results showed that soil bacterial diversity was the highest in urban areas, followed by suburban areas, and was the lowest in exurbs; however, fungal diversity did not vary significantly among the three areas. Plant traits, i.e., tree richness, shrub richness, the number of tree stems, diameter at breast height of trees, and soil properties, i.e., pH, soil organic carbon, soil exchangeable calcium and magnesium, and soil water content, were only significantly influenced bacterial diversity, but not fungal diversity. The effect of trees and shrubs was higher than that of herbs on microbial composition. Soil organic carbon, pH, soil available nitrogen, soil exchangeable calcium, and magnesium were the major soil factors influencing the soil bacterial and fungal composition. Soil properties had a greater influence on bacterial than on fungal composition at genus level, while plant traits contributed more to fungal than to bacterial composition at genus level. Our study suggests that the urban-to-rural gradient affect the composition and diversity of bacterial community as well as the fungal composition, but not the fungal diversity.

Effects of sediment physicochemical factors and heavy metals on the diversity, structure, and functions of bacterial and fungal communities from a eutrophic river

Soil microorganisms play an important role in the circulation of materials and nutrients between plants and soil ecosystems, but the drivers of microbial community composition and diversity remain uncertain in different vegetation restoration patterns. We studied soil physicochemical properties (i.e., soil moisture, bulk density, pH, soil nutrients, available nutrients), plant characteristics (i.e., Shannon index [HPlant] and Richness index [SPlant], litter biomass [LB], and fine root biomass [FRB]), and microbial variables (biomass, enzyme activity, diversity, and composition of bacterial and fungal communities) in different plant succession patterns (Robinia pseudoacacia [MF], Caragana korshinskii [SF], and grassland [GL]) on the Loess Plateau. The herb communities, soil microbial biomass, and enzyme activities were strongly affected by vegetation restoration, and soil bacterial and fungal communities were significantly different from each other at the sites. Correlation analysis showed that LB and FRB were significantly positively correlated with the Chao index of soil bacteria, soil microbial biomass, enzyme activities, Proteobacteria, Zygomycota, and Cercozoa, while negatively correlated with Actinobacteria and Basidiomycota. In addition, soil water content (SW), pH, and nutrients have important effects on the bacterial and fungal diversities, as well as Acidobacteria, Proteobacteria, Actinobacteria, Nitrospirae, Zygomycota, and microbial biomass. Furthermore, plant characteristics and soil properties modulated the composition and diversity of soil microorganisms, respectively. Overall, the relative contribution of vegetation and soil to the diversity and composition of soil bacterial and fungal communities illustrated that plant characteristics and soil properties may synergistically modulate soil microbial communities, and the composition and diversity of soil bacterial and fungal communities mainly depend on plant biomass and soil nutrients.