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Diagrams depicting community composition and relative abundance at phylum levels: (A), bacteria; (B), fungi. https://doi.org/10.1371/journal.pone.0254065.g003
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Environmental properties are important factors in structuring soil microbial communities. The primary driving factors vary in different ecosystems. In the present work, we analyzed the microbial communities of rhizosphere and bulk soils associated with the halophyte Alhagi sparsifolia across three salt/water gradients in the desert area around Ebin...
Context in source publication
Context 1
... of the bacterial OTUs belonged to 643 genera, 267 families, 104 classes, and 46 phyla. The abundant phyla were Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Cyanobacteria, and Acidobacteria (Fig 3). The relative abundances of the dominant bacterial phylum Actinobacteria in the rhizosphere and bulk soils in the H plot were 23.3% and 32.0%, in the M plot were 34.9% and 23.2%, and in the L plot were 53.8% and 48.5%, respectively. ...
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Citations
... In China, T. chinensis is often used as the principal plant in the restoration of saline-alkaline land. It performs varied ecological functions, thereby playing an important role in maintaining biogeochemical cycles while stabilizing factors such as soil pH, electric conductivity, and cations [27,28]. However, the response characteristics of the phyllosphere colonizers of the salt-secreting halophyte T. chinensis to salt secretion remain unclear. ...
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.
... Similarly, differences were expected between the dry and rainy seasons due to the significant influence of higher soil moisture and lower temperatures in the rainy season, which are more conducive to microbial activity. As suggested by Li et al. 17 and Lacerda-Junior et al. 18 , soil moisture and temperature emerge as primary factors driving variations in soil microbial communities. On the other hand, we did not observe a clear effect of restoration on altering the bacterial structure compared to degraded soil. ...
Land degradation by deforestation adversely impacts soil properties, and long-term restoration practices have been reported to potentially reverse these effects, particularly on soil microorganisms. However, there is limited knowledge regarding the short-term effects of restoration on the soil bacterial community in semiarid areas. This study evaluates the bacterial community in soils experiencing degradation (due to slash-and-burn deforestation) and restoration (utilizing stone cordons and revegetation), in comparison to a native soil in the Brazilian semiarid region. Three areas were selected: (a) under degradation; (b) undergoing short-term restoration; and (c) a native area, and the bacterial community was assessed using 16S rRNA sequencing on soil samples collected during both dry and rainy seasons. The dry and rainy seasons exhibited distinct bacterial patterns, and native sites differed from degraded and restoration sites. Chloroflexi and Proteobacteria phyla exhibited higher prevalence in degraded and restoration sites, respectively, while Acidobacteria and Actinobacteria were more abundant in sites undergoing restoration compared to degraded sites. Microbial connections varied across sites and seasons, with an increase in nodes observed in the native site during the dry season, more edges and positive connections in the restoration site, and a higher occurrence of negative connections in the degradation site during the rainy season. Niche occupancy analysis revealed that degradation favored specialists over generalists, whereas restoration exhibited a higher prevalence of generalists compared to native sites. Specifically, degraded sites showed a higher abundance of specialists in contrast to restoration sites. This study reveals that land degradation impacts the soil bacterial community, leading to differences between native and degraded sites. Restoring the soil over a short period alters the status of the bacterial community in degraded soil, fostering an increase in generalist microbes that contribute to enhanced soil stability.
... Total genome DNA from samples was extracted using CTAB method. DNA concentration and purity were monitored on 1% agarose gel [19]. According to the concentration, DNA was diluted to 1 ng/μL using sterile water. ...
Objective
The mechanism of cervical ripening in late pregnancy is still unclear. The vaginal microbiome has been reported to correlate with the preterm birth and short cervix in pregnant women. However, the associations between the cervical maturity and the vaginal microbiome are still poorly understood. We aim to analyze the cervicovaginal microflora in women with ripe cervix and in those who are unripe when delivering at term.
Methods
Cervicovaginal swabs were collected between 40 and 41 weeks of gestation from the following 2 different groups of patients: ripe group (n = 25) and unripe group (n = 25). Samples were tested using 16S ribosomal RNA gene high-throughput sequencing and analyzed by bioinformatics platform.
Results
This study highlights the relationship between cervical maturity during late pregnancy and the composition of the cervicovaginal microflora. Both α- and β-diversity analyses demonstrated significant differences between women with a ripe cervix and those with an unripe cervix. Notably, the Lactobacillus profile was found to be closely linked to cervical maturity. There was a significant difference in the vaginal community state type, with CST IV being more prevalent in women with an unripe cervix. Furthermore, the association between CST IV and the unripe cervix group, as indicated by the odds ratio of 8.6, underscores its relevance in evaluating cervical maturity, when compared to other Lactobacillus -dominant community state types. Additionally, several bacterial taxa, particularly Lactobacillus , exhibited differential relative abundances between the two groups.
Conclusion
This study provided significant evidence regarding the relationship between the vaginal microbiome and cervical maturity, highlighting the differential diversity, community state types, and specific bacterial taxa, such as Lactobacillus , that are associated with cervical maturation status. These findings contributed to our understanding of the dynamics of the cervicovaginal microflora during late pregnancy and its implications for cervical health.
... Low soil moisture content may be one factor contributing to overall lower population abundances (0.002-0.004%) in drier soils, such as in Saudi Arabia [68]. However, chytrid populations can increase as the soil water content increases, as was observed in arid soil in China [120]. Chytrids are reliant upon the presence of moisture to stimulate zoosporulation and, subsequently, aid in dispersal. ...
... Chytrid tolerance to more extreme pH ranges has been further shown in vitro [131], but this tolerance is species specific and does not account for the influence of other soil factors. For example, chytrid populations have been observed to have a positive correlation with soil factors, including for properties such as fine texture, electric conductivity, sulphate concentration, and soil phosphorus, nitrogen, and carbon content [120,132]. The methods used in Zhou et al. (2021) [66] clearly mapped out both the microbiological and biochemical changes in a soil ecosystem and provide an experimental guide for future investigations. ...
Chytridiomycota (zoosporic true fungi) have a consistent presence in soils and have been frequently identified within many diverse terrestrial environments. However, Chytridiomycota and other early-diverging fungi have low representation in whole-genome sequencing databases compared to Dikarya. New molecular techniques have provided insights into the diversity and abundance of chytrids in soils and the changes in their populations both spatially and temporally. Chytrids complete their life cycle within rapidly changing soil environments where they may be more common within micropores due to protection from predation, desiccation, and extreme temperatures. Reproductive and morphological changes occur in response to environmental changes including pH, fluctuating nutrient concentrations, and metals at levels above toxic thresholds. Rhizoids share some features of hyphae, including the spatial regulation of branching and the ability to attach, adapt to, and proliferate in different substrates, albeit on a microscale. Soil chytrids provide a pool of novel enzymes and proteins which enable a range of lifestyles as saprotrophs or parasites, but also can be utilised as alternative tools with some biotechnological applications. Thus, 3D live-cell imaging and micromodels such as MicroCT may provide insight into zoospore functions and rhizoid plasticity, respectively, in response to various conditions. A combination of classical techniques of soil chytrid baiting with simultaneous molecular and ecological data will provide insights into temporal population changes in response to environmental change. The authors emphasise the need to review and improve DNA-based methodologies for identifying and quantifying chytrids within the soil microbiome to expand our knowledge of their taxonomy, abundance, diversity, and functionality within soil environments.
... Whereas, fungal alpha-diversity based on the OTU richness and Shannon diversity index were the highest in non-treated samples on 44th day (Supplementary Table 2). Rhizosphere bacterial and fungal communities were altered by various environmental factors such as climate and soil properties (Li et al., 2021), as well as host factors such as plant genotype and plant age (Fazal et al., 2021). Our results indicated that microbial richness and diversity increase with time and plant development. ...
Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.
... Whereas, fungal alpha-diversity based on the OTU richness and Shannon diversity index were the highest in non-treated samples on 44th day (Supplementary Table 2). Rhizosphere bacterial and fungal communities were altered by various environmental factors such as climate and soil properties (Li et al., 2021), as well as host factors such as plant genotype and plant age (Fazal et al., 2021). Our results indicated that microbial richness and diversity increase with time and plant development. ...
... Some studies have shown that the water-salt content of soils in the riparian zone of the Achiksu River, which is located in the reserve, is high and decreases with increasing distance from the river [24]. Thus far, scholars have been conducting more research on the structure of soil microbial communities and their relationship with the environment in the arid zone of the Lake Ebinur basin, but most of the resulting studies mainly focus on the response of microbial communities to a single environment, such as land type, soil physicochemical factors, seasonal changes, etc., rarely addressing the interaction relationship within the soil microbial communities and the joint response mechanism of environmental factors [21,[25][26][27][28][29]. Based on this, the present study was conducted to explore the process of soil microbial community assembly and influencing factors under different water-salt gradients via a field investigation and soil sample analysis in a typical desert ecosystem in Lake Ebinur Wetland Nature Reserve in order to answer the following scientific questions: (1) What are the differences in the community composition of the soil microbiome in an arid zone under different water-salt gradients? ...
Exploring the structural characteristics of arid soil microbial communities and their assembly mechanisms is important for understanding the ecological characteristics of arid zone soils and promoting ecological restoration. In this study, we used Illumina high-throughput sequencing technology to study soils in the arid zone of the Lake Ebinur basin, determined the differences among soil microbial community structures in the study area under different water–salt gradients, and investigated the effects of environmental factors on microbial community structure and assembly mechanisms. The results show the following: the microbial community alpha diversity exhibited a significantly higher low water–salt gradient (L) than high water–salt gradient (H) and medium water–salt gradient (M). The pH was most strongly correlated with soil microbial community structure, where the alpha diversity indices of the bacterial community and fungal community were significantly negatively correlated with pH, and the Bray–Curtis distance of bacterial community was significantly positively correlated with pH (p < 0.05). The complexity of bacterial community co-occurrence networks showed a significantly higher L than H and M, and the complexity of fungal community co-occurrence network showed a significantly lower L than H and M. The cooperative relationship of H and M in the co-occurrence networks was stronger than that of the L, and the key species of the microbial co-occurrence network were different under different water–salt gradients. Stochastic processes dominated the assembly mechanism of the microbial community structure of soil, and the explanation rates of deterministic and stochastic processes were different under different water–salt gradients, with the highest explanation rate of stochastic processes on the L accounting for more than 90%. In summary, the soil microbial community structure and assembly mechanisms significantly differed across water–salt gradients, and these findings can help provide a reference for further research on soil microbiology in arid zones.
... Soil pH can be an important determinant of the growth and distribution of Alhagi in arid areas by affecting soil microbial communities. Salinity, water content, total nitrogen and total phosphorus in the soil are the other important factors that influence soil microbial communities in an Alhagi rangeland (Li et al., 2021). Soil pH can modify the spatial distribution of bacterial communities in semi-arid and arid environments by changing the individual abundance of bacterial communities (Wang et al., 2015). ...
In this research, the growth and distribution of Alhagi camelorum Medic. as a potential crop was monitored for producing forage in hypersaline and hyperarid regions. For this purpose, seven Alhagi-dominated rangelands were selected in its original homeland at the south of the Great Salt Desert. The soil salinity of selected regions is very variable, and ranged from 3.6 dS m⁻¹ to 725 dS m⁻¹ and from 0.4 dS m⁻¹ to 366 dS m⁻¹ at 0–30 cm and 30–60 cm soil depths, respectively. The annual mean of maximum and minimum air temperature is around 30 and 6 °C, respectively, and the mean annual precipitation is less than 150 mm. The plant growth characteristics assessed by canopy cover, canopy height, shoot fresh weight (SFW), and dry weight (SDW) had a negative relationship with soil salinity and pH. The highest SFW (24.97 t ha⁻¹) and SDW (6.98 t ha⁻¹) of Alhagi were obtained where soil salinity was 13 dS m⁻¹ and soil pH was the lowest (7.1). Alhagi maintained the minimal growth and production of 20 cm canopy height and 50% canopy cover even in the saltiest conditions with a soil salinity of 395 dS m⁻¹; hence it can serve as a potential crop for haloculture systems. In Aqda, the canopy cover increased with increase in the soil salinity up to 7–10 dS m⁻¹ but decreased as the salinity levels increased further. The study revealed that A. camelorum not only has a very high tolerance to salinity but a moderate salinity up to 10 dS m⁻¹ can also stimulate the growth. However, soil pH had a greater effect on growth, and Alhagi does not have a high tolerance to soil alkalinity. Therefore, Alhagi species could not be a bio-indicator for soil salinity, while well-established plants with good canopy could be considered as a sign for low alkalinity in arid terrestrial ecosystems.
... A large number of studies have shown that soil cultivation and plant species are the main factors affecting the structure of soil microbial communities (Nüsslein and Tiedje, 1999;Calderón et al., 2000;Tang et al., 2020;Li et al., 2021d). Different cultivation patterns have varied impacts on soil microbes (Cookson et al., 2008). ...
Forage monoculture and grass (Gramineae)-legume mixtures are the two most commonly used planting patterns for establishing farming grasslands, but the effects of these planting patterns on the rhizosphere bacterial community and forage production are still unclear. In this study, we carried out a field experiment on the Tibetan Plateau, and observed that grass-legume mixtures significantly increased forage production over monocultures (P < 0.05). We investigated the effects of these two planting patterns on rhizosphere and bulk soil bacterial communities, and found that the grass-legume mixtures altered the community structure and composition of the grass rhizosphere bacterial community, while the bacterial community of bulk soils remained unchanged. Source tracker analysis demonstrated that 50.77% and 34.72% of the changes in mixture rhizosphere of two gramineous grasses were derived from the legume, illustrating that the legume greatly influenced the grass rhizosphere in grass-legume planting. The molecular ecological network analysis demonstrated that network vulnerability and robustness of the mixtures were significantly higher than that of monoculture, indicating that the grass-legume mixtures provided a favorable condition for microbial interactions. Besides, by using structural equation modeling, it was found that the stability and complexity of the bacterial community network had significant positive correlations with forage production, while the soil physicochemical properties had no significant direct correlations, suggesting the rhizosphere bacterial community played a critical role in enhancing plant growth in grass-legume mixtures. This study provides a new insight into the mechanism behind the enhancement of forage production in the grass-legume mixture planting pattern.
... Subsoiling + rotary tillage significantly decreased the bacterial abundance and diversity in the 10-20 cm soil layer (p < 0.05), and the bacterial colony abundance and diversity showed a downward trend with the increase in soil depth ( Table 2). In addition, soil pH is the key factor driving the change in soil microbial activity and community diversity [52]. In this study, the Chao1 and Shannon indices of cultivator colonies were negatively correlated with pH, while the Simpson index was positively correlated with pH (Figure 7), indicating that soil pH was an important factor affecting the abundance and diversity of cultivator bacterial communities. ...
This study was carried out to investigate effects of subsoiling on the diversity and composition of the bacterial community in a wheat–maize rotation field in the Guanzhong area of Shaanxi Province, China. After the wheat harvest, surface soil samples were collected under two tillage methods (single rotary tillage (RT) and subsoiling + rotary tillage (ST)) to perform high-throughput sequencing and bioinformatics analysis. Soil properties and root length density (RLD) of winter wheat at booting and flowering stages were also studied. Results showed that ST treatment significantly raised the water storage, organic carbon and total nitrogen contents of deep soil (>40 cm), and notably increased the total soil pH, ammonium nitrogen content and RLD in the tillage layer from 0–70 cm at booting stage and 0~100 cm at flowering stage, but the residual nitrate nitrogen significantly decreased by 17.74%. Compared with RT, soil bacterial richness and diversity in the 10~20 cm layer of ST treatment showed a significantly decreased trend. The relative abundances of GAL15, Actinobacteria, Nitrospirae, Rhizobiales, Burkholderiales, Pseudomonas and Serratia in the 10–20 cm layer were remarkably increased in ST. Principal Component Analysis (PCA) and Redundancy Analysis (RDA) results showed that surface soil pH, ammonium nitrogen and nitrate nitrogen contents have the strongest effect on the bacterial structure. In addition, there were positive correlations between the RLD and the relative abundances of Rhizobiales, Burkholderiales, Pseudomonas and the ammonium nitrogen content. In conclusion, although subsoiling was not conducive to improving soil bacterial community richness and diversity, it significantly increased soil beneficial bacteria (biological nitrogen-fixing bacteria, ammonifying bacteria, nitrobacteria) abundances, reduced the nitrogen loss caused by denitrifying bacteria, promoted earlier root development and improved the plant utilization ratio of soil nutrients.
