Distribution patterns of Acidobacteriota in different fynbos soils

Interruption after Short-Term Nitrogen Additions Improves Ecological Stability of Larix olgensis Forest Soil by Affecting Bacterial Communities

Atmospheric nitrogen deposition can alter soil microbial communities and further impact the structure and function of forest ecosystems. However, most studies are focused on positive or negative effects after nitrogen addition, and few studies pay attention to its interruption. In order to investigate whether interruption after different levels of short-term N additions still benefit soil health, we conducted a 2-year interruption after a 4-year short-term nitrogen addition (10 and 20 kg N·hm-2·yr-1) experiment; then, we compared soil microbial diversity and structure and analyzed soil physicochemical properties and their correlations before and after the interruption in Larix olgensis forest soil in northeast China. The results showed that soil ecological stabilization of Larix olgensis forest further improved after the interruption compared to pre-interruption. The TN, C:P, N:P, and C:N:P ratios increased significantly regardless of the previous nitrogen addition concentration, and soil nutrient cycling was further promoted. The relative abundance of the original beneficial microbial taxa Gemmatimonas, Sphingomonas, and Pseudolabrys increased; new beneficial bacteria Ellin6067, Massilia, Solirubrobacter, and Bradyrhizobium appeared, and the species of beneficial soil microorganisms were further improved. The results of this study elucidated the dynamics of the bacterial community before and after the interruption of short-term nitrogen addition and could provide data support and a reference basis for forest ecosystem restoration strategies and management under the background of global nitrogen deposition.

Acidification induce chemical and microbial variation in tea plantation soils and bacterial degradation of the key acidifying phenolic acids

Camellia sinensis is an important economic plant grown in southern subtropical hilly areas, especially in China, mainly for the production of tea. Soil acidification is a significant cause of the reduction of yield and quality and continuous cropping obstacles in tea plants. Therefore, chemical and microbial properties of tea growing soils were investigated and phenolic acid-degrading bacteria were isolated from a tea plantation. Chemical and ICP-AES investigations showed that the soils tested were acidic, with pH values of 4.05-5.08, and the pH negatively correlated with K (p < 0.01), Al (p < 0.05), Fe and P. Aluminum was the highest (47-584 mg/kg) nonessential element. Based on high-throughput sequencing, a total of 34 phyla and 583 genera were identified in tea plantation soils. Proteobacteria and Acidobacteria were the main dominant phyla and the highest abundance of Acidobacteria was found in three soils, with nearly 22% for the genus Gp2. Based on the functional abundance values, general function predicts the highest abundance, while the abundance of amino acids and carbon transport and metabolism were higher in soils with pH less than 5. According to Biolog Eco Plate™ assay, the soil microorganisms utilized amino acids well, followed by polymers and phenolic acids. Three strains with good phenolic acid degradation rates were obtained, and they were identified as Bacillus thuringiensis B1, Bacillus amyloliquefaciens B2 and Bacillus subtilis B3, respectively. The three strains significantly relieved the inhibition of peanut germination and growth by ferulic acid, p-coumaric acid, p-hydroxybenzoic acid, cinnamic acid, and mixed acids. Combination of the three isolates showed reduced relief of the four phenolic acids due to the antagonist of B2 against B1 and B3. The three phenolic acid degradation strains isolated from acidic soils display potential in improving the acidification and imbalance in soils of C. sinensis.

Effects of biochar pyrolysis temperature on uranium immobilization in soil remediation: Revealed by 16S rDNA and metabolomic analyses

Uranium-stressed soil caused by nuclear industry development and energy acquisition have attracted extensive attentions for a long time. This study investigated the effects of biochar application with different pyrolysis temperatures (300 ℃, 500 ℃ and 700 ℃) on remediation of uranium-stressed soil. The results showed that higher pyrolysis temperature (700 ℃) was benefit for ryegrass growing and caused a lower uranium accumulation in plants. At the same time, uranium immobilization was more effective at higher biochar pyrolysis temperature. Careful investigations indicated that activities of soil urease and sucrase were promoted, and bacterial diversity was strengthened in C700 group, which may contribute to uranium immobilization. The biochar application could activate metabolic of lipids and amino acids, organic acids and derivatives, and organic oxygen compounds. Nicotinate and nicotinamide metabolism, and Benzoxazinoid biosynthesis were unique metabolic pathways in the C700 group, which could enhance the uranium tolerance from different perspectives. Based on these results, we recommend to use biochar with 700 °C pyrolysis temperature when processing remediation of uranium-stressed soil. This study will facilitate the implementation of biochar screening and provide theoretical helps for remediation of uranium-stressed soil.

Exploring the impact of fungicide exposure and nutritional stress on the microbiota and immune response of the Cape honey bee (Apis mellifera capensis)

Honey bees (Apis mellifera) harbour a stable core microbial community within their gut, that is suggested to play a role in metabolic functioning, immune regulation, and host homeostasis. This microbiota presents a unique opportunity to observe the effects of stressors on honey bee health. We examined the effects of two common honey bee stressors: indirect fungicide contamination and nutrient limitation. These effects were observed through changes in their hind- and midgut microbiota using Automated Ribosomal Intergenic Spacer Analysis (ARISA), alongside high-throughput amplicon sequencing. Expression of the honey bees' immune response was examined through the expression of three immune-related genes, namely, immune deficiency (imd), proPhenolOxidase (proPO), and spaetzle (spz). Additionally, longevity of the honey bees was monitored through observation of the expression levels of Vitellogenin (Vg). Both treatment groups were compared to a negative control, and a diseased positive control. There was no effect on the hindgut microbiota due to the stressors, while significant changes in the midgut was observed. This was also observed in the expression of the immune-related genes within the treatment groups. The Imd pathway was substantially downregulated, with upregulation in the prophenoloxidase pathway. However, no significant effect was observed in the expression of spz, and only the pollen treatment group showed reduced longevity through a downregulation of Vg. Overall, the effect of these two common stressors indicate a compromise in honey bee immunity, and potential vulnerabilities within the immune defence mechanisms.

Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity

BACKGROUND

The visual organ plays a crucial role in sensing environmental information. However, its mucosal surfaces are constantly exposed to selective pressures from aquatic or airborne pathogens and microbial communities. Although few studies have characterized the conjunctival-associated lymphoid tissue (CALT) in the ocular mucosa (OM) of birds and mammals, little is known regarding the evolutionary origins and functions of immune defense and microbiota homeostasis of the OM in the early vertebrates.

RESULTS

Our study characterized the structure of the OM microbial ecosystem in rainbow trout (Oncorhynchus mykiss) and confirmed for the first time the presence of a diffuse mucosal-associated lymphoid tissue (MALT) in fish OM. Moreover, the microbial communities residing on the ocular mucosal surface contribute to shaping its immune environment. Interestingly, following IHNV infection, we observed robust immune responses, significant tissue damage, and microbial dysbiosis in the trout OM, particularly in the fornix conjunctiva (FC), which is characterized by the increase of pathobionts and a reduction of beneficial taxa in the relative abundance in OM. Critically, we identified a significant correlation between viral-induced immune responses and microbiome homeostasis in the OM, underscoring its key role in mucosal immunity and microbiota homeostasis.

CONCLUSIONS

Our findings suggest that immune defense and microbiota homeostasis in OM occurred concurrently in early vertebrate species, shedding light on the coevolution between microbiota and mucosal immunity. Video Abstract.

Biochar and organic fertilizer drive the bacterial community to improve the productivity and quality of Sophora tonkinensis in cadmium-contaminated soil

Excessive Cd accumulation in soil reduces the production of numerous plants, such as Sophora tonkinensis Gagnep., which is an important and widely cultivated medicinal plant whose roots and rhizomes are used in traditional Chinese medicine. Applying a mixture of biochar and organic fertilizers improved the overall health of the Cd-contaminated soil and increased the yield and quality of Sophora. However, the underlying mechanism between this mixed fertilization and the improvement of the yield and quality of Sophora remains uncovered. This study investigated the effect of biochar and organic fertilizer application (BO, biochar to organic fertilizer ratio of 1:2) on the growth of Sophora cultivated in Cd-contaminated soil. BO significantly reduced the total Cd content (TCd) in the Sophora rhizosphere soil and increased the soil water content, overall soil nutrient levels, and enzyme activities in the soil. Additionally, the α diversity of the soil bacterial community had been significantly improved after BO treatment. Soil pH, total Cd content, total carbon content, and dissolved organic carbon were the main reasons for the fluctuation of the bacterial dominant species. Further investigation demonstrated that the abundance of variable microorganisms, including Acidobacteria, Proteobacteria, Bacteroidetes, Firmicutes, Chloroflexi, Gemmatimonadetes, Patescibacteria, Armatimonadetes, Subgroups_ 6, Bacillus and Bacillus_ Acidiceler, was also significantly changed in Cd-contaminated soil. All these alterations could contribute to the reduction of the Cd content and, thus, the increase of the biomass and the content of the main secondary metabolites (matrine and oxymatrine) in Sophora. Our research demonstrated that the co-application of biochar and organic fertilizer has the potential to enhance soil health and increase the productivity and quality of plants by regulating the microorganisms in Cd-contaminated soil.

Long-term surface composts application enhances saline-alkali soil carbon sequestration and increases bacterial community stability and complexity

Organic composts could remediate saline-alkali soils on agricultural land by amending soil micro-environment which is one of the main strategies for resourceful treatment and recycling of livestock manure. However, it was still unknown how long-term surface application of organic composts affects the microhabitat and bacterial community characteristics and assembly processes on the profile. We examined the features of the soil properties, bacterial community, and assembly models after 7-years composts application. Physicochemical indicators, enzyme activities, and bacterial diversity of the saline-alkali farmland were all enhanced by the surface composts application, particularly in the 0-20 cm. The network analysis showed that the surface application of composts significantly enhanced the robustness and topological characteristics of the bacterial community and that bacteria from Acidobacteriota were the keystone of the saline-alkali soils improvement. Composts also greatly increased the ecological niche of the bacterial community, while stochastic processes (mainly dispersal limitation) significantly shaped the bacterial community compared to the control. Structural equation modeling indicated that composts application promoted bacterial community succession, which in turn promoted elevated total organic carbon and improved saline-alkali soils properties. Overall, the study linked the ecological characteristics of soil microhabitats and bacterial communities during the restoration of saline-alkali soils by long-term surface application of composts, providing the management and remediation of saline-alkali agricultural soil with a theoretical foundation and technological support.

Seasonal changes of soil microbiota and its association with environmental factors in coal mining subsidence area

BACKGROUND

As a special type of wetland, the new wetland in the coal mining subsidence area is highly sensitive to environmental changes. In recent years, more and more attention has been paid to the studies of soil microbial diversity in newly born wetlands in coal mining subsidence areas. However, there are few reports on the seasonal variation of soil microbial diversity and its relationship with soil physical and chemical properties.

METHODS

In this study, 16S rRNA gene sequencing technology was used to analyze the seasonal changes of soil microbial composition and functional diversity in newly formed wetlands in coal mining subsidence areas, and to determine the seasonal changes of soil nutrient elements and physical and chemical properties in coal mining subsidence areas, so as to analyze the correlation between soil microbial diversity and soil nutrient elements and physical and chemical properties in newly formed wetlands in coal mining subsidence areas.

RESULTS

A total of 16,050 OTUs were obtained after sample gene noise reduction. Proteobacteria, Acidobacteriota and Bacteroidota were the highest abundance in the coal mining subsidence area of Jining. The two seasons gathered separately, and temperature (Temp), total phosphorus (TP), available phosphorus (AP), total organic carbon (TOC) and dry matter content (DMC) were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining. The contents of Temp, AP and TP were significantly correlated with the abundance of soil microorganisms in summer subsidence area, while the contents of DMC and TOC were significantly correlated with the abundance of soil microorganisms in winter subsidence area.

CONCLUSION

Soil microbial diversity in coal mining subsidence area was correlated with the seasons. Temp, TP, AP, TOC and DMC were the key factors for the seasonal change of soil microbial community in the wetland of the coal mining subsidence area of Jining.

Exogenous microbial antagonism affects the bioaugmentation of humus formation under different inoculation using Trichoderma reesei and Phanerochaete chrysosporium

This study was aimed at exploring the effect of antagonism of Trichoderma reesei (T.r) and Phanerochaete chrysosporium (P.c) on humification during fermentation of rice (RS) and canola straw (CS). Results showed that exogeneous fungi accelerated straw degradation and enzyme activities of CMCase, xylanase and LiP. P.c inhibited the activity of LiP when co-existing with T.r beginning, it promoted the degradation of lignin and further increased the production of humus-like substances (HLS) and humic-like acid (HLA) in later fermentation when nutrients were insufficient. The HLS of RTP was 54.9 g/kg RS, higher than the other treatments, and displayed more complex structure and higher thermostability. Brucella and Bacillus were the main HLA bacterial producers. P.c was the HLA fungal producer, while T.r assisted FLA and polyphenol transformation. Therefore, RTP was recommended to advance technologies converting crop straw into humus resources.

Effects of different concentrations of biochar amendments and Pb toxicity on rhizosphere soil characteristics and bacterial community of red clover (Trifolium pretense L.)

Amending soil with biochar can reduce the toxic effects of heavy metals (HM) on plants and the soil. However, the effects of different concentrations of biochar on the properties and microbial activities in lead (Pb)-contaminated soils are unclear. In this study, two Pb concentrations were set (low, 1000 mg/kg; high, 5000 mg/kg), and five corn straw biochar (CSB) concentrations (0, 2.5, 5, 10 and 15%) were used to determine the response of the growth and rhizosphere of red clover (Trifolium pretense L.) (in terms of soil properties and bacteria) to CSB and Pb application. The results showed that 5% CSB better alleviated the toxicity of Pb on the shoot length of red clover, the biomass increased by 74.55 and 197.76% respectively and reduced the enrichment factor (BCF) and transport factor (TF) of red clover. Pb toxicity reduced soil nutrients, catalase (CAT), acid phosphatase (ACP) and urease activity, while the addition of CSB increased soil pH, soil organic matter (SOM) content and soil enzyme activity. 16S rDNA amplicon sequencing analysis showed that Pb toxicity reduced the diversity of rhizosphere bacteria in red clover and reduced the relative abundance of plant growth-promoting rhizobacteria such as Gemmatimonas, Devosia and Bryobacter. Spearman correlation analysis showed that the addition of alkaline CSB restored the relative abundance of rhizobacteria positively correlated with pH, such as Chitinophaga, Sphingomonas, Devosia and Pseudomonas, and thus restored the rhizosphere soil environment. This study demonstrates that 5% CSB can better alleviate the toxicity of Pb to red clover and soil. We also provide a theoretical basis for the subsequent use of beneficial bacteria to regulate the repair efficiency of red clover.

Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine

Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.

Vertical characterisation of phylogenetic divergence of microbial community structures, interaction, and sustainability in estuary and marine ecosystems

The changes in the aquatic environmental conditions often influence the microbial community assemblages and genome repertoire. Studies investigating the aquatic diversity and ecosystem services were primarily conducted in horizontal environments while neglecting the microbial phylogenetic divergences, biotrophic interactions, and eco-sustainability at water vertical layers. We investigated the mechanisms of microbial transitions, and the ecological significance of water depth layers in the estuary and marine ecosystems. The results demonstrated that the salinity and turbidity increased with increasing water depth (0-50 m), while temperature and pH decreased significantly. The bacterial and eukaryotic diversity and composition significantly increased with an elevating water depth. Bacterial phyla such as Desulfobacterota, Acidobacteriota, Myxococcota, Gemmatimonadota, Campilobacterota, and Latescibacterota were increased significantly. However, niche preference occurred, and some microbes showed differential nestedness at water vertical layers. In the eukaryotic community, Eustigmatales group were the only clades predominantly phylogenetically nested at the surface water depth. c_Conoidasida, o_Gregarinasina, f_Eugregarinorida, and g_Lankesteria were the most predominant at the middle depth. While Mediophyceae clades, p_SAR, and the Animalia clades were the most predominant groups nested at the bottom depths. The microbial interaction, structure, and stability were increased with increasing depth. The vertical phylogenetic turnover of the microbial community was related to the feeding mechanisms. Phototrophic organisms were particularly adapted at the surface, and middle depth by parasitic and pathogenic organisms, while the bottom was inhabited by diatoms, decomposers, and detritus protists. This study demonstrated that the bottom depth was the most ecologically stable area with more profound ecosystem services.

The biogeochemical responses of hyporheic groundwater to the long-run managed aquifer recharge: Linking microbial communities to hydrochemistry and micropollutants

Interactions of surface water and groundwater (SW-GW) in hyporheic zones produce biogeochemical hotspots. However, response patterns of hyporheic groundwater to external influences remain unclear. In this study, three datasets (hydrochemistry, antibiotics, and microbiome) were collected over a hydrological year to explore the influence of a 12-year managed aquifer recharge (MAR) project. We observed that the long-term MAR practice elevated nutrient and antibiotic levels while reduced redox potential in hyporheic groundwater, and these impacts depended on decreasing SW-GW interaction intensity with aquifer depth. In contrast, the long-term MAR practice increased community dissimilarity of 30-m groundwater but had little impact on 50-m or 80-m groundwater. Moreover, hyporheic community assembly was dominated by dispersal limitation, and thereby co-varied hydrochemistry and antibiotics only attributed to small community variability. The long-term MAR practice decreased species-interaction intensity and changed the abundance of metabolic functions in hyporheic groundwater. Furthermore, predicted community functions involving carbon, nitrogen, sulfur, and manganese cycles for 30-m groundwater showed higher abundances than those for 50- and 80-m groundwater. Collectively, we showed that hyporheic groundwater was sensitive to the SW-GW interaction and human activities, with the interactions of hydrochemistry, contaminants, and microbiome linking to hyporheic groundwater quality and ecosystem functioning.

Application of mixotrophic acidophiles for the bioremediation of cadmium-contaminated soils elevates cadmium removal, soil nutrient availability, and rice growth

A major challenge in radically alleviating the threats posed by Cd-contaminated paddy fields to human health is to reduce the Cd levels in both soils and rice grains. In this study, the microbial extraction (ME) treatment using a mixotrophic acidophilic consortium was used for the bioremediation of Cd-contaminated soils. The results showed that the ME treatment enhanced the total Cd (40%) and diethylenetriamine pentaacetic acid-soluble Cd (DTPA-Cd, 64%) removal efficiencies in contaminated soils. In addition, ME treatment decreased the levels of Cd acid-soluble and reducible fractions and thereby reduced Cd uptake in rice tissues. Microbial community analysis indicated that the indigenous soil microbial diversity and composition were not changed after the ME treatment, but the relative abundance of functional microbes associated with Cd removal was improved. Notably, soil available nutrient levels were elevated upon inoculation with mixotrophic acidophiles, resulting in an increase in rice growth and grain weight. This study provides a scientific basis for the potential application and evaluation of ME treatment in the field for remediating Cd-contaminated paddy soils.

Cadmium Speciation Distribution Responses to Soil Properties and Soil Microbes of Plow Layer and Plow Pan Soils in Cadmium-Contaminated Paddy Fields

Cadmium (Cd) speciation ratio in arable land determines the Cd exposure risk and Cd uptake in crops. However, the driving mechanisms of Cd speciation change on the vertical scale of paddy fields remain poorly understood. In this study, the effects of plow layer and plow pan on Cd speciation distribution were investigated in a long-term Cd-contaminated rice ecosystem. The Cd accumulative effect within rice grain was enhanced with high levels of activated Cd speciation ratios in soils. Activated Cd speciation ratios were higher in plow layer soils, while stabilized Cd speciation ratios were elevated in plow pan soils. Soil physicochemical properties and soil microbes synergistically affected the Cd speciation changes in different ways between the two soil layers. Soil pH and organic elements in plow layer environment directly hindered the transformation of stabilized Cd speciation, while in plow pan environment, soil pH and organic elements indirectly decreased activated Cd speciation ratios and resulted in the accumulation of stabilized Cd speciation via regulating the predominant bacterial taxa. This study will improve our understanding of how soil environments regulate Cd speciation distributions in rice ecosystems and help to seek effective remediation methods of Cd-contaminated paddy fields to reduce the Cd accumulation in rice.