Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere

Microbial-mediated carbon metabolism in the subtropical marine mangroves affected by shrimp pond discharge

Mangrove ecosystems exhibit high efficiency in carbon (C) sequestering within the global ecosystem. However, the rapid expansion of the shrimp farming industry poses a significant threat to these delicate ecosystems. The microbial mechanisms driving C metabolism in shrimp-affected sediments remain poorly understood. This study investigates the spatiotemporal dynamics of C metabolism-related microbial communities in shrimp pond and natural mangrove sediments in a subtropical region. Shrimp pond discharge altered soil properties, microbial diversity, and microbial stability, driven by factors such as salinity, sulfide, and total organic C (TOC). Metagenomic analyses reveals shifts in C degradation and oxidation, with a reduction in genes for cellulose and hemicellulose degradation. Microbial markers like Prolixibacteraceae and Nitrosopumilaceae reflect these changes. Co-occurrence network analysis indicates higher connectivity within shrimp pond groups, suggesting nutrient-driven changes in symbiotic relationships. PLS-PM analysis further confirms the interplay between microbial composition, nutrient levels, and C metabolism, with higher 16S rRNA operon copy numbers linked to increased C fixation. These findings demonstrate how shrimp pond discharge alters microbial networks and C metabolism, with implications for ecosystem resilience.

Effect of Compound Fertilizer on Foxtail Millet Productivity and Soil Environment

The effects of balanced fertilization with nitrogen, phosphorus, and potassium (NPK) on foxtail millet productivity and the soil environment under the same conditions of total nutrients have received limited research attention. Therefore, in this study, three balanced fertilization patterns of 27-14-10 (T1), 27-17-7 (T2), and 30-10-11 (T3), and one no fertilization treatment (CK), a total of four treatments, were set up through a two-year field experiment to study the effects of balanced fertilization patterns on foxtail millet yield and soil environment. Mantel analysis was conducted to reveal the correlation between soil environmental factors and the community and their contribution to productivity. The results showed that: (1) all balanced fertilization treatments significantly increased foxtail millet yield, with the highest yield in the T1 treatment. (2) The contents of EC, available K, available P, and alkaline-hydrolyzable nitrogen in the soil of the two-year TI treatments were higher than those of the other treatments and increased by 7.20-9.36%, 24.87-52.35%, 55.83-56.38%, and 21.05-43.95%, respectively, compared with CK. (3) Soil urease activity in the T1 treatment increased significantly by 26.67% and 9.00% compared with the control over the two years. Sucrase activity increased by 36.27% and 23.88% in the T1 treatment compared to CK, and glutaminase activity increased by 33.33% and 19.23% in the T1 treatment compared to CK. (4) T1 treatment significantly increased the OUT number and diversity index of the soil bacterial community. (5) Mantel analysis and principal component analysis showed that available soil nutrients and soil enzymes were positively correlated, and soil enzymes and soil nutrients contributed more to foxtail millet productivity. In this study, the 27-14-10 balanced fertilization pattern was more effective, providing a theoretical basis for the research and development of special fertilizers for foxtail millet and offering technical guidance for realizing the light simplified cultivation of foxtail millet and sustainable development of cost-saving and increased efficiency.

A preliminary study characterizing temporal changes in soil bacterial communities after dismembered bones were buried

Determining the burial time of skeletal remains is one of the most important issues of forensic medicine. We speculated that the microbiome of gravesoil may be a promising method to infer burial time by virtue of time-dependent. As we know, forensic scientists have established various models to predict the postmortem interval of a decedent based on the changes in body and soil microbiome communities. However, limited data are available on the burial time prediction for bones, especially dismembered bones. In this exploratory study, we initially conducted 16S rRNA amplicon high-throughput sequencing on the burial soil of 10 porcine femurs within a 120-day period and analyzed the changes in soil microbial communities. Compared with the control soil, a higher Shannon index in the microbial diversity of burial soil containing bones was observed. Correlation analysis identified 61 time-related bacterial families and the best subset selection method obtained best subset, containing Thermomonosporaceae, Clostridiaceae, 0319-A21, and Oxalobacteraceae, which were used to construct a simplified multiple linear regression model with a mean absolute error (MAE) of 56.69 accumulated degree day (ADD). An additional random forest model was established based on indicators for the minimum cross-validation error of Thermomonosporaceae, Clostridiaceae, 0319-A21, Oxalobacteraceae, and Syntrophobacteraceae, with an MAE of 55.65 ADD. The produced empirical data in this pilot study provided the evidence of feasibility that the microbial successional changes of burial soil will predict the burial time of dismembered bones and may also expand the current knowledge of the effects of bone burial on soil bacterial communities.

Variations in different preceding crops on the soil environment, bacterial community richness and diversity of tobacco-planting soil

Tobacco (Nicotiana tabacum L.) is a major cash crop, and soil quality played a significant role in the yield and quality of tobacco. Most farmers cultivate tobacco in rotation with other crops to improve the soil characteristics. However, the effects of different previous crops on the soil's nutrient status and bacterial community for tobacco cultivation still need to be determined. Three treatments were assessed in this study, i.e., tobacco-planting soil without treatment (CK), soil with barley previously cultivated (T1), and soil with rapeseed previously cultivated (T2). The soil physical and chemical properties and the 16S rRNA gene sequence diversity of the bacterial community were analyzed. The effects of different crops on the physical and chemical properties of tobacco-planting soil and the diversity and richness of the bacterial community were comprehensively discussed. The results of this study showed that different previously cultivated crops altered the nutrient status of the soil, with changes in the ratio of NH4 +-N to NO3 --N having the most significant impact on tobacco. In CK, the ratio of NH4 +-N to NO3 --N was 1:24.2, T1-1:9.59, and T2-1:11.10. The composition of the bacterial community in tobacco-planting soil varied significantly depending on the previously cultivated crops. The richness and diversity of the bacterial community with different crops were considerably higher than without prior cultivation of different crops. The dominant bacteria in different treatments were Actinobacteriota, Proteobacteria, and Chloroflexi with their relative abundance differed. In conclusion, our study revealed significant differences in nutrient status, bacterial community diversity, and the richness of tobacco-planting soil after the preceding cultivation of different crops. Suitable crops should be selected to be previously cultivated in tobacco crop rotations in near future for sustainable agriculture.

Harnessing sulfate-reducing bacteria with plants growing to revitalize metal-tainted coal mine soils in Midwest China: metal sequestration performance, ecological networking interaction, and functional enzymatic prediction

Heavy metal contamination from coal mining calls for advanced bioremediation, i.e., using sulfate-reducing bacteria (SRB) technology. Yet, the interaction of SRB with native soil microbiota during metal sequestration, especially in the presence of plants, remains ambiguous. In this study, we assessed the metal sequestration capabilities, ecological network interactions, and enzymatic functions in soils treated with a predominant SRB consortium, mainly Desulfovibrio (14 OTUs, 42.15%) and Desulfobulbus (7 OTUs, 42.27%), alongside Acacia dealbata (AD) and Pisum sativum (PS) plants. The SRB consortium notably enhanced the immobilization of metals such as Zn, Cu, As, and Pb in soil, with the conversion of metals to residual forms rising from 23.47 to 75.98%. Plant inclusion introduced variability, potentially due to changes in root exudates under metal stress. While AD flourished, PS demonstrated significant enhancement in conjunction with SRB, despite initial challenges. Comprehensive microbial analyses revealed the pivotal role of SRB in influencing microbial networking, underpinning critical ecological links. This interplay between plants and SRB not only enhanced microbial diversity but also enriched soil nutrients. Further, enzymatic assessments, highlighting enzymes like NADH:ubiquinone reductase and non-specific serine/threonine protein kinase, reinforced contribution of SRB to energy metabolism and environmental resilience of the entire soil microbial community. Overall, this research underscores the potential of SRB-driven bioremediation in revitalizing soils affected by coal mining.

Microbial Assemblages Associated with the Soil-Root Continuum of an Endangered Plant, Helianthemum songaricum Schrenk

The microbial network of the soil-root continuum plays a key role in plant growth. To date, limited information is available about the microbial assemblages in the rhizosphere and endosphere of endangered plants. We suspect that unknown microorganisms in roots and soil play an important role in the survival strategies of endangered plants. To address this research gap, we investigated the diversity and composition of the microbial communities of the soil-root continuum of the endangered shrub Helianthemum songaricum and observed that the microbial communities and structures of the rhizosphere and endosphere samples were distinguishable. The dominant rhizosphere bacteria were Actinobacteria (36.98%) and Acidobacteria (18.15%), whereas most endophytes were Alphaproteobacteria (23.17%) as well as Actinobacteria (29.94%). The relative abundance of rhizosphere bacteria was higher than that in endosphere samples. Fungal rhizosphere and endophyte samples had approximately equal abundances of the Sordariomycetes (23%), while the Pezizomycetes were more abundant in the soil (31.95%) than in the roots (5.70%). The phylogenetic relationships of the abundances of microbes in root and soil samples also showed that the most abundant bacterial and fungal reads tended to be dominant in either the soil or root samples but not both. Additionally, Pearson correlation heatmap analysis showed that the diversity and composition of soil bacteria and fungi were closely related to pH, total nitrogen, total phosphorus, and organic matter, of which pH and organic matter were the main drivers. These results clarify the different patterns of microbial communities of the soil-root continuum, in support of the better conservation and utilization of endangered desert plants in Inner Mongolia. IMPORTANCE Microbial assemblages play significant roles in plant survival, health, and ecological services. The symbiosis between soil microorganisms and these plants and their interactions with soil factors are important features of the adaptation of desert plants to an arid and barren environment. Therefore, the profound study of the microbial diversity of rare desert plants can provide important data to support the protection and utilization of rare desert plants. Accordingly, in this study, high-throughput sequencing technology was applied to study the microbial diversity in plant roots and rhizosphere soils. We expect that research on the relationship between soil and root microbial diversity and the environment will improve the survival of endangered plants in this environment. In summary, this study is the first to study the microbial diversity and community structure of Helianthemum songaricum Schrenk and compare the diversity and composition of the root and soil microbiomes.

Comparison of network connectivity and environmental driving factors of root-associated fungal communities of desert ephemeral plants in two habitat soils

Root-associated microorganisms regulate plant growth and development, and their distribution is likely influenced by habitat conditions. In this study, the responses of rhizosphere and root-endophytic fungi of dominant ephemeral plants to aeolian soil (AS) and grey desert soil (DS) in the Gurbantünggüt Desert were analyzed using high-throughput sequencing. This was done to understand the adaptation strategies of this vegetation in typical habitat soils from a microbial perspective. We found that the diversity of root-associated fungi of ephemeral plants differed in the two habitat soils. The diversity of rhizosphere fungi was relatively low in AS compared to DS, whereas the diversity of root-endophytic fungi was higher in AS. The community structure of root-associated fungi and relative abundances of some dominant taxa differed between the two soils. A co-occurrence network showed that the degree of coupling and interaction between root-associated fungal taxa were closer in AS than in DS and that most of the fungal taxa were cooperative in the two habitat soils. Additionally, the network properties of the root-endophytic fungi were apparent different between the two soils. Environmental factors, including electrical conductivity, soil organic carbon, carbon/nitrogen, and carbon/phosphorus ratios, were found to be key factors affecting rhizosphere fungi in DS, whereas soil available phosphorus was the main factor in AS. Several factors affect the root-endophytic fungal community and are more influential in DS than in AS. Overall, the root-associated fungal communities of ephemeral plants had different adaptation strategies to the two soils: increasing the diversity of rhizosphere fungi and their relationship with environmental factors in DS, and increasing the diversity and network relationships of root-endophytic fungi in AS. These findings provide insight into the assemblage of ephemeral plant root-associated microbial communities and the underlying environmental factors, which allows for a deeper understanding of how to construct an artificial core root microbiota to promote plant growth and resistance.

Functional interplay between antagonistic bacteria and Rhizoctonia solani in the tomato plant rhizosphere

Microbial interactions with plant roots play an imperial role in tomato plant growth and defense against the Rhizoctonia solani. This study performed a field experiment with two antagonistic bacteria (Pseudomonas and Bacillus) inoculated in healthy and Rhizoctonia solani treated soil in tomato rhizosphere to understand the metabolic pattern and microbial function during plant disease suppression. In the present study, we assessed soil and microbial enzymes, bacterial and fungal cell forming unit (CFU), and carbon utilization profiling through Bio-Eco plates of rhizoplane samples. Antagonist bacteria and pathogen interaction significantly (p < 0.05) influenced the bacterial count, soil enzymes (chitinase and glucanase), and bacterial function (siderophore and chitinase production). These results indicated that these variables had an imperial role in disease suppression during plant development. Furthermore, the metabolic profiling showed that carbon source utilization enhanced under fruit development and ripening stages. These results suggested that carbon sources were essential in plant/pathogen/antagonist interaction. Substrates like β-methyl-D-glucoside, D-mannitol, D-galacturonic acid, N-acetyl-D-glucosamine, and phenylethylamine strongly connect with the suppuration of root rot disease. These carbon sources may help to propagate a healthy microbial community to reduce the pathogen invasion in the plant root system, and these carbon sources can be stimulators of antagonists against pathogens in the future.

Responses and comprehensive evaluation of growth characteristics of ephemeral plants in the desert-oasis ecotone to soil types

The ecological environment of the Gurbantünggüt desert-oasis ecotone is extremely fragile. Ephemeral plants are an important part of the ecosystem and play an essential role in maintaining the ecological stability of the ecotone. However, few studies have focused on the growth, soil quality and system sustainability of ephemeral plants in different soils. This study was based on two typical soil types (grey desert soil, GS; aeolian soil, AS) in the aforementioned ecotone, considered four ephemeral plants (Tetracme recurvata, TR; Tetracme contorta, TC; Malcolmia scorpioides, MS; Isatis violascens, IV) as the research object, analysed plant characteristics and soil properties, and comprehensively evaluated the ephemeral plant system by analysing the soil quality index (SQI) and sustainability index (SI). The results showed that there were significant differences in biomass and nutrient accumulation between different ephemeral plants, which were significantly affected by soil types. In the two examined soils (GS and AS), the contents of nutrients and microbial carbon (MBC) and nitrogen (MBN) in the rhizosphere soil were higher than those in the bare soil (BS), and there were significant differences among different species. The key soil factors related to total biomass in GS and AS were also different. The SQI of ephemeral plants was significantly higher than that of the BS, and varied with soil types and plant species. The species with the highest SQI of the key factor data set in GS and AS were IV and TR, respectively. The SI analysis indicated that IV in GS and MS and IV in AS were sustainable, and the plant properties can be better used to assess the sustainability of ephemeral plant systems. In conclusion, ephemeral plants improved the soil quality and system sustainability of the study ecotone. Further, the growth of ephemeral plant and rhizosphere soil properties vary with plant species and soil types; thus, selecting suitable species for large-scale planting in different soil types is of great significance for improving the ecological stability of the ecotone.

Soil Microbial Communities Affect the Growth and Secondary Metabolite Accumulation in Bletilla striata (Thunb.) Rchb. f

Bletilla striata (Thunb.) Rchb.f. is a perennial herb belonging to the Orchidaceae family. Its tubers are used in traditional Chinese medicine to treat gastric ulcers, inflammation, silicosis tuberculosis, and pneumogastric hemorrhage. It has been reported that different soil types can affect the growth of B. striata and the accumulation of secondary metabolites in its tubers, but the biological mechanisms underlying these effects remain unclear. In this study, we compared agronomic traits and the accumulation of secondary metabolites (extractum, polysaccharide, total phenol, militarine) in B. striata grown in sandy loam or sandy clay soil. In addition, we compared physicochemical properties and microbial communities between the two soil types. In pot experiments, we tested how irradiating soil or transplanting microbiota from clay or loam into soil affected B. striata growth and accumulation of secondary metabolites. The results showed that sandy loam and sandy clay soils differed significantly in their physicochemical properties as well as in the structure and composition of their microbial communities. Sandy loam soil had higher pH, SOM, SOC, T-Ca, T-N, T-Mg, T-Mn, T-Zn, A-Ca, A-Mn, and A-Cu than sandy clay soil, but significantly lower T-P, T-K, T-Fe, and A-P content. Sandy loam soil showed 7.32% less bacterial diversity based on the Shannon index, 19.59% less based on the Ace index, and 24.55% less based on the Chao index. The first two components of the PCoA explained 74.43% of the variation in the bacterial community (PC1 = 64.92%, PC2 = 9.51%). Similarly, the first two components of the PCoA explained 58.48% of the variation in the fungal community (PC1 = 43.67%, PC2 = 14.81%). The microbiome associated with sandy clay soil can promote the accumulation of militarine in B. striata tubers, but it inhibits the growth of B. striata. The accumulation of secondary metabolites such as militarine in B. striata was significantly higher in sandy clay than in sandy loam soil. Conversely, B. striata grew better in sandy loam soil. The microbiome associated with sandy loam soil can promote the growth of B. striata, but it reduces the accumulation of militarine in B. striata tubers. Pot experiment results further confirmed that the accumulation of secondary metabolites such as militarine was higher in soil transplanted with loam microbiota than in soil transplanted with clay microbiota. These results may help guide efforts to improve B. striata yield and its accumulation of specific secondary metabolites.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

Microbial Community-Level Physiological Profiles and Genetic Prokaryotic Structure of Burned Soils Under Mediterranean Sclerophyll Forests in Central Chile

Forest fires alter soil microbial communities that are essential to support ecosystem recovery following land burning. These alterations have different responses according to soil abiotic pre- and post-fire conditions and fire severity, among others, and tend to decrease along vegetation recovery over time. Thus, understanding the effects of fires on microbial soil communities is critical to evaluate ecosystem resilience and restoration strategies in fire-prone ecosystems. We studied the state of community-level physiological profiles (CLPPs) and the prokaryotic community structure of rhizosphere and bulk soils from two fire-affected sclerophyll forests (one surveyed 17 months and the other 33 months after fire occurrence) in the Mediterranean climate zone of central Chile. Increases in catabolic activity (by average well color development of CLPPs), especially in the rhizosphere as compared with the bulk soil, were observed in the most recently affected site only. Legacy of land burning was still clearly shaping soil prokaryote community structure, as shown by quantitative PCR (qPCR) and Illumina MiSeq sequencing of the V4 region of the 16S rRNA gene, particularly in the most recent fire-affected site. The qPCR copy numbers and alpha diversity indexes (Shannon and Pielou’s evenness) of sequencing data decreased in burned soils at both locations. Beta diversity analyses showed dissimilarity of prokaryote communities at both study sites according to fire occurrence, and NO₃^– was the common variable explaining community changes for both of them. Acidobacteria and Rokubacteria phyla significantly decreased in burned soils at both locations, while Firmicutes and Actinobacteria increased. These findings provide a better understanding of the resilience of soil prokaryote communities and their physiological conditions in Mediterranean forests of central Chile following different time periods after fire, conditions that likely influence the ecological processes taking place during recovery of fire-affected ecosystems.