Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation.
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ABSTRACT:
SUBMITTER: Jayaramaiah RH
PROVIDER: S-EPMC8719800 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Irrigation and nitrogen (N) fertilization rates are widely used to increase crop growth and yield and promote the sustainable production of the maize crop. However, our understanding of irrigation and N fertilization in the soil microenvironment is still evolving, and further research on soil bacterial communities under maize crop with irrigation and N management in subtropical regions of China is needed. Therefore, we evaluated the responses of two irrigation levels (low and high irrigation water with 60 and 80% field capacity, respectively) and five N fertilization rates [i.e., control (N0), N200 (200 kg N ha-1), N250 (250 kg N ha-1), N300 (300 kg N ha-1), and N350 (350 kg N ha-1)] on soil bacterial communities, richness, and diversity. We found that both irrigation and N fertilization significantly affected bacterial richness, diversity index, and number of sequences. Low irrigation with N300 treatment has significantly higher soil enzymes activities, soil nutrient content, and bacterial alpha and beta diversity than high irrigation. In addition, the Proteobacteria, Actinobacteriota, Chloroflexi, and Firmicutes were the dominant bacterial phyla under both irrigation regimes. The acidic phosphates, acidic invertase, β-glucosidase, catalase, cellulase, and urease were positively correlated with the Shannon index under both low and high irrigation. Therefore, low irrigation improves soil nutrient utilization by boosting soil enzyme activity, directly affecting soil bacterial communities. It was concluded that greater soil nutrients, enzyme activities with higher bacterial diversity are the main indicators of soil reactivity to low irrigation water and N300 for maintaining soil fertility and soil microbial community balance.
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Project description:Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.
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Project description:The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr⁺ and mlr- bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr⁺ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr- strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr- bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention.
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Project description:Crop rotation is a typical agronomic practice to mitigate soil deterioration caused by continuous cropping. However, the mechanisms of soil biotic and abiotic factors in response to different cropping patterns in acidic and polyphenol-rich tea nurseries remain unclear. In this study, the composition and function of microbial communities were comparatively investigated in soils of tea seedlings continuously planted for 2 years (AC: autumn-cutting; SC: summer-cutting) and in soils rotation with strawberries alternately for 3 years (AR: autumn-cutting). The results showed that AR significantly improved the survival of tea seedlings but greatly reduced the contents of soil polyphenols. The lower soil polyphenol levels in AR were associated with the decline of nutrients (SOC, TN, Olsen-P) availability, which stimulates the proliferation of nutrient cycling-related bacteria and mixed-trophic fungi, endophytic fungi and ectomycorrhizal fungi, thus further satisfying the nutrient requirements of tea seedlings. Moreover, lower levels of polyphenols facilitated the growth of plant beneficial microorganisms (Bacillus, Mortierella, etc.) and suppressed pathogenic fungi (Pseudopestalotiopsis, etc.), creating a more balanced microbial community that is beneficial to plant health. Our study broadens the understanding of the ecological role of plant secondary metabolites and provides new insights into the sustainability of tea breeding.
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Project description:Bacteria are a crucial component of forest soil biodiversity and play an important role in numerous ecosystem processes. Here, we studied the patterns of soil bacterial community diversity and structure in a climax forest (Larix gmelinii; LG) compared with those in degraded forest ecosystems of four forest vegetation types (BD, Betula dahurica; BP, Betula platyphylla; QM, Quercus mongolica; and LGQM, a mixed coniferous-broadleaved forest composed of Larix gmelinii and Quercus mongolica) in the Heilongjiang Zhongyangzhan Black-billed Capercaillie Nature Reserve in northern China, using Illumina MiSeq sequencing of 16 S rRNA genes. Soil physicochemical properties (pH, soil organic carbon = SOC, total nitrogen = TN, carbon/nitrogen = C/N, total phosphorous = TP, available nitrogen = AN, available phosphorous = AP) differed significantly (p < .05) among the five forests. SOC, C/N, TP, AN, and AP were highest in QM, whereas SOC was lowest in LGQM. Soil pH was lowest in BD and highest in LGQM. α diversity was highest in LG and lowest in QM. The soil bacterial community composition in the climax forest was significantly different from that in the four degraded forests (p < .05). The dominant bacterial phyla were Acidobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Firmicutes, Chloroflexi, and Rokubacteria. The highest relative abundances of these phyla were: 30.7% for Acidobacteria in LGQM, 42.6% for Proteobacteria in LG, 17.6% for Verrucomicrobia in BD, 5.5% for Firmicutes in BP, and 6.9% for Actinobacteria in QM. The dominant bacterial genera across the five forest vegetation types were Bryobacter and some poorly characterized taxa (e.g., Candidatus_Udaeobacter and Candidatus_Solibacter). Redundancy analysis indicated that SOC, C/N, TP, AN, and AP were the main soil physicochemical properties that shaped the bacterial communities. Our study revealed distinct bacterial diversity and composition in the climax forest compared with values in degraded forests, suggesting that the biotic and abiotic factors associated with climax ecosystems play an important role in shaping soil bacterial community structure and thus biogeochemical functions. The results of this study contribute to a deeper understanding and better predictions of the network among belowground systems and of the functions and services of degraded forests compared with climax ecosystems.
| S-EPMC9682091 | biostudies-literature
Project description:Gravel-mulched land in China suffers from poor natural resources and fragile ecological environment, posing a challenge to effective restoration of ecological function. Lonicera japonica, a traditional Chinese herb used for treating human diseases, is a highly adaptable and resilient plant species, can effectively improve the soil properties, and may have important implications for the ecology and economy of gravel-mulched land. A study was conducted in a gravel-mulched field to measure the impact of planting the L. japonica (including control (CK), 1-year, 2-year, and 4-year cultivation of plants) on (i) dynamic changes in soil nutrient and enzyme activity properties, and (ii) soil rhizosphere microbial community structure characteristics. We found that the concentration of soil organic carbon, available nitrogen, available phosphorus and available potassium in L. japonica soil after cultivation for 1-4 years increased by 11-409%. The urease, phosphatase and catalase activities were increased by 11-560%, with the highest nutrient concentration and enzyme activity in 4-year plants. The pH value gradually decreased after cultivation. The improved soil environments increased soil bacterial community diversity. Planting L. japonica significantly increased the bacterial ACE, Chao1 index, Simpson index, and Shannon-Wiener index. The Firmicutes, Proteobacteria and Bacteroidetes were observed in dominant phyla. The relative abundance of eight genera, including Streptococcus, Veillonella and Rothia, was significantly reduced by more than 1%. Taken together, these soil indicators suggest that planting L. japonica in the short term would be a cost-effective strategy to combat soil degradation in a gravel-mulched ecosystem.
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Project description:Nutrient addition to forest ecosystems significantly influences belowground microbial diversity, community structure, and ecosystem functioning. Nitrogen (N) addition in forests is common in China, especially in the southeast region. However, the influence of N addition on belowground soil microbial community diversity in subtropical forests remains unclear. In May 2018, we randomly selected 12 experimental plots in a Pinus taiwanensis forest within the Daiyun Mountain Nature Reserve, Fujian Province, China, and subjected them to N addition treatments for one year. We investigated the responses of the soil microbial communities and identified the major elements that influenced microbial community composition in the experimental plots. The present study included three N treatments, i.e., the control (CT), low N addition (LN, 40 kg N ha-1 yr-1), and high N addition (HN, 80 kg N ha-1 yr-1), and two depths, 0-10 cm (topsoil) and 10-20 cm (subsoil), which were all sampled in the growing season (May) of 2019. Soil microbial diversity and community composition in the topsoil and subsoil were investigated using high-throughput sequencing of bacterial 16S rDNA genes and fungal internal transcribed spacer sequences. According to our results, 1) soil dissolved organic carbon (DOC) significantly decreased after HN addition, and available nitrogen (AN) significantly declined after LN addition, 2) bacterial ?-diversity in the subsoil significantly decreased with HN addition, which was affected significantly by the interaction between N addition and soil layer, and 3) soil DOC, rather than pH, was the dominant environmental factor influencing soil bacterial community composition, while AN and MBN were the best predictors of soil fungal community structure dynamics. Moreover, N addition influence both diversity and community composition of soil bacteria more than those of fungi in the subtropical forests. The results of the present study provide further evidence to support shifts in soil microbial community structure in acidic subtropical forests in response to increasing N deposition.
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Project description:IntroductionMicroorganisms, including the pioneer microorganisms that play a role in the early colonization of rock, are extremely important biological factors in rock deterioration. The interaction of microorganisms with limestone leads to biodeterioration, accelerates soil formation, and plays an important role in the restoration of degraded ecosystems that cannot be ignored. However, the process of microbial colonization of sterile limestone in the early stages of ecological succession is unclear, as are the factors that affect the colonization. Acid erosion (both organic and inorganic), nutrient availability, and water availability are thought to be key factors affecting the colonization of lithobiontic microorganisms.MethodsIn this study, organic acid (Oa), inorganic acid (Ia), inorganic acid + nutrient solution (Ia + Nut), nutrient solution (Nut), and rain shade (RS) treatments were applied to sterilized limestone, and the interaction between microorganisms and limestone was investigated using high-throughput sequencing techniques to assess the microorganisms on the limestone after 60 days of natural placement.ResultsThe results were as follows: (1) The abundance of fungi was higher than that of bacteria in the early colonization of limestone, and the dominant bacterial phyla were Proteobacteria, Bacteroidota, and Actinobacteriota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Chytridiomycota. (2) Acid erosion and nutrient availability shaped different microbial communities in different ways, with bacteria being more sensitive to the environmental stresses than fungi, and the higher the acidity (Ia and Oa)/nutrient concentration, the greater the differences in microbial communities compared to the control (based on principal coordinate analysis). (3) Fungal communities were highly resistant to environmental stress and competitive, while bacterial communities were highly resilient to environmental stress and stable.DiscussionIn conclusion, our results indicate that limestone exhibits high bioreceptivity and can be rapidly colonized by microorganisms within 60 days in its natural environment, and both nutrient availability and acid erosion of limestone are important determinants of early microbial colonization.
| S-EPMC10289080 | biostudies-literature
Project description:The widespread utilization of the herbicide imazethapyr presents significant challenges to crop rotation and results in detrimental soil degradation issues. Bacterial biodegradation has emerged as a promising and eco-friendly approach for mitigating pesticide residues contamination in the environment. In this study, a novel bacterium, identified as Brevibacterium sp. IM9601, was isolated and characterized based on morphological, physiological, and biochemical characteristics, as well as 16S rRNA gene sequence. This strain exhibited the ability to utilize imazethapyr as its sole carbon source for growth. Response surface methodology (RSM) was applied to optimize the degradation conditions. The most favorable conditions were determined to be a temperature of 27 °C, pH of 6.0, and an initial inoculum with a final OD600 of 0.15. Under these optimized condition, bacterial strain IM9601 exhibited substantial imazethapyr degradation, with removal rates of 90.08 and 87.05% for initial imazethapyr concentrations of 50 and 100 mg L-1, respectively, achieved within a 5-day incubation period. This investigation highlights imazethapyr-degrading capabilities of the Brevibacterium genus bacterial strain IM9601, marking it as a potentially novel and effective solution for addressing the environmental pollution resulting from the usage of imazethapyr. The study contributes to the growing body of research on bioremediation approaches, offering a sustainable and environmentally friendly method for mitigating the adverse impacts of herbicide contamination in agricultural settings.
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Project description:UnlabelledCell division in bacteria is driven by a cytoskeletal ring structure, the Z ring, composed of polymers of the tubulin-like protein FtsZ. Z-ring formation must be tightly regulated to ensure faithful cell division, and several mechanisms that influence the positioning and timing of Z-ring assembly have been described. Another important but as yet poorly understood aspect of cell division regulation is the need to coordinate division with cell growth and nutrient availability. In this study, we demonstrated for the first time that cell division is intimately linked to central carbon metabolism in the model Gram-positive bacterium Bacillus subtilis. We showed that a deletion of the gene encoding pyruvate kinase (pyk), which produces pyruvate in the final reaction of glycolysis, rescues the assembly defect of a temperature-sensitive ftsZ mutant and has significant effects on Z-ring formation in wild-type B. subtilis cells. Addition of exogenous pyruvate restores normal division in the absence of the pyruvate kinase enzyme, implicating pyruvate as a key metabolite in the coordination of bacterial growth and division. Our results support a model in which pyruvate levels are coupled to Z-ring assembly via an enzyme that actually metabolizes pyruvate, the E1? subunit of pyruvate dehydrogenase. We have shown that this protein localizes over the nucleoid in a pyruvate-dependent manner and may stimulate more efficient Z-ring formation at the cell center under nutrient-rich conditions, when cells must divide more frequently.ImportanceHow bacteria coordinate cell cycle processes with nutrient availability and growth is a fundamental yet unresolved question in microbiology. Recent breakthroughs have revealed that nutritional information can be transmitted directly from metabolic pathways to the cell cycle machinery and that this can serve as a mechanism for fine-tuning cell cycle processes in response to changes in environmental conditions. Here we identified a novel link between glycolysis and cell division in Bacillus subtilis. We showed that pyruvate, the final product of glycolysis, plays an important role in maintaining normal division. Nutrient-dependent changes in pyruvate levels affect the function of the cell division protein FtsZ, most likely by modifying the activity of an enzyme that metabolizes pyruvate, namely, pyruvate dehydrogenase E1?. Ultimately this system may help to coordinate bacterial division with nutritional conditions to ensure the survival of newborn cells.
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