scholarly journals Bacteria with Different Assemblages in the Soil Profile Drive the Diverse Nutrient Cycles in the Sugarcane Straw Retention Ecosystem

Diversity ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 194 ◽  
Author(s):  
Zhang ◽  
Tayyab ◽  
Abubakar ◽  
Yang ◽  
Pang ◽  
...  
Keyword(s):  
Nutrient Cycling ◽  
Soil Fertility ◽  
Soil Profile ◽  
Enzyme Activities ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Soil Parameters ◽  
Sugarcane Straw ◽  
Straw Retention ◽  
C And N

Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land.

scholarly journals Extreme niche partitioning promotes a remarkably high diversity of soil microbiomes across eastern Antarctica

2019 ◽  
Author(s):  
Eden Zhang ◽  
Loïc M. Thibaut ◽  
Aleks Terauds ◽  
Sinyin Wong ◽  
Josie van Dorst ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Niche Partitioning ◽  
Species Abundance ◽  
Soil Microbial Communities ◽  
Biodiversity Loss ◽  
Ecosystem Dynamics ◽  
Soil Parameters ◽  
Sequencing Data ◽  
Windmill Islands

AbstractTerrestrial Antarctica, a predominantly microbial realm, encompasses some of the most unique environments on Earth where resident soil microbiota play key roles in the sustainability and evolution of the ecosystem. Yet the fundamental ecological processes that govern the assemblage of these natural communities remain unclear. Here, we combined multivariate analyses, co-occurrence networks and fitted species abundance distributions of amplicon sequencing data to disentangle community assemblage patterns of polar soil microbiomes across two ice-free deserts (Windmill Islands and Vestfold Hills) situated along the coastline of eastern Antarctica. Our findings report that communities were predominantly structured by non-neutral processes, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. In contrast, both eukaryotic and archaeal communities exhibited multimodal distributions, indicating the potential emergence of neutrality. Between the three microbial domains, polar soil bacterial communities consistently demonstrated the greatest taxonomic diversity, estimated richness, network connectivity and linear response to contemporary environmental soil parameters. We propose that reduced niche overlap promotes greater phylogenetic diversity enabling more bacterial species to co-exist and essentially thrive under adversity. However, irrespective of overall relative abundance, consistent and robust associations between co-existing community members from all three domains of life highlights the key roles that diverse taxa play in ecosystem dynamics.SignificanceIn the face of a warming Antarctica, contemporary dynamics between polar soil microbial communities will inevitably change due to the climate-induced expansion of new ice-free areas. Increasing concern about disturbance and rapid biodiversity loss has intensified the need to better understand microbial community structure and function in high-latitude soils. We have taken an integrated approach to elucidate domain-level assemblage patterns across east Antarctic soil microbiomes. These assemblage patterns will be available to feed into policy management and conservation planning frameworks to potentially mitigate future biodiversity loss.

scholarly journals A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

2021 ◽  
Vol 22 (7) ◽  
pp. 3438
Author(s):  
Juan Liu ◽  
Xiangwei He ◽  
Jingya Sun ◽  
Yuchao Ma
Keyword(s):  
Soil Fertility ◽  
Microbial Diversity ◽  
Resistance Genes ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Antibiotics Resistance ◽  
Plant Growth Promoting Bacteria ◽  
Soil Microbial Diversity ◽  
Antibiotic Target ◽  
And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

Ammonium application mitigates the effects of elevated carbon dioxide on the carbon/nitrogen balance of Phoebe bournei seedlings

2021 ◽  
Author(s):  
Xiao Wang ◽  
Xiaoli Wei ◽  
Gaoyin Wu ◽  
Shengqun Chen
Keyword(s):  
Carbon Dioxide ◽  
Enzyme Activities ◽  
Atmospheric Carbon Dioxide ◽  
Global Climate ◽  
Co2 Concentration ◽  
Rubisco Activase ◽  
Plant Responses ◽  
N Metabolism ◽  
C And N ◽  
Phoebe Bournei

Abstract The study of plant responses to increases in atmospheric carbon dioxide (CO2) concentration is crucial to understand and to predict the effect of future global climate change on plant adaptation and evolution. Increasing amount of nitrogen (N) can promote the positive effect of CO2, while how N forms would modify the degree of CO2 effect is rarely studied. The aim of this study was to determine whether the amount and form of nitrogen (N) could mitigate the effects of elevated CO2 (eCO2) on enzyme activities related to carbon (C) and N metabolism, the C/N ratio, and growth of Phoebe bournei (Hemsl.) Y.C. Yang. One-year-old P. bournei seedlings were grown in an open-top air chamber under either an ambient CO2 (aCO2) (350 ± 70 μmol•mol−1) or an eCO2 (700 ± 10 μmol•mol−1) concentration and cultivated in soil treated with either moderate (0.8 g per seedling) or high applications (1.2 g per seedling) of nitrate or ammonium. In seedlings treated with a moderate level of nitrate, the activities of key enzymes involved in C and N metabolism (i.e., Rubisco, Rubisco activase and glutamine synthetase) were lower under eCO2 than under aCO2. By contrast, key enzyme activities (except GS) in seedlings treated with high nitrate or ammonium were not significantly different between aCO2 and eCO2 or higher under eCO2 than under aCO2. The C/N ratio of seedlings treated with moderate or high nitrate under eCO2was significantly changed compared with the seedlings grown under aCO2, whereas the C/N ratio of seedlings treated with ammonium was not significantly different between aCO2 and eCO2. Therefore, under eCO2, application of ammonium can be beneficial C and N metabolism and mitigate effects on the C/N ratio.

Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana

2021 ◽  
Author(s):  
Shen Jean Lim ◽  
Brenton Davis ◽  
Danielle Gill ◽  
John Swetenburg ◽  
Laurie C Anderson ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nutrient Cycling ◽  
Bacterial Communities ◽  
Structure And Function ◽  
Differentially Expressed ◽  
Seagrass Species ◽  
Bare Sand ◽  
And Function

Abstract Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic, and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides, and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes, and their environment.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals Soil Chemistry and Cucumber (Cucumis sativus L.) Yield as Influenced by 16 Years of Composted Poultry Litter Addition

2017 ◽  
Vol 10 (1) ◽  
pp. 325
Author(s):  
Hebert D. A. Abobi ◽  
Armand W. Koné ◽  
Bernard Y. Koffi ◽  
Saint Salomon F. Diahuissié ◽  
Stanislas K. Loukou ◽  
...  
Keyword(s):  
Soil Fertility ◽  
Growth Parameters ◽  
Block Design ◽  
C:N Ratio ◽  
Poultry Litter ◽  
Growth And Yield ◽  
Soil Parameters ◽  
Total N ◽  
Organic C ◽  
Litter Addition

Poultry litter is increasingly used as organic amendment in market gardening in Côte d’Ivoire. To know about the sustainability of this practice, its impacts on soil quality should be known. This study aimed at assessing the effect on soil fertility of composted poultry litter addition for 16 years following two distinct ways, and identifying soil parameters driving cucumber yield. Trials were laid out in a Fisher randomized block design with 3 treatments replicated 5 times each: Control (C), Surface-applied compost (SAC) and Buried compost (BC). Soil (0-20 cm) chemical characteristics and cucumber growth and yield parameters were measured. Values of all parameters were higher with compost addition compared to the control, except for the C:N ratio. SAC and BC showed similar values of organic C, total N, CEC, pH and available phosphorus. However, Ca2+, Mg2+, K+ and base saturation were higher in SAC than in BC. Relative to values in the control, the greatest changes in soil parameters were observed with exchangeable cations, followed by soil organic matter. Soil organic C and total N concentrations have doubled in SAC while Ca2+, Mg2+, and K+ increased at greater rate (702.4, 400.9 and 186.67% respectively). Also, cucumber growth parameters were the highest with compost addition compared to the control. Significant effect of the compost application way on cucumber was also observed: collar diameter, leaf area and fresh fruit yield in SAC (0.72±0.02 cm, 258.9±12.3 cm2, 11.1±1.3 t ha-1, respectively) were higher than in BC (0.56±0.01 cm, 230.2±2.5 cm2, 5.4±0.5 t ha-1 respectively). Fruit yields in SAC and BC were four times and twice higher than in the control (2.6±0.3 t ha-1), respectively. Cucumber growth parameters were determined by soil concentration in Mg2+ while yield was determined by Ca2+. Composted poultry litter should be promoted for a sustainable soil fertility management in vegetable farming systems.

scholarly journals Effects of continuous cropping of Pinellia ternata (Thunb.) Breit. on soil physicochemical properties, enzyme activities, microbial communities and functional genes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yuan Zhao ◽  
Xiao–Meng Qin ◽  
Xue–Ping Tian ◽  
Tao Yang ◽  
Rong Deng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Physicochemical Properties ◽  
Soil Fertility ◽  
Phenolic Acids ◽  
Relative Abundance ◽  
Enzyme Activities ◽  
Rhizosphere Soil ◽  
Functional Genes ◽  
Continuous Cropping ◽  
Pinellia Ternata

Abstract Background Pinellia ternata (Thunb.) Breit. is a commonly used herb in traditional Chinese medicine, and the main raw material of various Chinese patent medicines. Continuous cropping obstacle (CCO) is the main factor leading to the decline of crop yields and quality. Methods Metagenomics sequencing technology was used to analyze the microbial community and functional genes of continuous cropping (CC) and control (CK) soils of P. ternata. In addition, differences in physicochemical properties, enzyme activities, microbial community composition and the abundance of functional genes in CC and CK were evaluated, as well as the relationship between these factors and CCO. Results Results indicated that CC of P. ternata led to the decline of rhizosphere soil pH, nutrient imbalance and enzyme activity reduction. Metagenomic analysis indicted that CC also changed the composition of the microbial community, causing an increase in the relative abundance of pathogenic microorganisms such as Fusarium, Klebsiella oxytoca and Pectobacterium carotovorum in the P. ternata rhizosphere. The relative abundance of potentially beneficial Burkholderia and Bradyrhizobium was recorded to decrease. Results also showed that there were considerable differences in CC and CK about the abundances of functional genes related to soil enzymes and the degradation of P. ternata allelochemicals, as well as the microbial groups which they belong. These results clarified the effects of CC on the microbial community structure and functional genes of soil. In addition, Burkholderia and Bradyrhizobium might play important roles in enhancing soil fertility and reducing the toxicity of phenolic acids in rhizosphere soil. Conclusions CC of P. ternata changed the physicochemical properties, microbial community and functional genes of rhizosphere soil. Burkholderia and Bradyrhizobium for enhancing soil fertility and reducing the toxicity of phenolic acids might be potentially beneficial. These results provide theoretical guidance for bioremediation of CCO soil of P. ternata and other staple crops. Graphic abstract

scholarly journals Microbial soil characteristics of grassland and arable soils linked to thermogravimetry data: correlations, use and limits

2021 ◽  
Author(s):  
Helena Doležalová-Weissmannová ◽  
Stanislav Malý ◽  
Martin Brtnický ◽  
Jiří Holátko ◽  
Michael Scott Demyan ◽  
...  
Keyword(s):  
Soil Properties ◽  
Soil Parameters ◽  
Organic Carbon Content ◽  
Regression Equations ◽  
Arable Soils ◽  
Grassland Soils ◽  
Simple Method ◽  
Organic C ◽  
Mass Losses ◽  
C And N

Abstract. Thermogravimetry (TG) is a simple method that enables rapid analysis of soil properties such as the content of total organic C, nitrogen, clay and C fractions with different stability. However, the possible link between TG data and microbiological soil properties has not been systematically tested yet and limits TG application for soil and soil organic matter assessment. This work aimed to search and to validate relationships of thermal mass losses (TML) to total C and N contents, microbial biomass C and N, basal and substrate-induced respiration, extractable organic carbon content, anaerobic ammonification, urease activity, short-term nitrification activity, specific growth rate, and time to reach the maximum respiration rate for two sample sets of arable and grassland soils. Analyses of the training soil set revealed significant correlations of TML with basic soil properties such as carbon and nitrogen content with distinguishing linear regression parameters and temperatures of correlating mass losses for arable and grassland soils. In a second stage the equations of significant correlations were used for validation with an independent second sample set. This confirmed applicability of developed equations for prediction of microbiological properties mainly for arable soils. For grassland soils was the applicability lower, which was explained as the influence of rhizosphere processes. Nevertheless, the application of TG can facilitate the understanding of changes in soil caused by microorganism’s activity and the different regression equations between TG and soil parameters reflect changes in proportions between soil components caused by land use management.

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