scholarly journals Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies

Agronomy ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 14 ◽  
Author(s):  
Yadong Yang ◽  
Peixin Wang ◽  
Zhaohai Zeng
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Hierarchical Cluster ◽  
Organic Manure ◽  
Community Structures ◽  
Long Term Effects ◽  
Inorganic Fertilizers ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Fertilization plays important roles in improving soil fertility and in increasing crop yield. Soil microbial communities are sensitive indicators of soil quality and health, which could be affected by fertilization strategy. However, our knowledge on how organic–inorganic fertilizers application affects soil bacterial communities remains largely poorly understood. In this study, we investigated the long-term effects of different organic–inorganic fertilization strategies: without fertilizer (CK), fertilizers NPK (CF), fertilizers NPK, plus 30% organic manure (CFM1), and fertilizers NPK plus 60% organic manure (CFM2) on soil bacterial communities in paddy fields. Results showed that the bacterial 16S ribosomal DNA (rDNA) gene abundances in treatments CF, CFM1, and CFM2 were 1.44, 1.54, and 1.28 times higher than that in CK and the ACE index in treatment CFM1 was 9.0% greater than that in treatment CFM2, respectively. Fertilization strategy significantly changed the relative abundance of Nitrospirae, Gemmatimonadetes, and unclassified bacteria at the phylum level and bacteria belonging to order Nitrospira, candidate bacterium SBR2076, unclassified bacteria, Syntrophobacterales, and Solibacterales at the order level, respectively. High organic–inorganic fertilizer application rates inhibited the growth of Nitrospirae by 20–35%, and stimulated the growth of Gemmatimonadetes by 14–77%, relative to the rest of the treatments, respectively. Hierarchical cluster and principal coordinate analysis (PCoA) showed that the fertilization strategy affected the bacterial community structures, and the organic–inorganic fertilized treatments possessed similar bacterial community structures. Furthermore, soil pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors altering the bacterial communities. Our results suggested that combined organic–inorganic fertilizers application increased soil nutrient contents and bacterial abundances, and this could be an optimized fertilization strategy in regulating soil bacterial communities for rice production.

scholarly journals Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

2009 ◽  
Vol 75 (15) ◽  
pp. 5111-5120 ◽  
Author(s):  
Christian L. Lauber ◽  
Micah Hamady ◽  
Rob Knight ◽  
Noah Fierer
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Spatial Scales ◽  
Bacterial Community Composition ◽  
Phylogenetic Structure ◽  
Soil Bacterial Communities ◽  
Soil Bacterial Community Structure ◽  
Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

scholarly journals Neutral processes and high inter-annual turnover shape the assembly of soil bacterial communities in a Mediterranean watershed

2019 ◽  
Author(s):  
Myrto Tsiknia ◽  
Stilianos Fodelianakis ◽  
Nikolaos P. Nikolaidis ◽  
Nikolaos V. Paranychianakis
Keyword(s):  
Stochastic Processes ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Ecosystem Functioning ◽  
Soil Microbial Communities ◽  
Soil Bacterial Communities ◽  
Environmental Selection ◽  
Mediterranean Landscapes ◽  
Soil Bacterial ◽  
Annual Turnover

AbstractThere is a renewed interest in recent years on the ecological processes (stochastic vs selective) driving the assembly of microbial communities. Such information could potentially improve our understanding on ecosystem functioning and resilience to disturbances, ecosystem response to environmental shifts, and adoption of sustainable soil management practices. Herein, employing a suite of existing methodologies, we show that stochastic processes have an important role on the assembly of soil bacterial communities at a Mediterranean watershed. Moreover, we document that the relative contribution of assembly processes varies over the years. The observed intensification of stochastic processes was accompanied by a decrease in the contribution of variable selection in favor of homogeneous selection and dispersal and this trend was only marginally affected by land use (natural vs agricultural lands) or soil depth. Our study also revealed a high inter-annual turnover of soil microbial communities that was likely stimulated by the weak environmental selection and the prevailing environmental conditions (drying-wetting cycles) in Mediterranean landscapes, implying potential impacts on ecosystem functioning and our ability to predict soil response to environmental shifts. Using nitrogen mineralization rate (NMR) as a representative function we document highly variable NMR over the sampling years, land uses and soil depths and lack of significant associations with the monitored environmental variables and individual taxa. In summary, our study provides novel insights on the organization and functioning of microbial communities at Mediterranean ecosystems and sets directions towards a more advanced understanding of the relationships among environmental factors, microbial community structure, and ecosystem functioning that could contribute to sustainable management of these severely degraded ecosystems.

scholarly journals Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1526
Author(s):  
Xiaoqin Yang ◽  
Yang Wang ◽  
Luying Sun ◽  
Xiaoning Qi ◽  
Fengbin Song ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Northeast China ◽  
Management Practice ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Crop Productivity ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

scholarly journals The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China

Forests ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 51 ◽  
Author(s):  
Jiangmei Qiu ◽  
Jianhua Cao ◽  
Gaoyong Lan ◽  
Yueming Liang ◽  
Hua Wang ◽  
...  
Keyword(s):  
Land Use ◽  
Surface Layer ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Yunnan Province ◽  
Soil Bacterial Community ◽  
Land Use Patterns ◽  
Use Patterns ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Land use patterns can change the structure of soil bacterial communities. However, there are few studies on the effects of land use patterns coupled with soil depth on soil bacterial communities in the karst graben basin of Yunnan province, China. Consequently, to reveal the structure of the soil bacterial community at different soil depths across land use changes in the graben basins of the Yunnan plateau, the relationship between soil bacterial communities and soil physicochemical properties was investigated for a given area containing woodland, shrubland, and grassland in Yunnan province by using next-generation sequencing technologies coupled with soil physicochemical analysis. Our results indicated that the total phosphorus (TP), available potassium (AK), exchangeable magnesium (E-Mg), and electrical conductivity (EC) in the grassland were significantly higher than those in the woodland and shrubland, yet the total nitrogen (TN) and soil organic carbon (SOC) in the woodland were higher than those in the shrubland and grassland. Proteobacteria, Verrucomicrobia, and Acidobacteria were the dominant bacteria, and their relative abundances were different in the three land use types. SOC, TN, and AK were the most important factors affecting soil bacterial communities. Land use exerts strong effects on the soil bacterial community structure in the soil’s surface layer, and the effects of land use attenuation decrease with soil depth. The nutrient content of the soil surface layer was higher than that of the deep layer, which was more suitable for the survival and reproduction of bacteria in the surface layer.

Effects of inoculation with organic-phosphorus-mineralizing bacteria on soybean (Glycine max) growth and indigenous bacterial community diversity

2017 ◽  
Vol 63 (5) ◽  
pp. 392-401 ◽  
Author(s):  
Wei Sun ◽  
Xun Qian ◽  
Jie Gu ◽  
Xiao-Juan Wang ◽  
Yang Li ◽  
...  
Keyword(s):  
Glycine Max ◽  
Carbon Source ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Organic Phosphorus ◽  
Community Diversity ◽  
Carbon Source Utilization ◽  
Soil Bacterial Communities ◽  
Bacterial Community Diversity ◽  
Soil Bacterial

Three different organic-phosphorus-mineralizing bacteria (OPMB) strains were inoculated to soil planted with soybean (Glycine max), and their effects on soybean growth and indigenous bacterial community diversity were investigated. Inoculation with Pseudomonas fluorescens Z4-1 and Brevibacillus agri L7-1 increased organic phosphorus degradation by 22% and 30%, respectively, compared with the control at the mature stage. Strains P. fluorescens Z4-1 and B. agri L7-1 significantly improved the soil alkaline phosphatase activity, average well color development, and the soybean root activity. Terminal restriction fragment length polymorphism analysis demonstrated that P. fluorescens Z4-1 and B. agri L7-1 could persist in the soil at relative abundances of 2.0%–6.4% throughout soybean growth. Thus, P. fluorescens Z4-1 and B. agri L7-1 could potentially be used in organic-phosphorus-mineralizing biofertilizers. OPMB inoculation altered the genetic structure of the soil bacterial communities but had no apparent influence on the carbon source utilization profiles of the soil bacterial communities. Principal components analysis showed that the changes in the carbon source utilization profiles of bacterial community depended mainly on the plant growth stages rather than inoculation with OPMB. The results help to understand the evolution of the soil bacterial community after OPMB inoculation.

scholarly journals The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6147 ◽  
Author(s):  
Shu-Hong Wu ◽  
Bing-Hong Huang ◽  
Jian Gao ◽  
Siqi Wang ◽  
Pei-Chun Liao
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Chemical Properties ◽  
Soil Chemical Properties ◽  
Soil Microbiome ◽  
Apparent Lack ◽  
Soil P ◽  
Soil Bacterial Communities ◽  
Abundant Otus ◽  
Soil Bacterial

Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.

scholarly journals Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

2019 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
Rhizosphere Soil ◽  
Photosynthetic Capacity ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Bacterial ◽  
The Impact

Abstract Background: Shade presents one of the major abiotic limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. Shade and live soil decreased LP growth but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in the live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Plant shade tolerance is mediated by soil-plant feedback and shade-induced changes in rhizosphere soil bacterial community structure in OJ and LP plants.

scholarly journals Effects of shade stress on turfgrasses morphophysiology and rhizosphere soil bacterial communities

2020 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
Soil Microorganisms ◽  
Rhizosphere Soil ◽  
Photosynthetic Capacity ◽  
Soil Bacterial Communities ◽  
Plant Soil ◽  
Soil Bacterial

Abstract Background: The shade represents one of the major environmental limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. The composition of the soil bacterial community was assayed using high-throughput sequencing. Results: OJ maintained higher photosynthetic capacity and root growth than LP under shade stress, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. The shade and live soil decreased LP growth, but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Shade stress had little impact on the diversity of the OJ and the LP bacterial communities, but instead impacted their composition. The OJ soil bacterial communities were mostly composed of Proteobacteria and Acidobacteria. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Soil microorganisms mediate plant responses to shade stress via plant-soil feedback and shade-induced change in the rhizosphere soil bacterial community structure for OJ and LP plants. These findings emphasize the importance of understanding plant-soil interactions and their role in the mechanisms underlying shade tolerance in shade-tolerant turfgrasses.

scholarly journals Effects of Vegetation Restoration on Soil Bacterial Communities, Enzyme Activities, and Nutrients of Reconstructed Soil in a Mining Area on the Loess Plateau, China

2019 ◽  
Vol 11 (8) ◽  
pp. 2295 ◽  
Author(s):  
Pengfei Li ◽  
Xingchang Zhang ◽  
Mingde Hao ◽  
Yongxing Cui ◽  
Shilei Zhu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Mining Area ◽  
Biochemical Properties ◽  
Vegetation Restoration ◽  
The Loess Plateau ◽  
Soil Biochemical Properties ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Reconstructed Soil

Soil microbes are the main driving forces and influencing factors of biochemical reactions in the environment. Study of ecological recovery after mining activities has prompted wider recognition of the importance of microbial diversity to ecosystem recovery; however, the response of soil bacterial communities to vegetation restoration types and soil biochemical properties remains poorly understood. The purpose of this research was to explore the soil bacterial communities and soil biochemical properties at four sampling sites (brushland (BL), forestland (FL), grassland (GL) and unreclaimed land (UL)) on the Loess Plateau, China, to evaluate the effect of vegetation restoration on the reconstructed soil in mining areas. In August 2017, samples were collected at the Heidaigou coal mine dumps. Illumina MiSeq sequencing was used to identify the structure of the soil bacterial community and evaluate its relationships with soil biochemical properties. The results showed that soil biochemical properties (soil organic matter, available phosphorus, urease, sucrase, microbial biomass carbon and microbial biomass nitrogen) were significantly increased in BL, FL and GL relative to UL, indicating that the soil quality was significantly improved by vegetation restoration. In addition, the results showed that the vegetation restoration on the reconstructed soil in the mining area could significantly improve the operational taxonomic units (OTUs), abundance (ACE and Chao1) and diversity (Shannon and Simpson) indices of bacterial community and the dominant phyla were Proteobacteria, Actinobacteria and Acidobacteria. With vegetation restoration, the relative abundance of Proteobacteria and Acidobacteria showed an increasing trend, while that of Actinobacteria showed a decreasing trend, and the dominant phyla were only significantly correlated with a few biochemical properties. Moreover, there were no changes in soil bacterial community structures across the four sampling sites and the response of the bacterial community to biochemical properties was not obvious. This implies that, although the region has experienced about 20 years of vegetation restoration, the microbial community still maintains good stability and lagging response to soil biochemical properties. Since the BL soil had better biochemical properties and higher bacterial richness and diversity, it was recommended as the optimum vegetation restoration type for soil reclamation in this area.

Variation in soil bacterial communities by long-term application of organic and inorganic fertilizers in rice

2019 ◽  
Vol 11 (3) ◽  
Author(s):  
Ashwini Shanthpure ◽  
Devaki Girija ◽  
Panchami Pottekkat Sidharthan ◽  
Moossa Puthen Peedikakkal ◽  
Sneha Sasidharan Nair
Keyword(s):  
Bacterial Communities ◽  
Inorganic Fertilizers ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
Organic And Inorganic Fertilizers
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