scholarly journals Ammonium and Nitrate Shift the Spatial Distribution of Soil Bacterial Communities and Association Networks Along a Distance from Maize Roots in an Acidic Red Soil

2020 ◽  
Author(s):  
Hao Qing Zhang ◽  
Xue Qiang Zhao ◽  
Yu Shi ◽  
Yuting Liang ◽  
Ren Fang Shen
Keyword(s):  
Spatial Distribution ◽  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Soil Ph ◽  
Bacterial Communities ◽  
Root Zone ◽  
Soil Bacterial Communities ◽  
Maize Roots ◽  
Soil Bacterial

Abstract Background: Ammonium (NH4+) and nitrate (NO3−) are two major inorganic nitrogen (N) forms available for plant growth. Soil microbes affect the availability and transformation of these N forms in the rhizosphere, and this affects the N-use efficiency of plants. However, little is known about the responses of the rhizosphere bacterial community structure to NH4+ and NO3−. Here, a rhizobox containing a root zone (root growing area) and various soil compartments (0–0.5 cm, 0.5–1 cm, 1–2 cm, 2–4 cm, and 4–9 cm from the root zone) was designed to investigate the spatial distribution of bacterial diversity, community structure, and co-occurrence patterns along a distance from maize (Zea mays L.) roots with the addition of 15N-labeled NH4+ or NO3− in an acidic red soil.Results: Addition of NH4+ and NO3− reduced soil bacterial diversity in the maize root zone. The structures of soil bacterial communities differed between NH4+ and NO3− in the root zone and 0.5 cm away from the root zone. Soil pH was the major driver of bacterial community assembly during plant uptake of N. Maize roots recruited potentially beneficial acidophilic bacteria (e.g. Acidibacter, Burkholderia, and Catenulispora) under NH4+ treatment, and recruited growth-promoting bacteria that prefer higher pH (e.g. Sphingomonas, Sphingobium, Azospirillum, and Novosphingobium) under NO3− treatment. In the N-fertilization treatments, the soil bacterial networks were more complex in the root zone and its adjacent 0.5–1 cm zone than in other soil compartments. The soil bacterial networks were more complex under NH4+ treatment than under NO3−. More bacterial taxa in the networks responded positively and negatively to soil residual NH4+ than to NO3− in all zones in the rhizobox.Conclusions: The combined effects of the N form and the rhizosphere influenced the spatial patterns and co-occurrence network of soil bacterial communities at different distances from the maize root zone, mainly because of changes in soil pH during the uptake of NH4+ and NO3− by maize roots. Regulating microbial communities by adjusting soil pH through NH4+ and NO3− supply may be an environmentally friendly option for promoting soil microbial functions in intensively managed agro-ecosystems.

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 Identifying the Biogeographic Patterns of Rare and Abundant Bacterial Communities Using Different Primer Sets on the Loess Plateau

2021 ◽  
Vol 9 (1) ◽  
pp. 139
Author(s):  
Quanchao Zeng ◽  
Shaoshan An
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Land Uses ◽  
The Loess Plateau ◽  
Soil Bacterial Diversity ◽  
Soil Bacterial ◽  
Rare Bacteria

High-throughput sequencing is commonly used to study soil microbial communities. However, different primers targeting different 16S rRNA hypervariable regions often generate different microbial communities and result in different values of diversity and community structure. This study determined the consequences of using two bacterial primers (338f/806r, targeting the V3-V4 region, and 520f/802r, targeting the V4 region) to assess bacterial communities in the soils of different land uses along a latitudinal gradient. The results showed that the variations in the soil bacterial diversity in different land uses were more evident based on the former pair. The statistical results showed that land use had no significant impact on soil bacterial diversity when primer pair 520f/802r was used. In contrast, when primer pair 338f/806r was used, the cropland and orchard soils had significantly higher operational taxonomic units (OTUs) and Shannon diversity index values than those of the shrubland and grassland soils. Similarly, the soil bacterial diversity generated by primer pair 338f/806r was significantly impacted by mean annual precipitation, soil total phosphorus (TP), soil total nitrogen (TN), and soil available phosphorus (AVP), while the soil bacterial diversity generated by primer pair 520f/802r showed no significant correlations with most of these environmental factors. Multiple regression models indicated that soil pH and soil organic carbon (SOC) shaped the soil bacterial community structure on the Loess Plateau regardless of what primer pair was used. Climatic conditions mainly affected the diversity of rare bacteria. Abundant bacteria are more sensitive than rare bacteria to environmental changes. Very little of the variation in the rare bacterial community was explained by environmental factors or geographic distance, suggesting that the communities of rare bacteria are unpredictable. The distributions of the abundant taxa were mainly determined by variations in environmental factors.

scholarly journals The Spatial Factor, Rather than Elevated CO2, Controls the Soil Bacterial Community in a Temperate Forest Ecosystem

2010 ◽  
Vol 76 (22) ◽  
pp. 7429-7436 ◽  
Author(s):  
Yuan Ge ◽  
Chengrong Chen ◽  
Zhihong Xu ◽  
Ram Oren ◽  
Ji-Zheng He
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Temperate Forest ◽  
Soil N ◽  
Soil Bacterial Communities ◽  
Spatial Factor ◽  
Soil Bacterial ◽  
Diversity Estimates ◽  
Total Soil N

ABSTRACT The global atmospheric carbon dioxide (CO2) concentration is expected to increase continuously over the next century. However, little is known about the responses of soil bacterial communities to elevated CO2 in terrestrial ecosystems. This study aimed to partition the relative influences of CO2, nitrogen (N), and the spatial factor (different sampling plots) on soil bacterial communities at the free-air CO2 enrichment research site in Duke Forest, North Carolina, by two independent techniques: an entirely sequencing-based approach and denaturing gradient gel electrophoresis. Multivariate regression tree analysis demonstrated that the spatial factor could explain more than 70% of the variation in soil bacterial diversity and 20% of the variation in community structure, while CO2 or N treatment explains less than 3% of the variation. For the effects of soil environmental heterogeneity, the diversity estimates were distinguished mainly by the total soil N and C/N ratio. Bacterial diversity estimates were positively correlated with total soil N and negatively correlated with C/N ratio. There was no correlation between the overall bacterial community structures and the soil properties investigated. This study contributes to the information about the effects of elevated CO2 and soil fertility on soil bacterial communities and the environmental factors shaping the distribution patterns of bacterial community diversity and structure in temperate forest soils.

scholarly journals Exploring Soil Bacterial Communities in Different Peanut-Cropping Sequences Using Multiple Molecular Approaches

2011 ◽  
Vol 101 (7) ◽  
pp. 819-827 ◽  
Author(s):  
Hari Sudini ◽  
Mark R. Liles ◽  
Covadonga R. Arias ◽  
Kira L. Bowen ◽  
Robin N. Huettel
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Plant Pathogens ◽  
Soil Sampling ◽  
Soil Microbial Community Structure ◽  
Soil Bacterial Communities ◽  
Soilborne Plant Pathogens ◽  
Soil Bacterial ◽  
Crop Health

Soil bacterial communities have significant influence on soilborne plant pathogens and, thus, crop health. The present study focuses on ribotyping soil bacterial communities in different peanut-cropping sequences in Alabama. The objective was to identify changes in microbial assemblages in response to cropping sequences that can play a role in managing soilborne plant pathogens in peanut. Four peanut-cropping sequences were sampled at the Wiregrass Research Station, Headland, AL in 2006 and 2007, including continuous peanut, 4 years of bahiagrass followed by peanut, peanut-cotton, and peanut-corn-cotton. Soil sampling was done at early and mid-season and at harvest. Bacterial community structure was assessed using ribosomal intergenic spacer analysis (RISA) combined with 16S rRNA cloning and sequencing. RISA results indicated >70% dissimilarities among different cropping sequences. However, 90% similarities were noticed among replicated plots of the same cropping sequences. Cropping sequences and time of soil sampling had considerable effect on soil microbial community structure. Bahiagrass rotation with peanut was found to have the highest bacterial diversity, as indicated by a high Shannon Weaver Diversity index. Overall, higher bacterial diversity was observed with bahiagrass and corn rotations compared with continuous peanut. The bacterial divisions Proteobacteria, Acidobacteria, Firmicutes, Bacteroidetes, and Actinomycetes were the predominant bacterial phyla found in all peanut-cropping sequences. The Proteobacteria taxa in these soils were negatively correlated with the abundance of members of division Firmicutes but, conversely, had a significant positive correlation with Gemmatimonadetes taxa. The prevalence of the division Actinomycetes was negatively correlated with the relative abundance of members of division Verrucomicrobia. These results indicate complex interactions among soil bacteria that are important contributors to crop health.

scholarly journals Effects of Manure and Chemical Fertilizer on Bacterial Community Structure and Soil Enzyme Activities in North China

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1017
Author(s):  
Zhiping Liu ◽  
Wenyan Xie ◽  
Zhenxing Yang ◽  
Xuefang Huang ◽  
Huaiping Zhou
Keyword(s):  
Alkaline Phosphatase ◽  
Community Structure ◽  
Bacterial Community ◽  
Enzyme Activities ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Organic Fertilizer ◽  
Chemical Fertilizer ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

The application of organic fertilizer affects soil microbes and enzyme activities. In this study, we explored the effects of various long-term different fertilization treatments (manure, M; chemical fertilizer, NP; manure + chemical fertilizer, MNP; and no fertilizer, CK) on bacterial community structure and soil sucrase, urease, and alkaline phosphatase activities in Shaping, Hequ, China. High-throughput sequencing was used to amplify the third to the fourth hypervariable region of the 16S ribosomal RNA for analysis of the bacterial community structure. Enzyme activities were determined by colorimetry. Soil treated with MNP had the highest bacterial Abundance-based Coverage Estimator index and enzyme activities. The principal coordinates analysis results showed significant differences among the various fertilization treatments (p < 0.001). Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi were consistently dominant in all soil samples. The redundancy analysis and Monte Carlo permutation tests showed that the soil bacterial communities were significantly correlated with alkali-hydrolyzable nitrogen, organic matter, urease, and alkaline phosphatase. Our results reveal the fundamentally different effects that organic and inorganic fertilizers have on soil bacterial communities and their functions.

scholarly journals Pavement Overrides the Effects of Tree Species on Soil Bacterial Communities

2021 ◽  
Vol 18 (4) ◽  
pp. 2168
Author(s):  
Yinhong Hu ◽  
Weiwei Yu ◽  
Bowen Cui ◽  
Yuanyuan Chen ◽  
Hua Zheng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Tree Species ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Soil Bacterial Community ◽  
Soil Bacterial Communities ◽  
Pine Stands ◽  
Soil Bacterial

Human disturbance and vegetation are known to affect soil microorganisms. However, the interacting effects of pavement and plant species on soil bacterial communities have received far less attention. In this study, we collected soil samples from pine (Pinus tabuliformis Carr.), ash (Fraxinus chinensis), and maple (Acer truncatum Bunge) stands that grew in impervious, pervious, and no pavement blocks to investigate the way pavement, tree species, and their interaction influence soil bacterial communities by modifying soil physicochemical properties. Soil bacterial community composition and diversity were evaluated by bacterial 16S amplicon sequencing. The results demonstrated that soil bacterial community composition and diversity did differ significantly across pavements, but not with tree species. The difference in soil bacterial community composition across pavements was greater in pine stands than ash and maple stands. Soil bacterial diversity and richness indices decreased beneath impervious pavement in pine stands, and only bacterial richness indices decreased markedly in ash stands, but neither showed a significant difference across pavements in maple stands. In addition, bacterial diversity did not differ dramatically between pervious pavement and no pavement soil. Taken together, these results suggest that pavement overwhelmed the effects of tree species on soil bacterial communities, and had a greater effect on soil bacterial communities in pine stands, followed by ash and maple stands. This study highlights the importance of anthropogenic disturbance, such as pavement, which affects soil microbial communities.

scholarly journals Soil Bacterial Community Response and Nitrogen Cycling Variations Associated with Subalpine Meadow Degradation on the Loess Plateau, China

2020 ◽  
Vol 86 (9) ◽  
Author(s):  
Zhengming Luo ◽  
Jinxian Liu ◽  
Tong Jia ◽  
Baofeng Chai ◽  
Tiehang Wu
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Loess Plateau ◽  
Bacterial Communities ◽  
N Cycling ◽  
The Loess Plateau ◽  
Soil Bacterial Communities ◽  
Subalpine Meadow ◽  
Soil Bacterial ◽  
Meadow Degradation

ABSTRACT Grassland degradation is an ecological problem worldwide. This study aimed to reveal the patterns of the variations in bacterial diversity and community structure and in nitrogen cycling functional genes along a subalpine meadow degradation gradient on the Loess Plateau, China. Meadow degradation had a significant effect on the beta diversity of soil bacterial communities (P < 0.05) but not on the alpha diversity (P > 0.05). Nonmetric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM) indicated that the compositions of bacterial and plant communities changed remarkably with increasing meadow degradation (all P < 0.05). The beta diversities of the plant and soil bacterial communities were significantly correlated (P < 0.05), while their alpha diversities were weakly correlated (P > 0.05) along the meadow degradation gradient. Redundancy analysis (RDA) showed that the structure of the bacterial community was strongly correlated with total nitrogen (TN), nitrate nitrogen (NO3−-N), plant Shannon diversity, plant coverage, and soil bulk density (all P < 0.05). Moreover, the abundances of N fixation and denitrification genes of the bacterial community decreased along the degradation gradient, but the abundance of nitrification genes increased along the gradient. The structure of the set of N cycling genes present at each site was more sensitive to subalpine meadow degradation than the structure of the total bacterial community. Our findings revealed compositional shifts in the plant and bacterial communities and in the abundances of key N cycling genes as well as the potential drivers of these shifts under different degrees of subalpine meadow degradation. IMPORTANCE Soil microbes play a crucial role in the biogeochemical cycles of grassland ecosystems, yet information on how their community structure and functional characteristics change with subalpine meadow degradation is scarce. In this study, we evaluated the changes in bacterial community structure and nitrogen functional genes in degraded meadow soils. Meadow degradation had a significant effect on bacterial community composition. Soil total nitrogen was the best predictor of bacterial community structure. The beta diversities of the plant and soil bacterial communities were significantly correlated, while their alpha diversities were only weakly correlated. Meadow degradation decreased the potential for nitrogen fixation and denitrification but increased the potential for nitrification. These results have implications for the restoration and reconstruction of subalpine meadow ecosystem on the Loess Plateau.

scholarly journals Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the Western Swiss Alps

2016 ◽  
Vol 82 (21) ◽  
pp. 6303-6316 ◽  
Author(s):  
Erika Yashiro ◽  
Eric Pinto-Figueroa ◽  
Aline Buri ◽  
Jorge E. Spangenberg ◽  
Thierry Adatte ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Water Content ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Swiss Alps ◽  
Content Type ◽  
Soil Bacterial ◽  
Western Swiss Alps

ABSTRACTMountain ecosystems are characterized by a diverse range of climatic and topographic conditions over short distances and are known to shelter a high biodiversity. Despite important progress, still little is known on bacterial diversity in mountain areas. Here, we investigated soil bacterial biogeography at more than 100 sampling sites randomly stratified across a 700-km2area with 2,200-m elevation gradient in the western Swiss Alps. Bacterial grassland communities were highly diverse, with 12,741 total operational taxonomic units (OTUs) across 100 sites and an average of 2,918 OTUs per site. Bacterial community structure was correlated with local climatic, topographic, and soil physicochemical parameters with high statistical significance. We found pH (correlated with % CaO and % mineral carbon), hydrogen index (correlated with bulk gravimetric water content), and annual average number of frost days during the growing season to be among the groups of the most important environmental drivers of bacterial community structure. In contrast, bacterial community structure was only weakly stratified as a function of elevation. Contrasting patterns were discovered for individual bacterial taxa.Acidobacteriaresponded both positively and negatively to pH extremes. Various families within theBacteroidetesresponded to available phosphorus levels. Different verrucomicrobial groups responded to electrical conductivity, total organic carbon, water content, and mineral carbon contents. Alpine grassland bacterial communities are thus highly diverse, which is likely due to the large variety of different environmental conditions. These results shed new light on the biodiversity of mountain ecosystems, which were already identified as potentially fragile to anthropogenic influences and climate change.IMPORTANCEThis article addresses the question of how microbial communities in alpine regions are dependent on local climatic and soil physicochemical variables. We benefit from a unique 700-km2study region in the western Swiss Alps region, which has been exhaustively studied for macro-organismal and fungal ecology, and for topoclimatic modeling of future ecological trends, but without taking into account soil bacterial diversity. Here, we present an in-depth biogeographical characterization of the bacterial community diversity in this alpine region across 100 randomly stratified sites, using 56 environmental variables. Our exhaustive sampling ensured the detection of ecological trends with high statistical robustness. Our data both confirm previously observed general trends and show many new detailed trends for a wide range of bacterial taxonomic groups and environmental parameters.

scholarly journals Changes in the Soil Bacterial Community in a Chronosequence of Temperate Walnut-Based Intercropping Systems

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 299 ◽  
Author(s):  
Pengxiang Gao ◽  
Xiaofeng Zheng ◽  
Lai Wang ◽  
Bin Liu ◽  
Shuoxin Zhang
Keyword(s):  
Bacterial Community ◽  
Soil Ph ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Agroforestry System ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Phyla ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Agroforestry (tree-based intercropping) is regarded as a promising practice in sustainable agricultural management. However, the impacts of converting cropland to an agroforestry system on microbial communities remain poorly understood. In this study, we assessed the soil bacterial communities in conventional wheat monoculture systems and a chronosequence (5–14 years) walnut-wheat agroforestry system through the high-throughput sequencing of 16S rRNA genes to investigate the effect of agroforestry age on soil bacterial communities and the correlation between soil properties and bacterial communities in the agroecosystem. Our results demonstrate that establishing and developing walnut tree-based agroforestry increased soil bacterial diversity and changed bacterial community structure. Firmicutes, Proteobacteria, Actinobacteria and Acidobacteria were the dominant soil bacterial phyla and Bacillus was the dominant genus. Crop monoculture systems were characterized by the Bacillus (Firmicutes)-dominated microbial community. The relative abundance of Bacillus decreased with agroforestry age; however, subgroups of Proteobacteria and Actinobacteria increased. Of the selected soil physicochemical properties, soil pH and bulk density were significantly correlated with bacterial alpha diversity, and soil pH and organic carbon were the principal drivers in shaping the soil microbial structure as revealed by redundancy analysis (RDA).

scholarly journals Cracks Reinforce the Interactions among Soil Bacterial Communities in the Coal Mining Area of Loess Plateau, China

2019 ◽  
Vol 16 (24) ◽  
pp. 4892 ◽  
Author(s):  
Zhanbin Luo ◽  
Jing Ma ◽  
Fu Chen ◽  
Xiaoxiao Li ◽  
Huping Hou ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Loess Plateau ◽  
Bacterial Communities ◽  
Nutrient Loss ◽  
Community Diversity ◽  
Available Phosphorus ◽  
Soil Microbial Community Structure ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Soil microorganisms play a key role in global biogeochemical changes. To understand the interactions among soil bacterial communities and their responses to extreme environments, the soil properties and bacterial community diversity were determined in the post-mining ecosystem of the Loess Plateau, China. The results showed that the soil temperature, pH, organic matter, available phosphorus, and available potassium values were significantly reduced in the post-mining cracks area. However, the richness and uniformity of soil bacterial communities increased by about 50% in the post-mining cracks area. Soil microbial community structure and the network interactions tended to be complex and strengthened in the post-mining cracks area. Moreover, soil nutrient loss caused the differences in soil bacterial community structure compositions in the post-mining cracks area. Furthermore, the relationships between soil physicochemical properties and different modules of the soil bacterial molecular ecological network were changed in a complex manner in the post-mining cracks area. This study provides a theoretical basis for adaptive management and response to cracks in post-mining areas and under other extreme conditions.

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