scholarly journals Drivers of Soil Bacterial Diversity in Sandy Grasslands in China

2021 ◽  
Author(s):  
Chengchen Pan ◽  
Qi Feng ◽  
Yulin Li ◽  
Xiaoya Yu ◽  
Shilong Ren
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Community Structure ◽  
Rrna Gene ◽  
Sandy Land ◽  
Α Diversity ◽  
Soil Bacterial ◽  
Sandy Grasslands

Abstract Bacteria constitute great abundances and groups on Earth and control many important processes in terrestrial ecosystems. However, our understanding of the interactions between soil bacteria and environmental factors remains limited, especially in sensitive and fragile ecosystems. In this study, geographic patterns of bacterial diversity across the four sandy grasslands along a 1600 km north-south transect in northern China were characterized by high-throughput 16S rRNA gene sequencing. Then, we analyzed the driving factors behind the patterns in bacterial diversity. The results showed that of the 21 phyla detected, the most abundant were Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes (average relative abundance > 5%). Soil bacterial α diversity, calculated as the bacterial phylotype richness and Faith’s phylogenetic diversity, was highest in the Otingdag Sandy Land and lowest in the Mu Us Sandy Land. Soil EC was the most influential factor driving bacterial α diversity. The bacterial communities differed significantly among the four sandy grasslands, and the bacterial community structure was significantly affected by environmental factors and geographic distance. Of the environmental variables examined, climatic factors (MAT and MAP) and edaphic properties (pH and EC) explained the highest proportion of the variation in bacterial community structure. Biotic factors such as plant species richness and aboveground biomass exhibited weak but significant associations with bacterial α diversity. Our findings revealed the important role of climate and salinity factors in controlling bacterial diversity; understanding these roles is critical for predicting the impacts of climate change and promoting sustainable management strategies for ecosystem services in these sandy lands.

scholarly journals Different Responses of Soil Environmental Factors, Soil Bacterial Community, and Root Performance to Reductive Soil Disinfestation and Soil Fumigant Chloropicrin

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Zhan ◽  
Ning Yan ◽  
Xinyue Miao ◽  
Qiong Li ◽  
Changbao Chen
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Community Structure ◽  
Treated Soil ◽  
Soil Disinfestation ◽  
Soil Fumigant ◽  
Soil Bacterial ◽  
Soil Environmental Factors

Reductive soil disinfestation (RSD) and soil fumigant chloropicrin (SFC) are two common agricultural strategies for the elimination of soil-borne pathogens. However, the differences in soil environmental factors, soil bacterial microbiome, and root performance between SFC and RSD are poorly understood. In this study, three soil treatments, untreated control (CK), SFC with 0.5 t⋅ha–1 chloropicrin, and RSD with 15 t⋅ha–1 animal feces, were compared. We evaluated their effects on soil environmental factors, bacterial community structure, and root activity using chemical analysis and high-throughput sequencing. RSD treatment improved soil composition structure, bacterial diversity, and root performance to a greater extent. Carbon source utilization preference and bacterial community structure were strikingly altered by SFC and RSD practices. Bacterial richness, diversity, and evenness were notably lowered in the SFC- and RSD-treated soil compared with the CK-treated soil. However, RSD-treated soil harbored distinct unique and core microbiomes that were composed of more abundant and diverse potentially disease-suppressive and organic-decomposable agents. Also, soil bacterial diversity and composition were closely related to soil physicochemical properties and enzyme activity, of which pH, available Na (ANa), available Mg (AMg), available Mn (AMn), total Na (TNa), total Ca (TCa), total Cu (TCu), total Sr (TSr), urease (S-UE), acid phosphatase (S-ACP), and sucrase (S-SC) were the main drivers. Moreover, RSD treatment also significantly increased ginseng root activity. Collectively, these results suggest that RSD practices could considerably restore soil nutrient structure and bacterial diversity and improve root performance, which can be applied as a potential agricultural practice for the development of disease-suppressive soil.

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 Effects of Residue Retention and Removal Following Thinning on Soil Bacterial Community Composition and Diversity in a Larix olgensis Plantation, Northeast China

Forests ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 559
Author(s):  
Xue Dong ◽  
Xin Du ◽  
Zhi-Hu Sun ◽  
Xiang-Wei Chen
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Soil Bacteria ◽  
Soil Bacterial Community ◽  
Soil Bacterial Communities ◽  
Α Diversity ◽  
Soil Bacterial Community Structure ◽  
Soil Bacterial ◽  
Residue Retention

Thinning is an important management practice for reducing plant competition and improving wood production in forests. The residues from thinning can contain large amounts of carbon (C) and nitrogen (N), and the management methods applied directly after thinning can affect the input of nutrients to soil, change the availability of substrates to soil bacterial communities, and thus affect soil bacterial community structure. Our objective was to determine the effects of different thinning residue treatments on soil bacterial community structure and diversity. Illumina high-throughput sequencing technology was used to sequence the bacterial 16SrRNA V3–V4 variable region of the soil (0–10 cm) of a Larix olgensis plantation to compare the composition and diversity of soil bacterial communities following removal of thinning residues (tree stems plus tree crowns) (RM) and retention of thinning residues (crowns retained with stem removal) (RT) treatments. Total soil carbon (TC) and nitrogen (TN) content in the residue retention treatment were significantly greater than in residue removal treatments (p < 0.05). The relative abundance of the dominant soil bacteria phyla were, in descending order: Proteobacteria, Verrucomicrobia, Acidobacteria, Chloroflexi, Actinobacteria, Nitrospirae, Planctomycetes, Gemmatimonadetes, and Bacteroidetes, with a total relative abundance of more than 80%. Acidobacteria were enriched in the RM treatment, while Proteobateria, Actinobacteria and Bacteroidetes were greater in the RT treatment. Rhizobiales and Rhodospirillales (belonging to the α-Proteobacteria) were enriched in the RM treatment. Soil bacteria α diversity was not significantly different among different treatments. Spearman correlation analysis showed that the α diversity index was significantly negatively correlated with TC and TN. Lefse analysis revealed that 42 significant soil bacteria from phylum to genus were found in the two different thinning residue treatments. Redundancy analysis showed that soil TC and TN were the major drivers of variation in soil bacterial community structure. Overall, thinning residue retention increased the availability of resources to the soil bacterial community, thus changing bacterial community structure. This research provides a theoretical basis for the regulation of plantation forest soil fertility and quality.

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 Effects of Simulated Nitrogen Deposition on the Bacterial Community of Urban Green Spaces

2021 ◽  
Vol 11 (3) ◽  
pp. 918
Author(s):  
Lingzi Mo ◽  
Augusto Zanella ◽  
Xiaohua Chen ◽  
Bin Peng ◽  
Jiahui Lin ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Negative Impact ◽  
Bacterial Community Composition ◽  
N Deposition ◽  
Soil Bacterial Community ◽  
Rrna Gene ◽  
Soil Dna ◽  
Urban Green ◽  
Soil Bacterial

Continuing nitrogen (N) deposition has a wide-ranging impact on terrestrial ecosystems. To test the hypothesis that, under N deposition, bacterial communities could suffer a negative impact, and in a relatively short timeframe, an experiment was carried out for a year in an urban area featuring a cover of Bermuda grass (Cynodon dactylon) and simulating environmental N deposition. NH4NO3 was added as external N source, with four dosages (N0 = 0 kg N ha−2 y−1, N1 = 50 kg N ha−2 y−1, N2 = 100 kg N ha−2 y−1, N3 = 150 kg N ha−2 y−1). We analyzed the bacterial community composition after soil DNA extraction through the pyrosequencing of the 16S rRNA gene amplicons. N deposition resulted in soil bacterial community changes at a clear dosage-dependent rate. Soil bacterial diversity and evenness showed a clear trend of time-dependent decline under repeated N application. Ammonium nitrogen enrichment, either directly or in relation to pH decrease, resulted in the main environmental factor related to the shift of taxa proportions within the urban green space soil bacterial community and qualified as a putative important driver of bacterial diversity abatement. Such an impact on soil life induced by N deposition may pose a serious threat to urban soil ecosystem stability and surrounding areas.

scholarly journals Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere

2010 ◽  
Vol 76 (24) ◽  
pp. 8117-8125 ◽  
Author(s):  
Paul J. Hunter ◽  
Paul Hand ◽  
David Pink ◽  
John M. Whipps ◽  
Gary D. Bending
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Population Diversity ◽  
Microbial Interactions ◽  
Soluble Carbohydrates ◽  
Rrna Gene ◽  
Species Variation ◽  
Clone Libraries ◽  
Microbe Interactions

ABSTRACT Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.

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