scholarly journals Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

2021 ◽  
Vol 9 (7) ◽  
pp. 1419
Author(s):  
Saheed Akinola ◽  
Ayansina Ayangbenro ◽  
Olubukola Babalola
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Stress Responses ◽  
Sampling Site ◽  
Diversity Indices ◽  
Influential Factor ◽  
Forward Selection ◽  
Shotgun Metagenomics ◽  
Maize Rhizosphere

The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant’s rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO3 (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls > Rs > Rc > Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms.

Bacterial community structure in a latitudinal gradient of lakes: the roles of spatial versus environmental factors

2011 ◽  
Vol 56 (10) ◽  
pp. 1973-1991 ◽  
Author(s):  
M. ROMINA SCHIAFFINO ◽  
FERNANDO UNREIN ◽  
JOSEP M. GASOL ◽  
RAMON MASSANA ◽  
VANESSA BALAGUÉ ◽  
...  
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Latitudinal Gradient

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 Continental-Scale Paddy Soil Bacterial Community Structure, Function and Biotic Interaction

2020 ◽  
Author(s):  
Zhijian Zhang ◽  
Hong-Yi Li ◽  
Hang Wang ◽  
Xing-Hua Tao ◽  
Xian-Zhe Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Paddy Soil ◽  
Bacterial Community Structure ◽  
Soil Bacteria ◽  
Paddy Soils ◽  
Continental Scale ◽  
Soil Sustainability

Abstract Background: Rice paddy soil-associated microbiota participate in biogeochemical processes that underpin rice yield and soil sustainability, yet continental-scale biogeographic patterns of paddy soil microbiota remain elusive. Here, the soil bacteria of four typical Chinese rice-growing regions were characterized over large-scale space and compared with adjacent non-paddy soils.Results: The geographic patterns of paddy soil bacteria were significantly different from non-paddy soils, with lower alpha diversity, unique taxonomic and functional composition, and distinct co-occurrence network topology. Both stochastic and deterministic processes shaped soil bacteria assembly, but paddy exhibited a stronger deterministic signature than non-paddy samples, especially due to the roles of climate determinants. The continental biogeographic variance in bacterial community structure was driven by the competition between two mutually-exclusive bacterial modules in the co-occurrence network, and suggested antagonistic species-to-species interactions as potential selective forces may greatly shape their community structures. Keystone taxa identified in network models, such as Actinobacteria, Chloroflexi, and Proteobacteria, were demonstrated to be preferentially affected by environmental factors than other community members and showed high sensitivity to environmental changes, whereby the environmental factors greatly shaped the paddy soil bacterial communities by leveraging changes in keystones.Conclusions: The strong interplay between biotic/abiotic factors may greatly construct paddy soil microbial community and their uniqueness as compared with non-paddy soils. Microbial biogeographical analyses with novel insights into underlying determinants investigated on intensively-cultivated paddy field soils may aid in elucidating microbial changes subjected to land-use changes following the transformation between natural and agro-ecosystem, and also facilitate microbial community manipulation for better crop productivity and soil sustainability worldwide.

scholarly journals Shift of anammox bacterial community structure along the Pearl Estuary and the impact of environmental factors

2015 ◽  
Vol 120 (4) ◽  
pp. 2869-2883 ◽  
Author(s):  
Bingbing Fu ◽  
Jiwen Liu ◽  
Hongmei Yang ◽  
Ting Chang Hsu ◽  
Biyan He ◽  
...  
Keyword(s):  
Community Structure ◽  
Environmental Factors ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
The Impact

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.

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