Soil pH is the primary factor driving the distribution and function of microorganisms in farmland soils in northeastern China

Abstract Purpose To understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil. Method A broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions. Result The dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.

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

Applied and Environmental Microbiology ◽

10.1128/aem.00335-09 ◽

2009 ◽

Vol 75 (15) ◽

pp. 5111-5120 ◽

Cited By ~ 1989

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.

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Field-Scale Transplantation Experiment To Investigate Structures of Soil Bacterial Communities at Pioneering Sites

Applied and Environmental Microbiology ◽

10.1128/aem.05778-11 ◽

2011 ◽

Vol 77 (23) ◽

pp. 8241-8248 ◽

Cited By ~ 30

Author(s):

Anna Lazzaro ◽

Andreas Gauer ◽

Josef Zeyer

Keyword(s):

Bacterial Community ◽

Environmental Conditions ◽

Bacterial Communities ◽

Seasonal Pattern ◽

Dry Weight ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Reciprocal Transplantation ◽

Temperature And Precipitation ◽

Soil Bacterial

ABSTRACTStudies on the effect of environmental conditions on plants and microorganisms are a central issue in ecology, and they require an adequate experimental setup. A strategy often applied in geobotanical studies is based on the reciprocal transplantation of plant species at different sites. We adopted a similar approach as a field-based tool to investigate the relationships of soil bacterial communities with the environment. Soil samples from two different (calcareous and siliceous) unvegetated glacier forefields were reciprocally transplanted and incubated for 15 months between 2009 and 2010. Controls containing local soils were included. The sites were characterized over time in terms of geographical (bedrock, exposition, sunlight, temperature, and precipitation) and physicochemical (texture, water content, soluble and nutrients) features. The incubating local (“home”) and transplanted (“away”) soils were monitored for changes in extractable nutrients and in the bacterial community structure, defined through terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA gene. Concentrations of soluble ions in most samples were more significantly affected by seasons than by the transplantation. For example, NO3−showed a seasonal pattern, increasing from 1 to 3 μg NO3−(g soil dry weight)−1after the melting of snow but decreasing to <1 μg NO3−(g soil dry weight)−1in autumn. Seasons, and in particular strong precipitation events occurring in the summer of 2010 (200 to 300 mm of rain monthly), were also related to changes of bacterial community structures. Our results show the suitability of this approach to compare responses of bacterial communities to different environmental conditions directly in the field.

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Urbanization-induced environmental changes strongly affect wetland soil bacterial community composition and diversity

Environmental Research Letters ◽

10.1088/1748-9326/ac444f ◽

2021 ◽

Author(s):

Xinyu Yi ◽

Chen Ning ◽

Shuailong Feng ◽

Haiqiang Gao ◽

Jianlun Zhao ◽

...

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Environmental Changes ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Environmental Drivers ◽

Wetland Soil ◽

Rrna Gene ◽

Soil Microbial ◽

Soil Bacterial

Abstract Soil microbial communities potentially serve as indicators for their responses to changes in various ecosystems at scales from a region to the globe. However, changes in wetland soil bacterial communities and how they are related to urbanization intensities remains poorly understood. Here, we collected sixty soil samples along urbanization intensity gradients from twenty wetlands. We measured a range of environmental factors and characterized bacterial communities structure using 16S rRNA gene amplicon sequencing that targeted the V4-V5 region. Our results revealed the dominant soil microbial phyla included Proteobacteria (39.3%), Acidobacteria (21.4%) and Chloroflexi (12.3%) in the wetlands, and showed a significant divergence of composition in intensive urbanization area (UI_4) than other places. A critical "threshold" exists in the soil bacterial diversity, demonstrating different patterns: a gradual increase in the areas of low-to-intermediate disturbances but a significant decrease in highly urbanized areas where metabolic functions were significantly strong. Additionally, soil pH, total phosphorus (TP), available phosphorus (AP ) and ammonia nitrogen (NH4+-N) made a significant contribution to variations in bacterial communities, explaining 49.6%, 35.1%, 26.2% and 30.7% of the total variance, respectively. pH and NH4+-N were identified as the main environmental drivers to determine bacterial community structure and diversity in the urban wetlands. Our results highlight collective changes in multiple environmental variables induced by urbanization rather than by the proportion of impervious surface area (ISA), which were potentially attributed to the spatial heterogeneity along different urbanization gradients.

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Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.03191-14 ◽

2014 ◽

Vol 81 (2) ◽

pp. 522-532 ◽

Cited By ~ 34

Author(s):

Wan-Ying Xie ◽

Jian-Qiang Su ◽

Yong-Guan Zhu

Keyword(s):

Bacterial Community ◽

Paddy Soil ◽

Bacterial Communities ◽

Bacterial Species ◽

Rrna Gene ◽

Core Microbiome ◽

Content Type ◽

Soil Ecosystems ◽

Α Diversity ◽

Floating Macrophytes

ABSTRACTThe phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We tookWolffia australianaas a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere ofW. australianaharbored considerably rich communities of bacteria, withProteobacteriaandBacteroidetesas the predominant phyla. The core microbiome in the phyllosphere contained genera such asAcidovorax,Asticcacaulis,Methylibium, andMethylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.

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The Growth of Plants and Indigenous Bacterial Community Were Significantly Affected by Cadmium Contamination in Soil-Plant System

10.21203/rs.3.rs-181936/v1 ◽

2021 ◽

Author(s):

Yunyan Du ◽

Dawei Zhang ◽

Dinggang Zhou ◽

Lili Liu ◽

Jinfeng Wu ◽

...

Keyword(s):

Heavy Metals ◽

Bacterial Community ◽

Oilseed Rape ◽

Bacterial Communities ◽

Anthropogenic Activities ◽

Ecosystem Functions ◽

Plant System ◽

Α Diversity ◽

Soil Bacterial ◽

The Impact

Abstract Concentrations of heavy metals continue to increase in soil environments as a result of both anthropogenic activities and natural processes. Cadmium (Cd) is one of the most toxic heavy metals and poses health risks to both humans and the ecosystem. Herein, we explore the impacts of Cd on a soil-plant system composed of oilseed rape (Brassica napus and Brassica juncea) and bacteria. The two species of oilseed rape displayed a similar variation trend under Cd treatment. Cd accumulation within plant tissues enhanced with increasing concentrations of Cd in soils, and Cd treatment decreased chlorophyll content and suppressed plant growth. Meanwhile, Cd stress induced the changes of antioxidative enzymes activities including elevating SOD and POD activities and reducing CAT activity. The impact of Cd on the bacterial communities of soils was greater than bacterial communities of plants (phyllosphere and endophyte). The α-diversity of bacterial community in soils declined significantly under higher Cd concentration (30 mg/kg). In addition, soil bacterial communities composition and structure were altered in the presence of higher Cd concentration. Meanwhile, the bacterial community of bulk soil was significantly correlated with Cd, while the variation of rhizosphere soil bacterial community was markedly correlated with Cd and other environmental factors of both soils and plants. These results suggested that Cd could affect both the growth of plants and the indigenous bacterial community in soil-plant system, which might further change ecosystem functions in soils.

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Drivers of Soil Bacterial Diversity in Sandy Grasslands in China

10.21203/rs.3.rs-141689/v1 ◽

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

Forests ◽

10.3390/f10040299 ◽

2019 ◽

Vol 10 (4) ◽

pp. 299 ◽

Cited By ~ 3

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).

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pH affects bacterial community composition in soils across the Huashan Watershed, China

Canadian Journal of Microbiology ◽

10.1139/cjm-2015-0783 ◽

2016 ◽

Vol 62 (9) ◽

pp. 726-734 ◽

Cited By ~ 1

Author(s):

Rui Huang ◽

Dayong Zhao ◽

Jin Zeng ◽

Feng Shen ◽

Xinyi Cao ◽

...

Keyword(s):

Bacterial Community ◽

Soil Properties ◽

Soil Ph ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Mantel Test ◽

Soil Samples ◽

Dominant Factor ◽

Bioinformatics Analyses ◽

Soil Bacterial

To investigate soil bacterial richness and diversity and to determine the correlations between bacterial communities and soil properties, 8 soil samples were collected from the Huashan watershed in Anhui, China. Subsequently, 454 high-throughput pyrosequencing and bioinformatics analyses were performed to examine the soil bacterial community compositions. The operational taxonomic unit richness of the bacterial community ranged from 3664 to 5899, and the diversity indices, including Chao1, Shannon–Wiener, and Faith’s phylogenetic diversity ranged from 7751 to 15 204, 7.386 to 8.327, and 415.77 to 679.11, respectively. The 2 most dominant phyla in the soil samples were Actinobacteria and Proteobacteria. The richness and diversity of the bacterial community were positively correlated with soil pH. The Mantel test revealed that the soil pH was the dominant factor influencing the bacterial community. The positive modular structure of co-occurrence patterns at the genus level was discovered by network analysis. The results obtained in this study provide useful information that enhances our understanding of the effects of soil properties on the bacterial communities.

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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

10.21203/rs.3.rs-41492/v1 ◽

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.

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Rhizosphere bacteria community and functions under typical natural halophyte communities in North China salinized areas

PLoS ONE ◽

10.1371/journal.pone.0259515 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0259515

Author(s):

Fating Yin ◽

Fenghua Zhang ◽

Haoran Wang

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Acid Metabolism ◽

Rhizosphere Soil ◽

Soil Bacterial Community ◽

Rhizosphere Bacteria ◽

Community Diversity ◽

Rrna Gene ◽

Soil Bacterial ◽

Suaeda Glauca

Soil salinity is a serious environmental issue in arid China. Halophytes show extreme salt tolerance and are grow in saline-alkaline environments. There rhizosphere have complex bacterial communities, which mediate a variety of interactions between plants and soil. High-throughput sequencing was used to investigated rhizosphere bacterial community changes under the typical halophyte species in arid China. Three typical halophytes were Leymus chinensis (LC), Puccinellia tenuiflora (PT), Suaeda glauca (SG). The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Acidobacteria and Bacteroidetes, Suaeda glauca rhizosphere has stronger enrichment of Nitrospirae and Cyanobacteria. The Ace, Chao and Shannon indices were significantly higher in soils under LC and SG (P<0.05). Functional predictions, based on 16S rRNA gene by PICRUSt, indicated that Energy metabolism, Amino acid metabolism, Carbohydrate metabolism and Fatty acid metabolism are dominant bacterial functions in three halophytes rhizosphere soil. Carbon metabolism, Oxidative phosphorylation, Methane metabolism, Sulfur metabolism and Nitrogen metabolism in SG were significantly higher than that in LC and PT. Regression analysis revealed that rhizosphere soil bacterial community structure is influenced by soil organic matter (SOM) and soil water content (SWC), while soil bacterial community diversity is affected by soil pH. This study contributes to our understanding of the distribution characteristics and metabolic functions under different halophyte rhizosphere bacterial communities, and will provide references for the use of rhizosphere bacteria to regulate the growth of halophytes and ecological restoration of saline soil.

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