Local Environmental Factors Drive Divergent Grassland Soil Bacterial Communities in the 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.

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Difference in Rhizosphere Soil Bacterial Community was among Six Cinnamomum camphora Chemotypes

10.20944/preprints202111.0158.v1 ◽

2021 ◽

Author(s):

Zufei Xiao ◽

Beihong Zhang ◽

Yangbao Wang ◽

Zhinong Jin ◽

Feng Li ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Rhizosphere Soil ◽

Soil Nutrient ◽

Soil Bacterial Community ◽

Cinnamomum Camphora ◽

Close Relationship ◽

Soil Bacterial

Abstract: Plant types and soil bacterial communities had a close relationship, understanding the profound association between them contributes to better learn bacterial ecological function for plant growth. In this study, rhizosphere soil of six different chemotype Cinnamomum camphora trees were collected, including C. bodinieri var. citralifera, [C. camphora (Linn.) Presl], camphora-type, cineole-type, linalool-type and isoborneol-type. Soil properties content and bacterial communities were analyzed. Two chemotype C. camphora, including [C. camphora (Linn.) Presl] and linalool-type, shaped similar bacterial community structure, decreased Firmcutes relative abundance. richness estimators (Chao1 index and Ace index) of [C. camphora (Linn.) Presl] were decreased compared with the others. Furthermore, soil bacterial community structure was also similar among bodinieri var. citralifera, camphora-type, cineole-type and isoborneol-type. Hence, different chemotype C. camphora altered soil nutrient and shaped rhizosphere bacterial communities.

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

Microorganisms ◽

10.3390/microorganisms9010139 ◽

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.

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

Agronomy ◽

10.3390/agronomy11051017 ◽

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.

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Responses of Bacterial Communities to Simulated Climate Changes in Alpine Meadow Soil of the Qinghai-Tibet Plateau

Applied and Environmental Microbiology ◽

10.1128/aem.00557-15 ◽

2015 ◽

Vol 81 (17) ◽

pp. 6070-6077 ◽

Cited By ~ 46

Author(s):

Junpeng Rui ◽

Jiabao Li ◽

Shiping Wang ◽

Jiaxing An ◽

Wen-tso Liu ◽

...

Keyword(s):

Bacterial Community ◽

Climate Warming ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Climate Changes ◽

Tibet Plateau ◽

Content Type ◽

Soil Bacterial Communities ◽

Soil Bacterial ◽

Qinghai Tibet Plateau

ABSTRACTThe soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, microbial responses to climate warming or cooling remain poorly understood, limiting our ability to predict the consequences of future climate changes. To address this issue, it is critical to identify microbes sensitive to climate change and key driving factors shifting microbial communities. In this study, alpine soil transplant experiments were conducted downward or upward along an elevation gradient between 3,200 and 3,800 m in the Qinghai-Tibet plateau to simulate climate warming or cooling. After a 2-year soil transplant experiment, soil bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. The results showed that the transplanted soil bacterial communities became more similar to those in their destination sites and more different from those in their “home” sites. Warming led to increases in the relative abundances inAlphaproteobacteria,Gammaproteobacteria, andActinobacteriaand decreases inAcidobacteria,Betaproteobacteria, andDeltaproteobacteria, while cooling had opposite effects on bacterial communities (symmetric response). Soil temperature and plant biomass contributed significantly to shaping the bacterial community structure. Overall, climate warming or cooling shifted the soil bacterial community structure mainly through species sorting, and such a shift might correlate to important biogeochemical processes such as greenhouse gas emissions. This study provides new insights into our understanding of soil bacterial community responses to climate warming and cooling.

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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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The impacts of a biochar application on selected soil properties and bacterial communities in an Albic Clayic Luvisol

Soil and Water Research ◽

10.17221/19/2019-swr ◽

2020 ◽

Vol 15 (No. 2) ◽

pp. 85-92

Author(s):

Chengsen Zhao ◽

Qingqing Xu ◽

Lin Chen ◽

Xiaoqing Li ◽

Yutian Meng ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Soil Properties ◽

Bulk Density ◽

Relative Abundance ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Soil Layer ◽

Total Carbon ◽

Soil Bacterial

In this four-year study, we focused on the impacts of a biochar application on physicochemical soil properties (soil total carbon, total nitrogen, total potassium, total phosphorus, available nitrogen, available potassium, available phosphorus, pH, bulk density and moisture) and bacterial communities in an Albic Clayic Luvisol. The biochar was applied to plots only once with rates of 0, 10, 20 and 30 t/ha at the beginning of the experiment. The soil samples were collected from the surface (0–10 cm) and second depth (10–20 cm) soil layers after four years. The results showed that that the soil total carbon (TC) and pH increased, but the soil bulk density (BD) decreased with the biochar application. The soil bacterial sequences determined by the Illumina MiSeq method resulted in a decrease in the relative abundance of Acidobacteria, but an increase in the Actinobacteria with the biochar application. The bacterial diversity was significantly influenced by the biochar application. The nonmetric multidimensional scaling (NMDS) and canonical correspondence analysis (CCA) indicated that the soil bacterial community structure was affected by both the biochar addition and the soil depth. The Mantel test analysis indicated that the bacterial community structure significantly correlated to a soil with a pH (r = 0.525, P = 0.001), bulk density (r = 0.539, P = 0.001) and TC (r = 0.519, P = 0.002) only. In addition, most of the differences in the soil properties, bacterial relative abundance and community composition in the second depth soil layer were greater than those in the surface soil layer.

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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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Soil bacterial community and functional shifts in response to thermal insulation in moist acidic tundra of Northern Alaska

10.5194/soil-2015-89 ◽

2016 ◽

Cited By ~ 2

Author(s):

M. P. Ricketts ◽

R. S. Poretsky ◽

J. M. Welker ◽

M. A. Gonzalez-Meler

Keyword(s):

Climate Change ◽

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Chemical Properties ◽

Winter Precipitation ◽

Snow Accumulation ◽

Soil Bacterial Communities ◽

Soil Bacterial

Abstract. Soil microbial communities play a central role in the cycling of carbon (C) in Arctic tundra ecosystems, which contain a large portion of the global C pool. Climate change predictions for Arctic regions include increased temperature and precipitation (i.e. more or less snow), resulting in increased winter soil insulation, increased soil temperature and moisture, and shifting plant community composition. We utilized an 18-year snowfence study site designed to examine the effects of increased winter precipitation on Arctic tundra soil bacterial communities within the context of ecosystem response to climate change. Soil was collected from three pre-established treatment zones representing varying degrees of snow accumulation (DEEP, INT, LOW), soil physical properties (temperature, moisture, active layer thaw depth) were measured, and samples were analysed for C content, nitrogen (N) content, and pH. DNA was extracted and the 16S rRNA gene was sequenced to reveal phylogenetic community differences between samples and determine how soil bacterial communities might respond (structurally and functionally) to changes in winter precipitation and soil chemistry. We analysed relative abundance changes of the six most abundant phyla and found four (Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi) responded to deepened snow. All six phyla correlated with at least one of the soil chemical properties (%C, %N, C:N, pH), however a single predictor was not identified suggesting that each bacterial phylum responds differently to soil characteristics. Overall bacterial community structure (beta diversity) was found to be associated with snow accumulation treatment and all soil chemical properties. Bacterial functional potential was inferred using ancestral state reconstruction to approximate functional gene abundance, revealing a decreased abundance of genes required for soil organic matter (SOM) decomposition in the organic horizon of the deep snow accumulation zones. These results suggest that predicted climate change scenarios may result in altered soil bacterial community structure and function, and indicate either a reduction in decomposition potential that may limit C loss from the system, or alleviated temperature limitations on enzymatic efficiency, or both. The fate of stored C in Arctic soils ultimately depends on the balance between these mechanisms.

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Effects of Chemical and Solar Soil-Disinfection Methods on Soil Bacterial Communities

Sustainability ◽

10.3390/su12239833 ◽

2020 ◽

Vol 12 (23) ◽

pp. 9833

Author(s):

Cuixia Yun ◽

Enke Liu ◽

Massimo Rippa ◽

Pasquale Mormile ◽

Dongbao Sun ◽

...

Keyword(s):

Activated Carbon ◽

Community Structure ◽

Solar Radiation ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Disinfection Methods ◽

Soil Disinfection ◽

Soil Bacterial

The actctivated carbon + solar radiation membrane is an eco-friendly soil disinfestations method for managing soil-borne plant pathogens. However, little was known the impact of Activated carbon + solar radiation membrane on bacterial community structure in strawberry production systems under field conditions. A comprehensive evaluation of the impacts of different soil disinfection methods on the bacterial community structure is fundamental to understand the role of disinfection in maintaining soil health. The changes in the soil bacterial diversity and community composition were detected using realtime fluorescence quantitative PCR (RTFQ PCR) and next-generation sequencing techniques to better understand the effect of soil disinfection. The bacterial community composition was monitored after disinfection using dazomet (DZ), chloropicrin (CP), 100 kg/ha activated carbon + solar radiation membrane (AC1), 200 kg/ha activated carbon + solar radiation membrane (AC2), and 300 kg/ha activated carbon + solar radiation membrane (AC3) and compared with the control (CT). The results indicated that the different dosages of activated carbon (AC1, AC2, and AC3) did not affect the bacterial community structure. On the other hand, DZ and CP considerably reduced the soil biomass and abundance of bacterial species. Chemical fumigants influenced the bacterial community structure, with DZ treatment leading to the dominance of the phylum Firmicutes, accounting for approximately 54%. After fumigation with CP, Proteobacteria and Acidobacteria were the dominant phyla. Beta diversity analysis and principal coordinate analysis revealed that the bacterial communities in the soil treated with DZ and CP formed clusters. Redundancy analysis indicated that soil pH, available potassium, and available phosphorus were the key factors influencing microbial metabolic functional diversity. Thus, it was verified that the damage caused by activated carbon + solar radiation membrane—a potential alternative for chemical fumigant—to the soil bacterial community was less than that caused by chemicals DZ and CP.

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Effects of Different Vegetable Rotations on the Bacterial Community Structure and Tomato Growth in a Continuous Tomato Cropping Substrate

10.21203/rs.3.rs-196685/v1 ◽

2021 ◽

Author(s):

Li Jin ◽

Jihua Yu ◽

Ning Jin ◽

Jianming Xie ◽

Yue Wu ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Crop Rotation ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Total N ◽

Healthy Growth ◽

Dominant Bacteria ◽

Substrate Ph

Abstract Purpose In this study, MiSeq pyrosequencing was used to analyze the effects of different vegetable rotations on the bacterial diversity and community structure in a substrate that was used for continuous tomato cropping (CK). Methods The vegetable rotations tested were cabbage/tomato (B), kidney bean/tomato (D), and celery/tomato (Q). Results The results revealed that the substrate bacterial diversity and richness of each crop rotation were higher than those of CK. The highest bacterial diversity was found in the B substrate, followed by the Q and D substrates. Further comparison showed that the bacterial community structure of Q substrate was significantly different to that of CK. Compared with the CK, the Q substrate had a significantly higher relative abundance of several dominant microflora, such as Acidobacteria, Chloroflexi, and Firmicutes. Additionally, the Q rotation significantly increased the abundance of beneficial bacteria, such as Actinobacteria_unclassified and Anaerolineaceae_unclassified. A redundancy analysis showed that Most dominant bacteria correlated positively with the substrate pH, total N, and alkali-hydrolyzable N but negatively with the available P, available K, total P, total K, and organic matter contents and substrate EC. The substrates after crop rotation improved the growth and physiological condition of the subsequent tomato plants, among which those from the Q rotation performed the best. Conclusion Therefore, celery rotation not only increased the richness and diversity of bacterial communities in the substrate but also significantly increased the richness of the beneficial bacterial communities, allowing better maintenance of the substrate microenvironment for the healthy growth of crops.

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