scholarly journals Phylogenetic Structure of Soil Bacterial Communities along Age Sequence of Subtropical Cunninghamia Lanceolata Plantations

2020 ◽  
Vol 12 (5) ◽  
pp. 1864
Author(s):  
Jiling Cao ◽  
Yuxiong Zheng ◽  
Yusheng Yang
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Filtering ◽  
Cunninghamia Lanceolata ◽  
Community Diversity ◽  
Stand Age ◽  
Phylogenetic Structure ◽  
Soil Bacterial

Despite increasing investigations having studied the changing patterns of soil microbial communities along forest plantation development age sequences, the underlying phylogenetic assemblages are seldom studied for microbial community. Here, the soil bacterial taxonomic and phylogenetic diversity as well as the phylogenetic structure were examined to elucidate the community diversity and assembly in three typical ages (young, middle and mature) of Cunninghamia lanceolata plantations, a dominant economic tree species in southern China. Results indicated that the soil bacterial phylogenetic not taxonomic diversity increased with the increasing in stand age. The bacterial community composition differed significantly among the young, middle and mature plantations. Phylogenetic signals showed that bacterial communities were phylogenetically clustered and structured by environmental filtering in all studied plantations. In mature plantation, the effect of environmental filtering becomes stronger and bacteria taxa tend to intraspecific interact more complexly as characterized by co-occurrence network analysis. This suggests that ecological niche-based environmental filtering could be a dominant assembly process that structured the soil bacterial community along age sequences of Cunninghamia lanceolata plantations.

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 Effects of shade stress on morphophysiology and rhizosphere soil bacterial communities of two contrasting shade-tolerant turfgrasses

2019 ◽  
Author(s):  
Juanjuan Fu ◽  
Yilan Luo ◽  
Pengyue Sun ◽  
Jinzhu Gao ◽  
Donghao Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Shade Tolerance ◽  
Rhizosphere Soil ◽  
Photosynthetic Capacity ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Bacterial ◽  
The Impact

Abstract Background: Shade presents one of the major abiotic limitations for turfgrass growth. Shade influences plant growth and alters plant metabolism, yet little is known about how shade affects the structure of rhizosphere soil microbial communities and the role of soil microorganisms in plant shade responses. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the growth and photosynthetic capacity of two contrasting shade-tolerant turfgrasses, shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrass (Lolium perenne, LP). We also examined soil-plant feedback effects on shade tolerance in the two turfgrass genotypes. Bacterial community composition was assayed using high-throughput sequencing. Results: Our physiochemical data showed that under shade stress, OJ maintained higher photosynthetic capacity and root growth, thus OJ was found to be more shade-tolerant than LP. Shade-intolerant LP responded better to both shade and soil microbes than shade-tolerant OJ. Shade and live soil decreased LP growth but increased biomass allocation to shoots in the live soil. The plant shade response index of LP is higher in the live soil than sterile soil, driven by weakened soil-plant feedback under shade stress. In contrast, there was no difference in these values for OJ under similar shade and soil treatments. Illumina sequencing data revealed that shade stress had little impact on the diversity of the OJ and LP’s bacterial communities, but instead impacted the composition of bacterial communities. The bacterial communities were mostly composed of Proteobacteria and Acidobacteria in OJ soil. Further pairwise fitting analysis showed that a positive correlation of shade-tolerance in two turfgrasses and their bacterial community compositions. Several soil properties (NO3--N, NH4+-N, AK) showed a tight coupling with several major bacterial communities under shade stress, indicating that they are important drivers determining bacterial community structures. Moreover, OJ shared core bacterial taxa known to promote plant growth and confer tolerance to shade stress, which suggests common principles underpinning OJ-microbe interactions. Conclusion: Plant shade tolerance is mediated by soil-plant feedback and shade-induced changes in rhizosphere soil bacterial community structure in OJ and LP plants.

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

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.

scholarly journals Rhizobacterial communities of five co-occurring desert halophytes

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5508 ◽  
Author(s):  
Yan Li ◽  
Yan Kong ◽  
Dexiong Teng ◽  
Xueni Zhang ◽  
Xuemin He ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Community Diversity ◽  
Species Identity ◽  
Halostachys Caspica ◽  
Lycium Ruthenicum ◽  
Limonium Gmelinii

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity ofHalostachys caspica,Halocnemum strobilaceumandKalidium foliatumassociated bacterial communities was lower than that ofLimonium gmeliniiandLycium ruthenicumcommunities. Furthermore, the composition of the bacterial communities ofHalostachys caspicaandHalocnemum strobilaceumwas very different from those ofLimonium gmeliniiandLycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

scholarly journals Diversity of Soil Bacterial Community Is Influenced by Spatial Location and Time but Not Potato Cultivar

2020 ◽  
Vol 4 (3) ◽  
pp. 225-238
Author(s):  
Kamrun Nahar ◽  
Jean-Baptiste Floc’h ◽  
Claudia Goyer ◽  
Bernie J. Zebarth ◽  
Sean Whitney
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Common Scab ◽  
Potato Cultivar ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Streptomyces Spp ◽  
Β Diversity ◽  
Soil Bacterial ◽  
Spatial Locations

Potato cultivars susceptible to common scab were previously reported to harbor five to six times more abundant pathogenic Streptomyces spp. in the rhizosphere soils compared with tolerant cultivars. It is still unclear if the diversity of soil bacterial communities is related to the abundance of pathogenic Streptomyces spp. This study evaluated the effects of potato cultivar on the diversity of bacterial communities in three spatial locations (soil located close to the plant [SCP], in the rhizosphere soil [RS], and in the geocaulosphere soil [GS]) in 2013 and 2014. Common scab tolerant (Goldrush and Hindenburg) and susceptible cultivars (Green Mountain and Agria) were planted in a field infested with pathogenic Streptomyces spp. causing common scab. The β-diversity of the bacterial community was significantly different between years and on dates within each year according to a permutational multivariate analysis of variance. The β-diversity also varied significantly among spatial locations (i.e., SCP, RS, and GS), probably due to changes in soil properties, but did not change significantly among potato cultivars. The architecture of the bacterial network in RS in 2014 was more complex compared with 2013 with a 2.5-fold increase in the number of bacteria included according to a co-occurrence analysis. These results indicated that the soil bacterial community diversity changed temporally and spatially. However, bacterial community diversity and richness were not affected by potato cultivar, suggesting that there were no relationships between bacterial community diversity or richness and the abundance of pathogenic Streptomyces spp.

scholarly journals Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1526
Author(s):  
Xiaoqin Yang ◽  
Yang Wang ◽  
Luying Sun ◽  
Xiaoning Qi ◽  
Fengbin Song ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Northeast China ◽  
Management Practice ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Chemical Properties ◽  
Crop Productivity ◽  
Rrna Gene ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

Effects of inoculation with organic-phosphorus-mineralizing bacteria on soybean (Glycine max) growth and indigenous bacterial community diversity

2017 ◽  
Vol 63 (5) ◽  
pp. 392-401 ◽  
Author(s):  
Wei Sun ◽  
Xun Qian ◽  
Jie Gu ◽  
Xiao-Juan Wang ◽  
Yang Li ◽  
...  
Keyword(s):  
Glycine Max ◽  
Carbon Source ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Organic Phosphorus ◽  
Community Diversity ◽  
Carbon Source Utilization ◽  
Soil Bacterial Communities ◽  
Bacterial Community Diversity ◽  
Soil Bacterial

Three different organic-phosphorus-mineralizing bacteria (OPMB) strains were inoculated to soil planted with soybean (Glycine max), and their effects on soybean growth and indigenous bacterial community diversity were investigated. Inoculation with Pseudomonas fluorescens Z4-1 and Brevibacillus agri L7-1 increased organic phosphorus degradation by 22% and 30%, respectively, compared with the control at the mature stage. Strains P. fluorescens Z4-1 and B. agri L7-1 significantly improved the soil alkaline phosphatase activity, average well color development, and the soybean root activity. Terminal restriction fragment length polymorphism analysis demonstrated that P. fluorescens Z4-1 and B. agri L7-1 could persist in the soil at relative abundances of 2.0%–6.4% throughout soybean growth. Thus, P. fluorescens Z4-1 and B. agri L7-1 could potentially be used in organic-phosphorus-mineralizing biofertilizers. OPMB inoculation altered the genetic structure of the soil bacterial communities but had no apparent influence on the carbon source utilization profiles of the soil bacterial communities. Principal components analysis showed that the changes in the carbon source utilization profiles of bacterial community depended mainly on the plant growth stages rather than inoculation with OPMB. The results help to understand the evolution of the soil bacterial community after OPMB inoculation.

scholarly journals Dynamics of Bacterial Communities in a 30-Year Fertilized Paddy Field under Different Organic–Inorganic Fertilization Strategies

Agronomy ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 14 ◽  
Author(s):  
Yadong Yang ◽  
Peixin Wang ◽  
Zhaohai Zeng
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Hierarchical Cluster ◽  
Organic Manure ◽  
Community Structures ◽  
Long Term Effects ◽  
Inorganic Fertilizers ◽  
Soil Bacterial Communities ◽  
Soil Bacterial

Fertilization plays important roles in improving soil fertility and in increasing crop yield. Soil microbial communities are sensitive indicators of soil quality and health, which could be affected by fertilization strategy. However, our knowledge on how organic–inorganic fertilizers application affects soil bacterial communities remains largely poorly understood. In this study, we investigated the long-term effects of different organic–inorganic fertilization strategies: without fertilizer (CK), fertilizers NPK (CF), fertilizers NPK, plus 30% organic manure (CFM1), and fertilizers NPK plus 60% organic manure (CFM2) on soil bacterial communities in paddy fields. Results showed that the bacterial 16S ribosomal DNA (rDNA) gene abundances in treatments CF, CFM1, and CFM2 were 1.44, 1.54, and 1.28 times higher than that in CK and the ACE index in treatment CFM1 was 9.0% greater than that in treatment CFM2, respectively. Fertilization strategy significantly changed the relative abundance of Nitrospirae, Gemmatimonadetes, and unclassified bacteria at the phylum level and bacteria belonging to order Nitrospira, candidate bacterium SBR2076, unclassified bacteria, Syntrophobacterales, and Solibacterales at the order level, respectively. High organic–inorganic fertilizer application rates inhibited the growth of Nitrospirae by 20–35%, and stimulated the growth of Gemmatimonadetes by 14–77%, relative to the rest of the treatments, respectively. Hierarchical cluster and principal coordinate analysis (PCoA) showed that the fertilization strategy affected the bacterial community structures, and the organic–inorganic fertilized treatments possessed similar bacterial community structures. Furthermore, soil pH, total nitrogen (TN), and soil organic carbon (SOC) were the main driving factors altering the bacterial communities. Our results suggested that combined organic–inorganic fertilizers application increased soil nutrient contents and bacterial abundances, and this could be an optimized fertilization strategy in regulating soil bacterial communities for rice production.

scholarly journals Quality of Irrigation Water Affects Soil Functionality and Bacterial Community Stability in Response to Heat Disturbance

2017 ◽  
Vol 84 (4) ◽  
Author(s):  
Sammy Frenk ◽  
Yitzhak Hadar ◽  
Dror Minz
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Resource Availability ◽  
Bacterial Communities ◽  
Anthropogenic Activities ◽  
Bacterial Community Composition ◽  
Treated Wastewater ◽  
Soil Bacterial Communities ◽  
High Resource ◽  
Soil Bacterial

ABSTRACTAnthropogenic activities alter the structure and function of a bacterial community. Furthermore, bacterial communities structured by the conditions the anthropogenic activities present may consequently reduce their stability in response to an unpredicted acute disturbance. The present mesocosm-scale study exposed soil bacterial communities to different irrigation water types, including freshwater, fertilized freshwater, treated wastewater, and artificial wastewater, and evaluated their response to a disturbance caused by heat. These effectors may be considered deterministic and stochastic forces common in agricultural operations of arid and semiarid regions. Bacterial communities under conditions of high mineral and organic carbon availability (artificial wastewater) differed from the native bacterial community and showed a proteobacterial dominance. These bacterial communities had a lower resistance to the heat treatment disturbance than soils under conditions of low resource availability (high-quality treated wastewater or freshwater). The latter soil bacterial communities showed a higher abundance of operational taxonomic units (OTUs) classified asBacilli. These results were elucidated by soil under conditions of high resource availability, which lost higher degrees of functional potential and had a greater bacterial community composition change. However, the functional resilience, after the disturbance ended, was higher under a condition of high resource availability despite the bacterial community composition shift and the decrease in species richness. The functional resilience was directly connected to the high growth rates of certainBacteroidetesand proteobacterial groups. A high stability was found in samples that supported the coexistence of both resistant OTUs and fast-growing OTUs.IMPORTANCEThis report presents the results of a study employing a hypothesis-based experimental approach to reveal the forces involved in determining the stability of a soil bacterial community to disturbance. The resultant postdisturbance bacterial community composition dynamics and functionality were analyzed. The paper demonstrates the relatedness of community structure and stability under cultivation conditions prevalent in an arid area under irrigation with water of different qualities. The use of common agricultural practices to demonstrate these features has not been described before. The combination of a fundamental theoretical issue in ecology with common and concerning disturbances caused by agricultural practice makes this study unique. Furthermore, the results of the present study have applicable importance regarding soil conservation, as it enables a better characterization and monitoring of stressed soil bacterial communities and possible intervention to reduce the stress. It will also be of valued interest in coming years, as fresh water scarcity and the use of alternative water sources are expected to rise globally.

scholarly journals Perennials but not slope aspect affect the diversity of soil bacterial communities in the northern Negev Desert, Israel

Soil Research ◽  
2018 ◽  
Vol 56 (2) ◽  
pp. 123 ◽  
Author(s):  
Ahuva Vonshak ◽  
Menachem Y. Sklarz ◽  
Ann M. Hirsch ◽  
Osnat Gillor
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Plant Litter ◽  
Negev Desert ◽  
Slope Aspect ◽  
Desert Shrubs ◽  
Soil Bacterial

Underneath the canopy of perennials in arid regions, moderate soil temperature and evaporation, as well as plant litter create islands of higher fertility in the low-productivity landscape, known as ‘resource islands’. The sparse distribution of these resource islands is mirrored by soil microbial communities, which mediate a large number of biogeochemical transformations underneath the plants. We explored the link between the bacterial community composition and two prevalent desert shrubs, Zygophyllum dumosum and Artemisia herba-alba, on northern- and southern-facing slopes in the northern highlands of the Negev Desert (Israel), at the end of a drought winter mild rainy season. We sequenced the bacterial community and analysed the physicochemical properties of the soil under the shrub canopies and from barren soil in replicate slopes. The soil bacterial diversity was independent of slope aspect, but differed according to shrub presence or type. Links between soil bacterial community composition and their associated desert shrubs were found, enabling us to link bacterial diversity with shrub type or barren soils. Our results suggest that plants and their associated bacterial communities are connected to survival and persistence under the harsh desert conditions.

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