Exploring Soil Bacterial Communities in Different Peanut-Cropping Sequences Using Multiple Molecular Approaches

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands. Soil samples were collected from recycled organics plots treated with different types and quantity of organic wastes. The field experimental treatments included control (CK, without application of any organic wastes), low amount of GTW CO (COL), GTW CL (CLL), and MSW (ML), and high amounts of GTW CO (COH), GTW CL (CLH), and MSW compost (MH). Microbial DNA was extracted from soil samples and the 16S rRNA genes were polymerase chain reaction (PCR)-amplified. The PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and clone libraries constructed from the excised DGGE bands. DGGE-based analyses showed that application of the GTW CO, regardless of the amount applied, had significant negative effects on soil bacterial genotypic diversity and community structure compared with the control, while the applications of other organic wastes including the GTW CL and MSW had no clear effects. The effects of the rate of organic waste application on soil bacterial community characteristics varied with the types of organic wastes applied. Sequence-based analyses of 126 clones indicated that Proteobacteria (53.2%) was the dominant taxa at the experimental site, followed by Actinobacteria (9.5%), Bacteroidetes (7.9%), Firmicutes (7.9%), Gemmatimonadetes (5.6%), Chloroflexi (2.4%), Acidobacteria (1.6%) and the unclassified group (11.9%). In the COH treatment, Acidobacteria, Bacteroidetes, and Gemmatimonadetes were not detected; the percentages of Firmicutes, Proteobacteria, and Actinobacteria in the COH treatment were significantly different from those in CK. There is a significant positive correlation (r = 0.71, p = 0.002) between the C/N ratio of organic wastes and the bacterial genotypic communities. Both the type and the amount of GTW applied affected soil bacterial genotypic diversity and community structure. The different effects of various types of organic wastes on soil bacterial characteristics may be predicted by the differences in specific properties of organic wastes such as C/N ratio, as evidenced by the strong and significant positive relationship between the bacterial community distance and the environmental distance of C/N ratio. This also indicates that the C/N ratio of GTW applied can be a major driver for the shift in the soil bacterial community. Our results revealed that the effects of organic wastes on soil bacterial communities varied with the types of organic wastes, and depending on the rate of application. Application of the GTW CO led to significant shifts in soil bacterial community diversity and structure. The effects of different types of organic wastes on the soil bacterial characteristics can be predicted by the differences of specific properties of organic wastes, such as the C/N ratio. Sequence-based analyses of 126 clones indicated that Proteobacteria was the dominant taxa at the experimental site. Our results have important implications for developing sound regulatory guidelines for the beneficial reuse of organic wastes, indicating that GTW CO and similar organic waste treatments may not be suitable for application in agricultural soils due to its significant negative effect on soil bacterial community.

Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.

PDF HTML阅读 XML下载 导出引用 引用提醒 三江平原沼泽湿地垦殖及自然恢复对土壤细菌群落多样性的影响 DOI: 10.5846/stxb201601040015 作者: 作者单位: 黑龙江省农垦科学院,东北林业大学,东北林业大学,东北林业大学,呼伦贝尔市林业局 作者简介: 通讯作者: 中图分类号: 基金项目: 黑龙江省青年科学基金项目（QC2014C029）；国家水体污染控制与治理科技重大专项课题（2015ZX07201-008-03） Effect of cultivation and natural restoration on soil bacterial community diversity in marshland in the Sanjiang Plain Author: Affiliation: Heilongjiang Academy of Land Reclamation Sciences,Northeast Forestry University,Northeast Forestry University,Northeast Forestry University,Hulunbeier forestry administration Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为量化垦殖对我国东北沼泽湿地的影响程度，于2015年6月基于Illumina Miseq PE300第二代高通量测序平台，对黑龙江省洪河国家级自然保护区的原始沼泽、耕地、退耕湿地的土壤细菌16S rRNA基因高变区域进行测序，并分析沼泽湿地土壤细菌群落多样性和结构组成与垦殖的关系。结果表明：共获得358737条修剪序列且被划分为36个已知的菌门，在11个主要的土壤细菌门类中（相对丰度 > 1%），芽单胞菌门（P < 0.01）、拟杆菌门（P < 0.01）、厚壁菌门（P < 0.01）和绿菌门（P < 0.01）在不同生境类型样地差异显著，土壤细菌群落alpha多样性由高到低排序依次是：耕地、退耕湿地、原始沼泽。结合相关性分析和冗余分析可以证明，长期的耕作，特别是旱田耕作对沼泽湿地土壤细菌群落组成产生显著的影响，土壤pH、含水量、全碳、有机碳、可溶有机碳、碱解氮、微生物量碳、微生物量氮对土壤细菌的多样性和群落组成产生影响。总之，研究结果发现自然恢复可以显著促进土壤细菌群落多样性的恢复，但是沼泽湿地土壤细菌群落结构一旦被垦殖干扰改变将很难恢复到原始状态，强调了有效地利用土壤细菌群落对维护土壤生态系统平衡具有重要的意义。 Abstract:Different perturbation regimes, including disturbance caused by cultivation or the process of natural restoration, can have significant effects on the soil bacterial community in marshland. In this study, we investigated the relationship between soil bacterial community composition and perturbation in marshland to quantify the extent of such disturbance-related changes in northeast China. We assessed the diversity of bacterial communities in twelve samples of marsh soil collected from pristine marsh, neighboring cropland, and a wetland restoration area. High-throughput sequencing of a bacteria-specific genomic sequence, the internal transcribed spacer (16S rRNA) region, was used to identify bacterial taxa. We obtained 358,737 sequences that represented 2263 bacterial OTUs across the three types of sampling sites. Of these, 1411 OTUs occurred at all three site types, 99 were shared between cultivated land and pristine marshland, 322 were shared between cultivated land and wetland converted from cropland, and 126 were shared between pristine marshland and wetland converted from cropland. All sites also hosted unique fungal OTUs, with 218 OTUs exclusive to cultivated land, 52 exclusive to pristine marshland, and 35 exclusive to wetland converted from cropland. Sequences were affiliated to 36 different phyla throughout the dataset. Sequence abundance showed that members of the Proteobacteria were more frequently identified in all soil samples than Acidobacteria, and included members of Chloroflexi, Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Nitrospirae, Saccharibacteria, and Chlorobi, which represented an overwhelming proportion of the soil bacterial communities with an average relative abundance of > 1%, and another 25 phyla with an average relative abundance were <1%. The dominant phyla that showed the greatest variation among habitat types (> 1% of the average relative abundance) were Gemmatimonadetes (P < 0.01), Bacteroidetes (P < 0.01), Firmicutes (P < 0.01), and Chlorobi (P < 0.01). The soil bacterial community diversity decreased from a maximum in cultivated land, through the wetland restoration area, to a minimum in pristine marshland. Redundancy and correlation analyses demonstrated that chronic disturbance through cultivation, especially dry cultivation, significantly altered the bacterial community composition of marsh soil. The α-diversity of the soil bacterial community was most affected by soil moisture, soil pH, total carbon, soil organic carbon, soil dissolved organic carbon, available nitrogen, microbial biomass of carbon, and microbial biomass of nitrogen. Meanwhile, the soil bacterial community composition was significantly affected by soil moisture, soil pH, total carbon, soil organic carbon, and soil dissolved organic carbon. Overall, the results from our study showed that the state of soil carbon and nitrogen is affected by the disturbance by agricultural cultivation, causing long-term accumulated soil nutrients to become available as an energy source that can be rapidly mineralized by soil bacteria. In addition, our results also indicate that cultivation and natural restoration influenced the bacterial community structure and diversity. Natural restoration can significantly enhance the recovery of bacterial diversity; however, once the composition of the marshland bacterial community has been altered by cultivated disturbance, it might be difficult to restore to its original state. These findings highlight the importance of effectively managing the soil bacterial community to maintain a naturally functioning soil ecosystem. 参考文献 相似文献 引证文献

Heavy metal pollution poses a serious hazard to the soil bacterial community. In this study, the 16 s rRNA high-throughput sequencing technology was used to analyze bacterial diversity and structure of dry field soil at different levels of heavy metal pollution. Further, the relationships between soil parameters and bacterial community were analyzed. Based on the study findings, we classified the levels of heavy metal pollution in soil samples from the study area could be divided into four grades: high risk (HR), considerable risk (CR), moderate risk (MR) and low risk (LR). In this study, heavy metal concentrations and pH showed significant effect on bacterial community structure. The distribution of bacterial community richness and diversity was MR > LR > CR > HR. Bacterial communities such as Acidobacteria, Chloroflexi and Gemmatimonadetes were highly resistant to the lower pH (pH < 6.5) and the high levels of heavy metal pollution compared with other bacterial community, which were abundant in HR samples. However, Proteobacteria, Actinobacteria, Bacteroidetes and Latescibacteria were more abundant in alkaline soils (pH > 7.5). Further, available Cd, Pb and Zn concentrations were lower in alkaline soils than acidic soils, which reduced the impact of heavy metals on bacterial community diversity and structure.

Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&amp;amp;N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.

How do grassland management history and bacterial micro-localisation affect the response of bacterial community structure to changes in aboveground grazing regime?

Soil bacterial communities are a crucial biological indicator of soil health and crop performance; however, their response to climate change remains poorly understood. Wild blueberry farms are experiencing unprecedented temperature changes, which may exacerbate microbial responses and potentially harm the crop. Here, we aimed to elucidate the response of bacterial communities in wild blueberry fields to warming. We employed passive and active open-top chambers to simulate climate warming scenarios, which elevated atmospheric temperatures by 1.2 and 3.3°C, respectively. Soils in the active warming treatment exhibited significantly lower water content than in ambient conditions. Overall soil bacterial diversity and richness under the warming (passive and active) treatments and ambient controls did not demonstrate significant differences after 2 years of warming. However, we found significantly higher bacterial evenness and diversity under warming treatments in the early growing season (June). Our study found pronounced seasonal shifts in the evenness and diversity of bacteria in wild blueberry soils, suggesting that the variation in bacterial community structure may be more influenced by seasonal changes in temperature and plant activity than by warming treatments. Our study reveals the limited impact of warming on overall soil bacterial diversity in a temperate crop, but the seasonal dynamics of bacterial diversity and composition are sensitive to warming. The increased bacterial evenness and diversity under warming treatments in June could be attributed to advanced plant phenology, indicating a potential future shift in seasonal dynamics of bacterial activity under global warming.

Simple SummaryTropical forests play an important role in the global carbon cycle, especially in the context of global climate change. Soil microorganisms are essential to the functions, services, and productivity of terrestrial ecosystems as a link to maintain the connections and interactions between the aboveground and belowground ecosystems. The interactions between plants and the soil microbiome are crucial for plant growth, health, and resistance to stressors. However, information on the response of soil microbial communities to a chronosequence of woody plants is lacking, especially in tropical forests. This study compares the soil properties, diversity, composition, and co-occurrence patterns of bacterial communities in the rhizosphere and bulk soils along a teak plantation chronosequence. The results show that the composition and co-occurrence patterns of the bacterial communities are statistically different among the plantations, while stand age has no significant impact on soil bacterial alpha diversity. The results further show that soil nutrients play a key role in shaping the soil bacterial community. The study also provides information about the dynamics and characteristics of these soil bacterial communities and adds valuable information that may underpin new strategies for the management of teak plantations.Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.

One of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (P < 0.012), but they were not affected by texture (P > 0.553). Bacterial diversity increased at water potentials of <or=2.5 kPa in sand and <or=4.0 kPa in silt+clay, equivalent to <or=56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (P < 0.001) and was correlated with WFPS (sum of squared correlations [delta(2)] = 0.88, P < 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil.

Exploring the variations of soil bacterial communities can contribute to the sustainability of Chinese fir plantations (CFPs). As the living environments of soil bacteria, soil aggregates significantly affect the diversity and composition regarding soil bacterial communities in CFPs. However, the distribution characteristics exhibited by soil bacteria at the aggregate scale are still not clear. In the present research, the diversity and composition regarding soil bacterial communities (using high‐flux sequencing) in CFPs with diverse stand ages (3, 9, 17, and 26 years) were analyzed from the perspective of soil aggregates (&gt;2, 1–2, 0.25–1, &lt;0.25 mm) in Guangxi, China. According to the results, regardless of the aggregate size and the stand age, bacterial communities in soil were mainly composed of Proteobacteria, Chloroflexi, and Acidobacteria. During Chinese fir growth, the relative abundance (RA) of soil Proteobacteria first elevated and afterwards reduced, with the greatest level in the 17 years, while that of soil Chloroflexi exhibited an inverse trend. In addition, the RA of soil Acidobacteria increased over time. At the aggregate scale, the 17‐year‐old CFPs presented the greatest soil bacterial community diversity (based on the Chao 1 and Shannon indices). After 17 years, the destruction of coarse macroaggregates (&gt;2 mm) could induce the reduction of soil bacterial community diversity, as coarse macroaggregates, taking up the majority of bulk soil, offered suitable environments for soil bacteria to survive and thrive. Moreover, soil organic C and total N concentrations and soil pH also significantly affected the diversity and composition regarding soil bacterial communities over time. Hence, the conservation of coarse macroaggregates after 17 years of Chinese fir growth is important to sustain the soil health as well as the bacterial community diversity in Guangxi, China.

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

Crop replanting leads to soil degradation and soil productivity reduction, which is a challenge for sustainable agricultural development. We previously found that silicon fertilizers combined with additional microbial agents are an effective means to alleviate problems that occur in a variety of Chinese lily during replanting, but little is known about the changes in microbial structure during this process. In the present study, we applied four treatments: CK (control), SF (silicon fertilizer), MF (microbial agents), and SMF (combination of silicon fertilizer and microbial agents). We treated the soil constantly for three years and investigated the bacterial community structure and some specific microbial groups in the soil of the lily root zone using 16S rRNA high-throughput sequencing analysis. The results showed that silicon fertilizer and microbial agent treatment significantly improved the growth status of the plants and changed the diversity and structure of the bacterial community in the soil. The genus Pseudomonas significantly increased in the SF treatment, and the phylum Actinobacteria and the genera Nordella, Devosia, and Rhodoplanes significantly increased in the SMF treatment. The genera Nordella, Pedomicrobium, and Chthoniobacter correlated with the seedling index or available silicon content. In addition, the two genera Gaiella and Nocardioides were the key species linking the bacterial community in the soil. The soil physicochemical properties played an important role in restoring the soil bacterial community structures. In conclusion, silicon fertilizer and microbial agents changed the diversity and structure of the bacterial community. Under the fertilizer supplement model, the enrichment of the phylum Actinobacteria and the genus Pseudomonas played an important role in improving soil health and alleviating CRPs in lilies. In addition, organic matter, available phosphorus, available potassium, and available silicon were found to be the most important factors that have a great impact on the restoration of bacterial community structures.

Plants and soil bacteria exert a vital function in mediating soil ecosystem multifunctionality (EMF). Nevertheless, plant and soil bacteria interaction during forest secondary succession is poorly understood, and their roles in soil EMF remain largely unexplored. The dynamics of soil physicochemical properties and bacterial diversity was studied in southwest China during forest succession from coniferous to monsoon broadleaf evergreen. Interdomain ecological networks (IDEN) were adopted for investigating plant–bacteria associations. With the purpose of assessing how soil factors, bacterial community and plant diversity influenced soil EMF, the structural equation model (SEM) was used. It was discovered that both soil bacterial diversity and soil EMF gradually increased with the succession. IDEN analysis revealed that plant–bacteria ecological networks differed significantly across successional stages. Keystone plant species richness (KSR) increased with succession, which benefited soil bacteria diversity (path coefficient = 0.802, p &lt; 0.001) while having a direct negative impact on pH (path coefficient = −0.602, p &lt; 0.05) and C:N (path coefficient = −0.759, p &lt; 0.001). Soil pH and C:N ratio declines were observed during forest secondary succession and were found to be inversely related to soil EMF. Furthermore, soil pH was found to be inversely related to bacterial diversity. The SEM analysis explained 88.2% of the variation in soil multifunctionality. The findings suggested that keystone plant species played a key function in regulating the variations of soil bacterial community and EMF (total effect = 0.813). Our study clarified the critical functions of keystone species in driving soil bacterial diversity and multifunctionality during forest succession and provided a new perspective on the relationship between above‐ and below‐ground.

Impact of farmland mulching practices on the soil bacterial community structure in the semiarid area of the loess plateau in China

Microbes are key components of the soil environment, playing an important role in maintaining soil health, sustainability, and productivity. The composition and structure of soil bacterial communities were examined in winter wheat-rice (WR) and winter wheat-maize (WM) cropping systems derived from five locations in the Low-Middle Yangtze River plain and the Huang-Huai-Hai plain by pyrosequencing of the 16S ribosomal RNA gene amplicons. A total of 102,367 high quality sequences were used for multivariate statistical analysis and to test for correlation between community structure and environmental variables such as crop rotations, soil properties, and locations. The most abundant phyla across all soil samples were Proteobacteria, Acidobacteria, and Bacteroidetes. Similar patterns of bacterial diversity and community structure were observed within the same cropping systems, and a higher relative abundance of anaerobic bacteria was found in WR compared to WM cropping systems. Variance partitioning analysis revealed complex relationships between bacterial community and environmental variables. The effect of crop rotations was low but significant, and interactions among soil properties, locations, and crop rotations accounted for most of the explained variation in the structure of bacterial communities. Soil properties such as pH, available P, and available K showed higher correlations (positive or negative) with the majority of the abundant taxa. Bacterial diversity (the Shannon index) and richness (Chao1 and ACE) were higher under WR than WM cropping systems.