scholarly journals Intertillage during Natural Farming Rice Paddy Production Negatively Impacted the Microbial Abundances in Soils but Not Diversities

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Jin-Feng Lin ◽  
Eva-Maria Minarsch ◽  
Munehide Ishiguro ◽  
Yoshitaka Uchida
Keyword(s):  
Bacterial Community ◽  
Soil Microbial Communities ◽  
Soil Surface ◽  
Rice Paddy ◽  
Diversity Indices ◽  
Vegetative Stage ◽  
Rice Paddies ◽  
Community Structures ◽  
Natural Farming ◽  
Soil Bacterial

In natural farming rice paddies, intertillage (tillage between rows, during rice growth period) is often performed mainly to remove weeds without the use of chemicals. Also, the intertillage disturbs soil surfaces, potentially impacting the characteristics of soil microbial communities, such as their diversity and abundance. Natural farming systems aim to maintain biodiversity, but it remains unclear whether the intertillage impacts soil microbes in rice paddies. Thus, this study aimed to understand to what extent “five times intertillage” treatment (5T) influences soil bacterial abundance and community structures compared with no tillage (NT), under a natural farming rice paddy system. Soils were sampled at rice proximity, soil surface, and 10 cm depth in a natural farming rice paddy, during the early to late vegetative phase (June to July), in Hokkaido, Japan. The 16S rRNA community structures and abundance were analyzed by next generation sequencing (NGS) and quantitative PCR, respectively. We observed that NT had significantly higher bacterial abundances at the soil surface than 5T. However, there were no clear differences between 5T and NT, regarding the bacterial community structures, including their diversity indices. Instead, the sampling timings markedly impacted the bacterial community structures for the rice proximity and soil surface, showing increasing diversity indices at the late vegetative stage, compared to the early vegetative stage, suggesting the interaction between the crop growth and bacterial communities. In this study, we did not observe the significant difference between the rice yield from NT (2.3 ± 0.7 t·ha−1) and 5T plots (2.7 ± 0.9 t·ha−1); however, the 5T might have negatively impacted soil bacterial abundances but not the community structure of the bacteria.

scholarly journals Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices

2006 ◽  
Vol 72 (12) ◽  
pp. 7804-7812 ◽  
Author(s):  
Martin Hartmann ◽  
Franco Widmer
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Rflp Analysis ◽  
Diversity Indices ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Soil Microbial ◽  
Soil Bacterial

ABSTRACT 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.

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 Effects of novel bioorganic fertilizer application on soil enzymes and bacterial community in multi-site rice paddies in China

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zuren Li ◽  
Jincai Han ◽  
Haodong Bai ◽  
Di Peng ◽  
Lifeng Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Field Experiments ◽  
Chemical Properties ◽  
Soil Bacterial Community ◽  
General Function ◽  
Rice Paddies ◽  
Phylogenetic Groups ◽  
Total N ◽  
Bioorganic Fertilizer ◽  
Soil Bacterial

AbstractApplication of a novel bioorganic fertilizer (BIO) has been effectively used to inhibit weeds in rice paddies. To identify changes in soil bacterial community and enzymes in response to BIO treatments, field experiments were carried out in five major rice-growing areas in China. The dominant phylogenetic groups recorded included Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Acidobacteria. Anaeromyxobacter, Bacteroides, Bifidobacterium, Escherichia- Shigella, Geobacter and Haliangium were significantly different between BIO-treatment and untreated control and aided in general function (R), amino acid transport, metabolism (E) and transcription (K) clusters. The soil chemical properties and enzyme activities were less affected by BIO at these study sites. RDA analysis showed that soil bacterial community had a significant positive correlations among northern latitude, eastern longitude, exchangeable K, total K, total P, soil pH, and total N, except for organic matter, hydrolytic N and extractable P. Overall, our work showed that application of BIO does not alter the main community structure and functional diversity of soil bacteria in rice paddies and should be encouraged for use as a sustainable weed management strategy.

Soil bacterial community structures across biomes in artificial ecosystems

2020 ◽  
Vol 158 ◽  
pp. 106067
Author(s):  
Yerang Yang ◽  
Seung-Hoon Lee ◽  
Inyoung Jang ◽  
Hojeong Kang
Keyword(s):  
Bacterial Community ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Artificial Ecosystems ◽  
Soil Bacterial

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 Conservation tillage regulates soil bacterial community assemblies, network structures and ecological functions in black soils

2021 ◽  
Author(s):  
Zhuxiu Liu ◽  
Haidong Gu ◽  
Aizhen Liang ◽  
Lujun Li ◽  
Qin Yao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Soil Carbon ◽  
High Throughput Sequencing ◽  
Conservation Tillage ◽  
Conventional Tillage ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Tillage Practices ◽  
Degrading Bacteria ◽  
Soil Bacterial

Abstract Aims Conventional tillage is a serious threat to the stability of soil ecosystems. Understanding the response mechanisms of soil microbial community assemblies to anthropogenic activities is a major topic of ecological research. Methods Here, we investigated the bacterial community structures and assemblies in bulk and rhizosphere soils of soybeans grown with conventional tillage (moldboard plow, MP) and with conservation tillage that involved no-tillage (NT) or ridge tillage (RT) using high-throughput sequencing methods. Results We found that soil bacterial community compositions, structures and assembly processes were primarily altered by tillage practices. Briefly, in comparison to MP, NT and RT increased the relative abundances of the nitrogen-fixing bacteria Mesorhizobium sp., Bradyrhizobium sp. and Burkholderia sp., but decreased the abundance of soil carbon-degrading bacteria, especially Blastococcus sp., Streptomyces sp. and Sphingomonas sp. In addition, in comparison to MP, NT and RT resulted in more stable bacterial networks and more lower the relative contribution of homogenizing dispersal. Soil pH was the primary soil factor regulating both the bacterial community structures and assembly processes under the three tillage practices. Conclusions The altered functional bacteria under conservation tillage was mostly affiliated with biomarkers and keystone taxa, inferring that conservation tillage might contribute to biological nitrogen fixation and soil carbon sequestration.

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 The effects of exotic weed Flaveria bidentis with different invasion stages on soil bacterial community structures

2015 ◽  
Vol 14 (35) ◽  
pp. 2636-2643 ◽  
Author(s):  
Huangfu Chaohe ◽  
Li Huiyan ◽  
Chen Xinwei ◽  
Liu Hongmei ◽  
Yang Dianlin
Keyword(s):  
Bacterial Community ◽  
Soil Bacterial Community ◽  
Community Structures ◽  
Soil Bacterial ◽  
Flaveria Bidentis
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