Differences in the soil bacterial community under organic farming and conventional farming modes revealed by 16S rDNA sequencing

To more efficiently identify the microbial community of the yak rumen, the standardization of DNA extraction is key to ensure fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rDNA sequencing to determine the optimal DNA extraction methods whose DNA products reflect complete bacterial communities. The results indicate that method 6 (hexadecyltrimethylammomium bromide-lysozyme-physical lysis by bead beating) is recommended for the DNA isolation of the rumen microbial community due to its high yield, operational taxonomic unit, bacterial diversity, and excellent cell-breaking capability. The results also indicate that the bead-beating step is necessary to effectively break down the cell walls of all of the microbes, especially Gram-positive bacteria. Another aim of this study was to preliminarily analyze the bacterial community via 16S rDNA sequencing. The microbial community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. A comparative analysis showed some variations in the microbial community between yaks and cattle that may be attributed to diet and environmental differences. Interestingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is required to determine the specific functional and ecological roles of these bacteria in yak rumen. In summary, the investigation of the optimal DNA extraction methods and the preliminary evaluation of the bacterial community composition of yak rumen support further identification of the specificity of the rumen microbial community in yak and the discovery of distinct gene resources.

Download Full-text

Quantitative improvement of 16S rDNA DGGE analysis for soil bacterial community using real-time PCR

Journal of Microbiological Methods ◽

10.1016/j.mimet.2009.06.001 ◽

2009 ◽

Vol 78 (2) ◽

pp. 216-222 ◽

Cited By ~ 15

Author(s):

Jae-Hyung Ahn ◽

Yoo-Jeong Kim ◽

Taesung Kim ◽

Hong-Gyu Song ◽

ChulHee Kang ◽

...

Keyword(s):

Bacterial Community ◽

Real Time ◽

16S Rdna ◽

Real Time Pcr ◽

Soil Bacterial Community ◽

Dgge Analysis ◽

Soil Bacterial

Download Full-text

Organic farming practices change the soil bacteria community, improving soil quality and maize crop yields

PeerJ ◽

10.7717/peerj.11985 ◽

2021 ◽

Vol 9 ◽

pp. e11985

Author(s):

Ademir Durrer ◽

Thiago Gumiere ◽

Maurício Rumenos Guidetti Zagatto ◽

Henrique Petry Feiler ◽

Antonio Marcos Miranda Silva ◽

...

Keyword(s):

Bacterial Community ◽

Organic Farming ◽

Soil Bacteria ◽

Crop Yields ◽

Bacterial Community Composition ◽

Chemical Properties ◽

Soil Bacterial Community ◽

Organic Management ◽

Organic Systems ◽

Soil Bacterial

Background The importance of organic farming has increased through the years to promote food security allied with minimal harm to the ecosystem. Besides the environmental benefits, a recurring problem associated with organic management is the unsatisfactory yield. A possible solution may rely on the soil microbiome, which presents a crucial role in the soil system. Here, we aimed to evaluate the soil bacterial community structure and composition under organic and conventional farming, considering the tropical climate and tropical soil. Methodology Our organic management treatments were composed by composted poultry manure and green manure with Bokashi. Both organic treatments were based on low nitrogen inputs. We evaluated the soil bacterial community composition by high-throughput sequencing of 16S rRNA genes, soil fertility, and soil enzyme activity in two organic farming systems, one conventional and the last transitional from conventional to organic. Results We observed that both organic systems evaluated in this study, have higher yield than the conventional treatment, even in a year with drought conditions. These yield results are highly correlated with changes in soil chemical properties and enzymatic activity. The attributes pH, Ca, P, alkaline phosphatase, and β- glucosidase activity are positively correlated with organic systems, while K and Al are correlated with conventional treatment. Also, our results show in the organic systems the changes in the soil bacteria community, being phyla Acidobacteria, Firmicutes, Nitrospirae, and Rokubacteria the most abundant. These phyla were correlated with soil biochemical changes in the organic systems, helping to increase crop yields. Conclusion Different organic management systems, (the so-called natural and organic management systems, which use distinct organic sources), shift the soil bacterial community composition, implying changes in their functionalities. Also, our results contributed to the identification of target bacterial groups and changes in soil chemical properties and enzymatic activity in a trophic organic farming system, which may contribute to higher crop yields.

Download Full-text

Variations in bacterial community structure during a dinoflagellate bloom analyzed by DGGE and 16S rDNA sequencing

Aquatic Microbial Ecology ◽

10.3354/ame023119 ◽

2001 ◽

Vol 23 ◽

pp. 119-130 ◽

Cited By ~ 156

Author(s):

LB Fandino ◽

L Riemann ◽

GF Steward ◽

RA Long ◽

F Azam

Keyword(s):

Community Structure ◽

Bacterial Community ◽

16S Rdna ◽

Bacterial Community Structure ◽

16S Rdna Sequencing ◽

Rdna Sequencing ◽

Dinoflagellate Bloom

Download Full-text

Differences in Soil Bacterial Community Compositions in Paddy Fields under Organic and Conventional Farming Conditions

Microbes and Environments ◽

10.1264/jsme2.me18101 ◽

2019 ◽

Vol 34 (1) ◽

pp. 108-111

Author(s):

Kazuki Suzuki ◽

Manami Takemura ◽

Takaaki Miki ◽

Masanori Nonaka ◽

Naoki Harada

Keyword(s):

Bacterial Community ◽

Soil Bacterial Community ◽

Paddy Fields ◽

Conventional Farming ◽

Soil Bacterial ◽

Organic And Conventional Farming

Download Full-text

Analysis of the bacterial community and diversity in tea plantation soil via 16S rDNA sequencing

Acta Ecologica Sinica ◽

10.5846/stxb201808141733 ◽

2019 ◽

Vol 39 (22) ◽

Author(s):

杨广容 YANG Guangrong ◽

马燕 MA Yan ◽

蒋宾 JIANG Bin ◽

马会杰 MA Huijie ◽

谢瑾 XIE Jin ◽

...

Keyword(s):

Bacterial Community ◽

16S Rdna ◽

16S Rdna Sequencing ◽

Tea Plantation ◽

Rdna Sequencing

Download Full-text

Differences in the soil bacterial community under organic farming and conventional farming modes revealed by 16S rDNA sequencing

10.21203/rs.3.rs-21660/v1 ◽

2020 ◽

Author(s):

Yazhen Yang ◽

Mingke Fang ◽

Meiyan Wu ◽

Huaisheng Zhang ◽

Huizhen Li ◽

...

Keyword(s):

Soil Sample ◽

Bacterial Diversity ◽

Organic Farming ◽

Bacterial Communities ◽

Strong Positive Correlation ◽

Conventional Farming ◽

Available Nitrogen ◽

Linear Discriminant ◽

Rdna Sequencing ◽

Soil Bacterial

Abstract Background The bacterial communities is complex and different in various agricultural ecosystem. In this study, high-throughput Illumina MiSeq sequencing was conducted to assess the differences in soil bacterial communities between organic farming and conventional farming modes. Results A total of 3, 919 operational taxonomic units were identified and classified as 26 phyla, 42 classes, 78 orders, 120 families, 281 genera. The dominant genera were Lysobacter , Pseudomonas , Massilia , Pseudarthrobacter , Ferruginibacter , Flavobacterium , Flavisolibacter , Brevundimonas , Haliangium and Sphingomonas . Analysis of soil bacterial diversity showed that the soil under the organic farming had a greater bacterial diversity than that under the conventional farming. Linear discriminant analysis effect size analysis showed that the major bacterial groups identified in the soil sample CK1 (2015.4) and CK6 (2017.10) under conventional farming mode were largely different from those in the soil sample O6 (2017.10) under organic farming mode. Redundancy analysis demonstrated that available nitrogen was the most important factor regulating bacterial composition under the organic farming mode, followed by soil rapidly available phosphorous and potassium. Massilia , Pseudomonas , Lysobacter and Pseudarthrobacter abundances showed a strong positive correlation with the content of available nitrogen. Conclusions Organic farming could improve soil organic matter, available nitrogen, rapidly available phosphorus and retard soil acidification. This modification of soil can directly or indirectly relate to the bacterial communities in soil. The shifts of bacterial communities were complicated and dynamic with respect to all sorts of the measures of cultivation and management under organic farming mode.

Download Full-text

Soil bacterial community as impacted by addition of rice straw and biochar

Scientific Reports ◽

10.1038/s41598-021-99001-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhiqiang Tang ◽

Liying Zhang ◽

Na He ◽

Diankai Gong ◽

Hong Gao ◽

...

Keyword(s):

Bacterial Community ◽

Rice Straw ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Soil Bacterial Community ◽

Rice Soil ◽

Uncultured Bacterium ◽

Rice Growth ◽

Rdna Sequencing ◽

Soil Bacterial

AbstractThe application of straw and biochar can effectively improve soil quality, but whether such application impacts paddy soil bacterial community development remains to be clarified. Herein, the impacts of three different field amendment strategies were assessed including control (CK) treatment, rice straw (RS) application (9000 kg ha−1), and biochar (BC) application (3150 kg ha−1). Soil samples were collected at five different stages of rice growth, and the bacterial communities therein were characterized via high-throughput 16S rDNA sequencing. The results of these analyses revealed that soil bacterial communities were dominated by three microbial groups (Chloroflexi, Proteobacteria and Acidobacteria). Compared with the CK samples, Chloroflexi, Actinobacteria, Nitrospirae and Gemmatimonadetes levels were dominated phyla in the RS treatment, and Acidobacteria, Actinobacteria, Nitrospirae and Patescibacteria were dominated phyla in the BC treatment. Compared with the RS samples, Chloroflexi, Acidobacteria, Actinobacteria, and Verrucomicrobia levels were increased, however, Proteobacteria, Gemmatimonadetes, Nitrospirae, and Firmicute levels were decreased in the BC samples. Rhizosphere soil bacterial diversity rose significantly following RS and BC amendment, and principal component analyses confirmed that there were significant differences in soil bacterial community composition among treatment groups when comparing all stages of rice growth other than the ripening stage. Relative to the CK treatment, Gemmatimonadaceae, Sphingomonadaceae, Thiovulaceae, Burkholderiaceae, and Clostridiaceae-1 families were dominant following the RS application, while Thiovulaceae and uncultured-bacterium-o-C0119 were dominant following the BC application. These findings suggest that RS and BC application can improve microbial diversity and richness in paddy rice soil in Northeast China.

Download Full-text

Metabolite fingerprinting of novel Streptomyces UK-238 from the Himalayan forest

Current Pharmaceutical Analysis ◽

10.2174/1573412916666200206160836 ◽

2020 ◽

Vol 16 ◽

Author(s):

Nidhi Srivastava ◽

Indira P. Sarethy

Keyword(s):

Ethyl Acetate ◽

16S Rdna ◽

Retention Index ◽

Ethyl Acetate Extract ◽

Similarity Index ◽

Antimicrobial Drug ◽

16S Rdna Sequencing ◽

Metabolite Fingerprinting ◽

Streptomyces Sp ◽

Rdna Sequencing

Aims: Characterization of antimicrobial metabolites of novel Streptomyces sp. UK-238. Background: Novel antimicrobial drug discovery is urgently needed due to emerging multi antimicrobial drug resistance among pathogens. Since many years, natural products have provided the basic skeletons for many therapeutic compounds including antibiotics. Bioprospection of un/under explored habitats and focussing on selective isolation of actinobacteria as major reservoir of bio and chemodiversity has yielded good results. Objective: The main objectives of the study were the identification of UK-238 by 16S rDNA sequencing and antimicrobial metabolite fingerprinting of culture extracts. Method: In the present study, a promising isolate, UK-238, has been screened for antimicrobial activity and metabolite fingerprinting from the Himalayan Thano Reserve forest. It was identified by 16S rDNA sequencing. Ethyl acetate extract was partially purified by column chromatography. The pooled active fractions were fingerprinted by GC-MS and compounds were tentatively identified by collated data analysis based on Similarity Index, observed Retention Index from Databases and calculated Retention Index. Results: UK-238 was identified as Streptomyces sp. with 98.4% similarity to S. niveiscabiei. It exhibited broad-spectrum antibacterial and antifungal activity. GC-MS analysis of active fractions of ethyl acetate extract showed the presence of eighteen novel antimicrobial compounds belonging to four major categories- alcohols, alkaloid, esters and peptide. Conclusion: The study confirms that bioprospection of underexplored habitats can elaborate novel bio and chemodiversity.

Download Full-text