Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning

Kraková, Lucia; Šoltýs, Katarína; Budiš, Jaroslav; Grivalský, Tomáš; Ďuriš, František; Pangallo, Domenico; Szemes, Tomáš

doi:10.1007/s00792-016-0855-5

Cited by 18 publications

(5 citation statements)

References 53 publications

(54 reference statements)

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“…In addition, it can only detect the most abundant (‘the top one thousand’) members of the microbial community. Nevertheless, DGGE is still used in many studies because it directly and rapidly compares the composition and diversity of the dominant soil microorganisms between treatments (van Elsas & Boersma, ; Cabezas et al, ; Krakova et al, ). When they are employed together, Biolog EcoPlates and PCR‐DGGE can more effectively elucidate soil microbial community profiles than either one alone.…”

Section: Discussionmentioning

confidence: 99%

Economic and Soil Environmental Benefits of Using Controlled‐Release Bulk Blending Urea in the North China Plain

Zhou

Shen

et al. 2017

Land Degrad Dev

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Crop production must be increased in order to ensure a sustainable food supply for the growing world population. Controlled‐release urea (CRU) improves nutrient use efficiency and saves labor, but its use in crop production is limited due to its high cost. Bulk blending urea (BBU) consists of both CRU and conventional urea and could be an excellent substitute or replacement for CRU. Nevertheless, its economic benefits and soil environment impact are unknown. A 3‐year field experiment was conducted to investigate the effects of two different nitrogen management practices in terms of economic benefits, soil mineral nitrogen availability, aggregate stability, and soil microbial communities. Split applications of conventional urea (UREA) and a single application of BBU were tested on winter wheat (Triticum aestivum L.) and summer maize (Zea mays L.) in the North China Plain between 2010 and 2013. Crop yields were measured after each harvest, and soil environmental parameters were determined after the 3‐year crop sequence. Relative to UREA, BBU significantly increased net revenue, soil inorganic nitrogen concentration, and the functional diversity of the soil microbial community without adverse effects on the soil bacterial community composition. On the other hand, BBU reduced the amount of soil macro‐aggregates and the mean weight diameter value of soil water‐stable aggregates. Although BBU showed great potential for improving wheat–maize cropping systems in the North China Plain, future studies should focus on optimizing the nitrogen dosage and the CRU ratio in BBU to decrease nitrogen leaching, avoid soil aggregate deterioration, and maintain crop yield. Copyright © 2017 John Wiley & Sons, Ltd.

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Section: Discussionmentioning

confidence: 99%

Economic and Soil Environmental Benefits of Using Controlled‐Release Bulk Blending Urea in the North China Plain

Zhou

Shen

et al. 2017

Land Degrad Dev

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“…Advanced molecular methods such as quantitative real-time PCR (qPCR) and massively parallel sequencing of fragments of universal marker genes, such as 16S rRNA, are revealing the structures of microbial communities from complex environments (19,20). These techniques have also been successfully used to study functional groups of microorganisms, such as methanogens, by targeting a gene or transcript related to their function (21)(22)(23). Three different physiological groups of methanogens are known (hydrogenotrophic, aceticlastic, and methylotrophic) and have the gene encoding the alpha subunit of methyl coenzyme A reductase (mcrA), which catalyzes the last step of methanogenesis (24).…”

Section: Importancementioning

confidence: 99%

Targeting Bacteria and Methanogens To Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure

Habtewold

Sokolov

VanderZaag

et al. 2018

Appl Environ Microbiol

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Microbial communities in residual slurry left after removal of stored liquid dairy manure have been presumed to increase methane emission during new storage, but these microbes have not been studied. While actual manure storage tanks are filled gradually, pilot- and farm-scale studies on methane emissions from such systems often use a batch approach. In this study, six pilot-scale outdoor storage tanks with (10% and 20%) and without residual slurry were filled (gradually or in batch) with fresh dairy manure, and methane and methanogenic and bacterial communities were studied during 120 days of storage. Regardless of filling type, increased residual slurry levels resulted in higher abundance of methanogens and bacteria after 65 days of storage. However, stronger correlation between methanogen abundance and methane flux was observed in gradually filled tanks. Despite some variations in the diversity of methanogens or bacteria with the presence of residual slurry, core phylotypes were not impacted. In all samples, the phylum Firmicutes predominated (∼57 to 70%) bacteria: >90% were members of Clostridia . Methanocorpusculum dominated (∼57 to 88%) archaeal phylotypes, while Methanosarcina gradually increased with storage time. During peak flux of methane, Methanosarcina was the major player in methane production. The results suggest that increased levels of residual slurry have little impact on the dominant methanogenic or bacterial phylotypes, but large population sizes of these organisms may result in increased methane flux during the initial phases of storage. IMPORTANCE Methane is the major greenhouse gas emitted from stored liquid dairy manure. Residual slurry left after removal of stored manure from tanks has been implicated in increasing methane emissions in new storages, and well-adapted microbial communities in it are the drivers of the increase. Linking methane flux to the abundance, diversity, and activity of microbial communities in stored slurries with different levels of residual slurry can help to improve the mitigation strategy. Mesoscale and lab-scale studies conducted so far on methane flux from manure storage systems used batch-filled tanks, while the actual condition in many farms involves gradual filling. Hence, this study provides important information toward determining levels of residual slurry that result in significant reduction of well-adapted microbial communities prior to storage, thereby reducing methane emissions from manure storage tanks filled under farm conditions.

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“…The coverage rates in this sequencing are all above 0.98, indicating that the amount of sequencing this time is reasonable. The sequencing results meet the needs of sample analysis, and can fully reflect the characteristics of the microorganisms in the sample [25].…”

Section: Microbial Community Diversity Analysismentioning

confidence: 90%

Simultaneous Removal of Trivalent Arsenic and Nitrate Using Microbial Fuel Cells

et al. 2021

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A rectangular double chamber with trivalent arsenic as the electron donor of the biological anode was constructed by microbial fuel cells (MFC), and the feasibility of the MFC simultaneous degradation of trivalent arsenic and nitrate was studied. Experimental results show that the co-matrix-coupled MFC reactor oxidizes trivalent arsenic in an anode chamber and degrades nitrate in the cathode chamber. The removal rate of trivalent arsenic is about 63.35%, and the degradation rate of nitrate is about 55.95% during the complete and stable operation period. MFC can continuously output electric energy, and the maximum output voltage is 388 mV. We compared and analyzed the main functional microflora of biofilm microorganisms in an anode chamber. In the long-term arsenic-polluted environment, the activity of Acinetobacter, Pseudomonas bacteria with arsenic resistance, was improved. It is inferred that a fraction of trivalent arsenic was oxidized to pentavalent arsenic by electrode-attached microorganisms. While remaining trivalent, arsenic was taken up by the suspended bacterial biomass and converted into stable arsenide. The results of this study have theoretical reference value for the expansion of the MFC application scope.

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Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning

Cited by 18 publications

References 53 publications

Economic and Soil Environmental Benefits of Using Controlled‐Release Bulk Blending Urea in the North China Plain

Economic and Soil Environmental Benefits of Using Controlled‐Release Bulk Blending Urea in the North China Plain

Targeting Bacteria and Methanogens To Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure

Simultaneous Removal of Trivalent Arsenic and Nitrate Using Microbial Fuel Cells

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