scholarly journals Linkages of Soil Nutrients and Diazotrophic Microbiome under Sugarcane-Legume Intercropping

2018 ◽  
Author(s):  
Manoj Kumar Solanki ◽  
Chang-Ning Li ◽  
Fei-Yong Wang ◽  
Zhen Wang ◽  
Tao-Ju Lan ◽  
...  
Keyword(s):  
Soil Fertility ◽  
Soil Properties ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Nifh Gene ◽  
Cultivation Systems ◽  
Operational Taxonomic Units ◽  
Land Use Efficiency ◽  
Alpha Proteobacteria ◽  
The Impact

Intercropping significantly improves land use efficiency and soil fertility. This study examines the impact of three cultivation systems (monoculture sugarcane, peanut-sugarcane and soybean-sugarcane intercropping) on soil properties and diazotrophs. Sugarcane rhizosphere soil was sampled from the farmers’ field. Soil properties and nifH gene abundance were analyzed by high throughput sequencing. Moreover, a total of 436,458 nifH gene sequences were obtained and classified into the 3201 unique operational taxonomic units (OTUs). Maximum unique OTUs resulted with soybean-sugarcane intercropping (<375). The dominant groups across all cultivation were Alpha-proteobacteria and Beta-proteobacteria. On the basis of microbial community structure, intercropping systems were more diverse than monoculture sugarcane. In the genus level, Bradyrhizobium, Burkholderia, Pelomonas, and Sphingomonas were predominant in the intercropping systems. Moreover, diazotrophic bacterial communities of these cultivation systems were positively correlated to the soil pH and soil enzyme protease. Moreover, low available P recovered from intercropping system showed a strong correlation with higher nutrient uptake activity of soil microbes. Based on the results, our investigation concluded that intercropping system caused a positive effect on the growth of diazotrophic bacterial communities and it might boost the soil fertility and this kind of study helps to develop an eco-friendly technology for sustainable sugarcane production.

scholarly journals Next-generation sequencing showing potential leachate influence on bacterial communities around a landfill in China

2018 ◽  
Vol 64 (8) ◽  
pp. 537-549 ◽  
Author(s):  
Adharsh Rajasekar ◽  
Raju Sekar ◽  
Eduardo Medina-Roldán ◽  
Jonathan Bridge ◽  
Charles K.S. Moy ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Urban Site ◽  
Bacterial Consortia ◽  
Ecological Site ◽  
Operational Taxonomic Units ◽  
Specific Effects ◽  
The Impact ◽  
Urban Sites

The impact of contaminated leachate on groundwater from landfills is well known, but the specific effects on bacterial consortia are less well-studied. Bacterial communities in a landfill and an urban site located in Suzhou, China, were studied using Illumina high-throughput sequencing. A total of 153 944 good-quality reads were produced and sequences assigned to 6388 operational taxonomic units. Bacterial consortia consisted of up to 16 phyla, including Proteobacteria (31.9%–94.9% at landfill, 25.1%–43.3% at urban sites), Actinobacteria (0%–28.7% at landfill, 9.9%–34.3% at urban sites), Bacteroidetes (1.4%–25.6% at landfill, 5.6%–7.8% at urban sites), Chloroflexi (0.4%–26.5% at urban sites only), and unclassified bacteria. Pseudomonas was the dominant (67%–93%) genus in landfill leachate. Arsenic concentrations in landfill raw leachate (RL) (1.11 × 103 μg/L) and fresh leachate (FL2) (1.78 × 103 μg/L) and mercury concentrations in RL (10.9 μg/L) and FL2 (7.37 μg/L) exceeded Chinese State Environmental Protection Administration standards for leachate in landfills. The Shannon diversity index and Chao1 richness estimate showed RL and FL2 lacked richness and diversity when compared with other samples. This is consistent with stresses imposed by elevated arsenic and mercury and has implications for ecological site remediation by bioremediation or natural attenuation.

scholarly journals New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

2021 ◽  
Vol 9 (3) ◽  
pp. 659
Author(s):  
Elias Asimakis ◽  
Panagiota Stathopoulou ◽  
Apostolis Sapounas ◽  
Kanjana Khaeso ◽  
Costas Batargias ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mutual Exclusion ◽  
Bacterial Composition ◽  
Operational Taxonomic Units ◽  
Host Diet ◽  
Dominant Bacteria ◽  
High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

scholarly journals Effect of Organic Amendment Addition on Soil Properties, Greenhouse Gas Emissions and Grape Yield in Semi-Arid Vineyard Agroecosystems

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1477
Author(s):  
Antonio Marín-Martínez ◽  
Alberto Sanz-Cobeña ◽  
Mª Angeles Bustamante ◽  
Enrique Agulló ◽  
Concepción Paredes
Keyword(s):  
Soil Fertility ◽  
Soil Properties ◽  
Greenhouse Gas ◽  
Co2 Emissions ◽  
Organic Amendments ◽  
Organic N ◽  
N2o Emissions ◽  
The Impact ◽  
Semi Arid ◽  
Grape Yield

In semi-arid vineyard agroecosystems, highly vulnerable in the context of climate change, the soil organic matter (OM) content is crucial to the improvement of soil fertility and grape productivity. The impact of OM, from compost and animal manure, on soil properties (e.g., pH, oxidisable organic C, organic N, NH4+-N and NO3−-N), grape yield and direct greenhouse gas (GHG) emission in vineyards was assessed. For this purpose, two wine grape varieties were chosen and managed differently: with a rain-fed non-trellising vineyard of Monastrell, a drip-irrigated trellising vineyard of Monastrell and a drip-irrigated trellising vineyard of Cabernet Sauvignon. The studied fertiliser treatments were without organic amendments (C), sheep/goat manure (SGM) and distillery organic waste compost (DC). The SGM and DC treatments were applied at a rate of 4600 kg ha−1 (fresh weight, FW) and 5000 kg ha−1 FW, respectively. The use of organic amendments improved soil fertility and grape yield, especially in the drip-irrigated trellising vineyards. Increased CO2 emissions were coincident with higher grape yields and manure application (maximum CO2 emissions = 1518 mg C-CO2 m−2 d−1). In contrast, N2O emissions, mainly produced through nitrification, were decreased in the plots showing higher grape production (minimum N2O emissions = −0.090 mg N2O-N m−2 d−1). In all plots, the CH4 fluxes were negative during most of the experiment (−1.073−0.403 mg CH4-C m−2 d−1), indicating that these ecosystems can represent a significant sink for atmospheric CH4. According to our results, the optimal vineyard management, considering soil properties, yield and GHG mitigation together, was the use of compost in a drip-irrigated trellising vineyard with the grape variety Monastrell.

scholarly journals Antibiotic resistance in bacterial communities of the oyster Crassostrea rivularis from different salinity zones in Qinzhou Bay, Beibu Gulf, China

Elem Sci Anth ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ruixuan Wang ◽  
Bing Li ◽  
Li Zhang ◽  
Yuee Hou ◽  
Huajian Lin ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Resistant Bacteria ◽  
Beibu Gulf ◽  
Potential Health ◽  
Antibiotic Resistant ◽  
Low Salinity ◽  
Operational Taxonomic Units ◽  
Qinzhou Bay ◽  
The Impact ◽  
Rdna Analysis

The oyster is one of the most abundantly harvested shellfish in the world. To explore the impact of salinity on antibiotic-resistant bacteria (ARB) and the microbial community associated with farmed oysters, oysters were taken from high-, medium-, and low-salinity zones (labeled HS, MS, and LS, respectively) in Qinzhou Bay of Beibu Gulf, China. ARB were tested with the Kirby–Bauer method. Species of ARB were confirmed by 16 S rDNA analysis. Microbial communities were analyzed by high-throughput sequencing technology. The results indicate that HS-derived ARB (>60%) resisted β-lactams and aminoglycosides and that LS-derived strains resisted macrolide and tetracyclines. All strains resisted 4 or more antibiotics. A total of 542 operational taxonomic units were detected in the samples, with Shewanella, Vibrio, and Endozoicomonas being the dominant genera (>80%), although distributed differently among the different salinity samples. The oyster microbial richness ranked as MS > LS > HS. This study provides an important reference for future efforts to explain factors or mechanisms underlying correlations between ARB, the microbiome, and salinity and thus the potential health of oysters in this region.

Crop yield and soil fertility as affected by papermill biosolids and liming by-products

2013 ◽  
Vol 93 (3) ◽  
pp. 319-328 ◽  
Author(s):  
Noura Ziadi ◽  
Bernard Gagnon ◽  
Judith Nyiraneza
Keyword(s):  
Soil Fertility ◽  
Soil Properties ◽  
Crop Yield ◽  
Water Soluble ◽  
Strong Increase ◽  
Paper Mills ◽  
Dry Bean ◽  
Organic C ◽  
The Impact ◽  
By Products

Ziadi, N., Gagnon, B. and Nyiraneza, J. 2013. Crop yield and soil fertility as affected by papermill biosolids and liming by-products. Can. J. Soil Sci. 93: 319–328. Papermill biosolids (PB) in combination with alkaline industrial residuals could benefit agricultural soils while diverting these biosolids from landfill. A greenhouse study was conducted to evaluate the effect of three types of PB at rates of 0, 30, and 60 wet Mg ha−1, as well as five liming by-products at 3 wet Mg ha−1 along with 30 Mg PB ha−1 on crop yield, nutrient accumulation, and soil properties. De-inking paper biosolids (DB, C/N of 65) were applied to soybean [Glycine max (L.) Merr.], and two combined PB (PB1, C/N of 31; and PB2, C/N of 14) were applied to dry bean (Phaseolus vulgaris L.) and barley (Hordeum vulgare L.), respectively. The liming by-products included lime mud (LM), wood ash (WA) from paper mills, commercial calcitic lime (CL), Mg dissolution by-product (MgD), and Mg smelting and electrolysis work (MgSE). Compared with the control, PB2 increased barley yield and total Mg and Na accumulation, and both PB increased plant N, P, and Ca accumulation in barley and dry bean. The impact of DB on soybean was limited. The addition of liming by-products to PB or DB did not affect crop attributes except the combination with MgSE, which severely reduced the growth of dry bean and, to a lesser extent, soybean. Soil NO3-N was immobilized following DB application, whereas there was a net release with both PB. Combining PB and liming by-products produced the greatest changes in soil properties at harvest. Generally, LM and CL raised pH and Mehlich-3 Ca, and MgSE caused a strong increase in Mehlich-3 Mg and Na and water-soluble Cl. When used with appropriate crops, biosolids from paper mills and alkaline residuals other than MgSE can efficiently enhance soil fertility by providing organic C and macronutrients for balanced crop fertilization.

scholarly journals Impact of Virioplankton on Archaeal and Bacterial Community Richness as Assessed in Seawater Batch Cultures

2004 ◽  
Vol 70 (2) ◽  
pp. 804-813 ◽  
Author(s):  
Christian Winter ◽  
Arjan Smit ◽  
Gerhard J. Herndl ◽  
Markus G. Weinbauer
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Tropical Atlantic ◽  
Viral Lysis ◽  
Batch Cultures ◽  
Operational Taxonomic Units ◽  
The Impact

ABSTRACT During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.

scholarly journals Comparison of the diversity of cultured and total bacterial communities in marine sediment using culture-dependent and sequencing methods

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10060
Author(s):  
Meng Wang ◽  
Samina Noor ◽  
Ran Huan ◽  
Congling Liu ◽  
JiaYi Li ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Culture Collection ◽  
Medium Composition ◽  
Microbial Culture ◽  
Bacterial Strains ◽  
Marine Microbes ◽  
Natural Systems ◽  
Operational Taxonomic Units ◽  
The Impact ◽  
Culture Dependent

Despite recent great advances in microbial culture, most microbes have not yet been cultured, and the impact of medium composition on the isolation of microbes from natural systems has not been elucidated. To optimize media for culturing marine microbes, microbial communities in three sediment samples were described using high-throughput sequencing (HTS) and culture-dependent techniques. HTS revealed communities dominated by Gammaproteobacteria, and culture-based methods revealed communities dominated by Actinobacteria. Among the total operational taxonomic units (OTUs) from the HTS dataset, 6% were recovered in the culture collection. Four potentially novel bacterial strains belonging to Oceaniovalibus, Psychrobacter and Salegentibacter were isolated. The combination of media cultured more taxa than any single medium. Nutrient-rich and single-carbon/nitrogen-source media supported the growth of relatively few taxa, and the quality of nitrogen strongly influenced the types of bacteria isolated.

scholarly journals Zai Technology and Integrated Nutrient Management for Improved Soil Fertility and Increased Sorghum Yields in Kitui County, Kenya

2021 ◽  
Vol 5 ◽  
Author(s):  
Mercy Cheruto Kebenei ◽  
Monicah Mucheru-Muna ◽  
Felista Muriu-Ng'ang'a ◽  
Charles Kimani Ndung'u
Keyword(s):  
Electrical Conductivity ◽  
Soil Moisture ◽  
Soil Fertility ◽  
Soil Properties ◽  
Crop Yield ◽  
Total Nitrogen ◽  
Cattle Manure ◽  
Sub Saharan Africa ◽  
Cropping Seasons ◽  
The Impact

Deteriorating soil fertility, low unreliable rainfall and soil moisture stress has resulted to low crop yields among farmers of sub-Saharan Africa (SSA), necessitating a search for more sustainable production practices. Zai technology has the ability to promote soil moisture retention and enhances soil fertility. A four-seasons field experiment was conducted to assess the impact of Zai technology combined with cattle manure and inorganic fertilizer on selected soil properties and sorghum yields in Kabati, Kitui County. The experiment was set up in a Randomized Complete Block Design (RCBD) with eight treatments replicated thrice with sorghum Gadam as the test crop. Soil sampling was done at the beginning of the first season and at the end of the fourth season at a dept of 0–15 cm across each plot for laboratory analyses. From the results, the increase in electrical conductivity was significant at p < 0.05 in all the treatments after four cropping seasons. Total organic carbon significantly increased in Zai with cattle manure (p = 0.045), conventional with no input (p = 0.038) and conventional with cattle manure (p = 0.045). Available phosphorous significantly (p < 0.05) increased in treatments under Zai technology while total nitrogen significantly (p < 0.05) reduced after the four cropping seasons. There was a significant (p < 0.05) interactive effect of the tested factors on soil pH, electrical conductivity, total nitrogen, and available phosphorous at the end of the experiment. Moreover, there was significant (p < 0.05) interactive effects on grain yields (SR18 and SR19 seasons) and stover yields (SR18, LR19, and SR19 seasons), with higher yields being recorded in treatments under Zai technology. This study demonstrates the importance of Zai technology in increasing crop yield by trapping water and enhancing its retention and infiltration into the soil for uptake by plants. This study concluded that positive impacts on important soil properties and crop yield could be realized when Zai technology is utilized alongside either sole inorganics or a combination of organic and inorganic amendments and this could be used as a strategy to improve crop production in eastern Kenya and other similar areas.

scholarly journals Environmental characteristics and changes of bacterial communities in the meltwater runoff of glacier in Ny-Alesund, Arctic

2021 ◽  
Author(s):  
Lidong Lin ◽  
Nengfei Wang ◽  
Wenbing Han ◽  
Botao Zhang ◽  
Jiaye Zang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Diversity ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Operational Taxonomic Units ◽  
The Core ◽  
Meltwater Runoff ◽  
Glacial Runoff ◽  
Weighted Correlation

Abstract The present study assessed the diversity and composition of bacterial communities in glacial runoff and glacial soils in the Midre Lovénbreen glacier region of Svalbard. A total of 6,593 operational taxonomic units were identified by high-throughput sequencing. The results showed differences in bacterial community composition between the upper and lower reaches of glacial runoff. The abundance of Actinobacteria, Firmicutes, Betaproteobacteria and Gammaproteobacteria in the upper reaches of glacial runoff was higher than that in the lower reaches. In contrast, the the abundance of Cyanobacteria and Alphaproteobacteria in the downstream of glacial runoff was higher than that in the upstream. In addition, we compared bacterial diversity and composition between glacial runoff areas and soils. The chart analysis showed that bacterial diversity in glacial soil was higher than that in the glacial runoff. Some typical bacteria in the soil, such as Actinobacteria, entered glacial runoff through contact between them. The abundance of Acidobacteria, Sphingobacterium and Flavobacterium was higher in glacial soil. Weighted correlation network analysis showed that the core bacteria in glacial runoff and glacial soil were typical bacteria in different habitats. Distance-based redundancy analysis revealed that NO 2 - -N was the most significant factor affecting the distribution of soil bacterial community, while NO 3 - -N was the most significant factor affecting the distribution of glacial runoff bacterial community.

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