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 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 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 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.

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.

Analysis of the bacterial communities in the waterlogged wooden cultural relics of the Xiaobaijiao No. 1 shipwreck via high-throughput sequencing technology

Holzforschung ◽  
2018 ◽  
Vol 72 (7) ◽  
pp. 609-619 ◽  
Author(s):  
Qiuxia Li ◽  
Lixiang Cao ◽  
Wenfeng Wang ◽  
Hongming Tan ◽  
Tao Jin ◽  
...  
Keyword(s):  
High Throughput ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Diversity Index ◽  
Sequence Similarity ◽  
Species Number ◽  
Sequencing Technology ◽  
Α Diversity ◽  
Sea Area ◽  
Cultural Relics

AbstractThe microbial impact on waterlogged wooden cultural relics fromXiaobaijiao No. 1shipwreck was investigated by means of a high-throughput sequencing technology, while the focus was on the composition of prokaryotic microorganisms in 10 wood samples collected from different parts of the shipwreck. A total of 28 501 different operational taxonomic units (OTUs) were obtained based on 97% sequence similarity. The α-diversity index is for the bacterial diversity, which was the highest and the lowest in the samples SS8 and SS5, respectively. Proteobacteria was the largest category of bacterial abundance (47.3%) followed by Bacteroidetes (10%). α-Proteobacteria was the first largest bacteria class with the maximum abundance (21.0%) followed by γ-Proteobacteria (16.9%). Other groups rich in the following species were found: Bacteroidales (13.3%), Thiotrichales (5.0%), Rhodobacterales (4.2%), Rhizobiales (4.0%), Chromatiales (3.5%), Oceanospirillales (3.3%), Flavobacteriales (2.9%) and Sphingomonadales (2.8%). At the level of the bacterial genus,Marinomonaswas the most abundant one. Phylogenetic analysis revealed that there are some differences in the composition of bacterial communities from different wood samples. The species number of bacteria in the relics of this shipwreck was far more than that reported in those found in Europe, and in which species composition was similar to the benthic bacteria in the corresponding sea area. The coexistence of anaerobic and aerobic bacteria is remarkable.

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 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.

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 ◽  
High Throughput Sequencing ◽  
Rhizosphere Soil ◽  
Bacterial Community Composition ◽  
Soil Bacterial Communities ◽  
Soil Bacterial ◽  
The Impact

Abstract Background: Perturbations in the abiotic stress directly or indirectly affect plants and root-associated microbial communities. Shade stress presents one of the major abiotic limitations for turfgrass growth, as light availability is severely reduced under a leaf canopy. Studies have shown that shade stress influences plant growth and alters plant metabolism, yet little is known about how it affects the structure of rhizosphere soil bacterial communities. In this study, a glasshouse experiment was conducted to examine the impact of shade stress on the physiology of two contrasting shade-tolerant turfgrasses and their rhizosphere soil microbes. Shade-tolerant dwarf lilyturf (Ophiopogon japonicus, OJ) and shade-intolerant perennial turf-type ryegrasss (Lolium perenne, LP) were used. 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. 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: OJ was more shade-tolerant than LP. Shifts in rhizosphere soil bacterial community structure play a vital role in shade-tolerance of OJ plants.

scholarly journals Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay

2021 ◽  
Author(s):  
Sebastian Martinez
Keyword(s):  
High Throughput Sequencing ◽  
Fungal Communities ◽  
Fungal Community Composition ◽  
Bacterial Phyla ◽  
New Crops ◽  
Operational Taxonomic Units ◽  
Rotation System ◽  
Long Term Experiment ◽  
Well Differentiated ◽  
The Impact

Rice is an important crop in Uruguay associated mostly with livestock production in a rice and pasture rotation system since the 1920s. However, in recent years there has been interest in intensifying the production in some of these systems to satisfy market demands and increase income. Intensification occurs by augmenting the rice frequency in the rotation, including new crops like sorghum and soybean, or shortening the pasture phase. A long-term experiment was established in 2012 in the main rice producing area of Uruguay with the objective to study the impact of intensification in rice rotations. After the first cycle of rotation soils from seven rotation phases were sampled and microbial communities were studied by means of high-throughput sequencing of Illumina NovaSeq 6000. Archaeal/bacterial and fungal community composition were studied (16S rRNA and 18S gene regions) detecting 3662 and 807 bacterial and fungal Operational Taxonomic Units (OTUs), respectively. Actinobacteria, Firmicutes and Proteobacteria were the most common bacterial phyla. Among them, only Proteobacteria differed significantly between rotations. Although most fungal OTUs were unidentified, Ascomycota, Basidiomycota and Mucoromycota were the most abundant fungal classes within identified taxa. Bacterial communities differed between rotations forming three groups according to the percentage of rice in the system. Fungal communities clustered in four groups, although not well differentiated, and mostly associated with the antecessor crop. Only P and C:N varied between rotations among soil physicochemical variables after six years, and individual bacterial OTUs appeared weakly influenced by P, pH, Mg and fungal OTUs by P. The results suggest that after six years, bacteria/archaeal communities were influenced by the time with rice in the rotation, and fungal communities were more influenced by the antecessor crop. More studies are needed to associate fungal communities with certain rotational or environmental variables. Some taxa were associated with a particular rotation, and some bacterial taxa were identified as biomarkers. Fungal indicator taxa were not identified at the species level for any rotation.

scholarly journals Distribution of Bacterial Endophytes in the Non-lesion Tissues of Potato and Their Response to Potato Common Scab

2021 ◽  
Vol 12 ◽  
Author(s):  
Wencong Shi ◽  
Gaoya Su ◽  
Mingcong Li ◽  
Bing Wang ◽  
Rongshan Lin ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Global Economy ◽  
High Throughput Sequencing ◽  
Common Scab ◽  
Bacterial Endophytes ◽  
Potato Tubers ◽  
Substantial Impact ◽  
Operational Taxonomic Units ◽  
Α Diversity ◽  
Potato Common Scab

The response of plant endophytes to disease within infected tissues has been well demonstrated, but the corresponding response of endophytes in non-lesion tissues remains unclear. Here, we studied the composition and distribution of bacterial endophytes in potato roots (RE), stems (SE), and tubers (TE), and explored the response of endophytes in non-lesion tissues to potato common scab (PCS), which is a soil-borne disease caused by pathogenic Streptomyces and results in serious losses to the global economy every year. Via high-throughput sequencing, it was seen that the composition of endophytes in roots, stems, and tubers had significant differences (P < 0.05) and the distribution of the bacterial communities illustrated a gradient from soil to root to tuber/stem. PCS significantly reduced bacterial endophytes α-diversity indexes, including ACE and the number of observed operational taxonomic units (OTUs), of RE without significantly reducing the indexes of SE and TE. No significant effect on the composition of endophytes were caused by PCS in roots, tubers, or stems between high PCS severity (H) and low PCS severity (L) infections at the community level, but PCS did have a substantial impact on the relative abundance of several specific endophytes. Rhizobium and Sphingopyxis were significantly enriched in root endophytes with low PCS severity (REL); Delftia and Ochrobactrum were significantly enriched in stem endophytes with low PCS severity (SEL); Pedobacter, Delftia, and Asticcacaulis were significantly enriched in tuber endophytes with high PCS severity (TEH). OTU62, a potential PCS pathogen in this study, was capable of colonizing potato tubers, roots, and stems with few or no symptoms present. Co-occurrence networks showed that the number of correlations to OTU62 was higher than average in these three tissue types, suggesting the importance of OTU62 in endophytic communities. This study clarified the distribution and composition of potato endophytes in tubers, roots, and stems, and demonstrated the response of endophytes in non-lesion tissues to PCS.

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