scholarly journals Characterization of a Bacterial Community in an Abandoned Semiarid Lead-Zinc Mine Tailing Site

2008 ◽  
Vol 74 (12) ◽  
pp. 3899-3907 ◽  
Author(s):  
Monica O. Mendez ◽  
Julia W. Neilson ◽  
Raina M. Maier
Keyword(s):  
Bacterial Communities ◽  
Phylogenetic Analyses ◽  
Control Sample ◽  
Mine Tailing ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Semiarid Environment ◽  
Lead Zinc ◽  
Zinc Mine

ABSTRACT Bacterial diversity in mine tailing microbial communities has not been thoroughly investigated despite the correlations that have been observed between the relative microbial diversity and the success of revegetation efforts at tailing sites. This study employed phylogenetic analyses of 16S rRNA genes to compare the bacterial communities present in highly disturbed, extremely (pH 2.7) and moderately (pH 5.7) acidic lead-zinc mine tailing samples from a semiarid environment with those from a vegetated off-site (OS) control sample (pH 8). Phylotype richness in these communities decreased from 42 in the OS control to 24 in the moderately acidic samples and 8 in the extremely acidic tailing samples. The clones in the extremely acidic tailing sample were most closely related to acidophiles, none of which were detected in the OS control sample. The comparison generated by this study between the bacteria present in extremely acidic tailing and that in moderately acidic tailing communities with those in an OS control soil provides a reference point from which to evaluate the successful restoration of mine tailing disposal sites by phytostabilization.

scholarly journals Structure and diversity of native bacterial communities in soils contaminated with polychlorinated biphenyls

2020 ◽  
Author(s):  
Adalberto Zenteno-Rojas ◽  
Esperanza Martínez-Romero ◽  
Daniel Castañeda-Valbuena ◽  
Clara Ivette Rincón-Molina ◽  
Víctor Manuel Ruíz-Valdiviezo ◽  
...  
Keyword(s):  
Polychlorinated Biphenyls ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Burkholderia Cepacia ◽  
Control Sample ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Comamonas Testosteroni ◽  
Bacterial Strains ◽  
Bacterial Phyla

Abstract Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) are a group of high-risk synthetic substances for human and environmental health. Currently, the study of sites contaminated by the spillage of equipment PCBs containing have been considered targeted areas for the study of bacterial communities with potential for PCBs degradation. There in isolation of bacterial strains is vital for use in biodegradable processes, such as bacterial bioaugmentation, which accelerates the development of phenomena such as natural attenuation of contaminated sites. The objective of this study was to assess biodiversity of bacteria contained in anthropogenic contaminated soils (HS and HP) with PCBs compared to a control sample without contaminant and the modified forest (F) and agricultural (A) soil in the laboratory with 100 mg L-1 PCB. For the analysis of 16S rRNA genes amplified from DNA extracted from the soils evaluated, the latest generation of Illumina Miseq and Sanger sequencing for the cultivable strains were detected. The bacteria identified as the most abundant bacterial phyla for HS and HP soil was Proteobacteria (56.7%) and Firmicutes (22.9%), which decreased in F and A soils. The most abundant bacterial genera were Burkholderia, Bacillus, Acinetobacter, Comamonas and Cupriavidus. Several species identified in this study, such as Bacillus cereus, Burkholderia cepacia, Comamonas testosteroni and Acinetobacter pittii have been reported as PCBs degraders. Finally, by means of a principal component analysis (PCA), a correlation between the physical and chemical characteristics of the soils in relation to the relative abundances of the bacteria identified was obtained. The C/N ratio was directly related to the control soil (without contaminant), while SOM maintained a relationship with F and A soils and the bacterial abundances were directly related to Hs and Hp soils due to the presence of aroclor 1260. Bacteria with the ability to tolerate high concentrations of this pollutant are considered for future use in biostimulation and bioaugmentation processes in contaminated soils.

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

scholarly journals Variability of the Sheep Lung Microbiota

2016 ◽  
Vol 82 (11) ◽  
pp. 3225-3238 ◽  
Author(s):  
Laura Glendinning ◽  
Steven Wright ◽  
Jolinda Pollock ◽  
Peter Tennant ◽  
David Collie ◽  
...  
Keyword(s):  
Spatial Variability ◽  
Dna Sequences ◽  
Bacterial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Large Animal ◽  
Local Factors ◽  
Adult Sheep ◽  
Sequencing Technologies ◽  
Host Influence

ABSTRACTSequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n= 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota.IMPORTANCEUntil recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the “lung microbiota.” In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.

A description of the second species of the genus Bleptus Eaton, 1885 (Ephemeroptera: Heptageniidae) from Japan, and phylogenetic relationships of two Bleptus mayflies inferred from mitochondrial and nuclear gene sequences

Zootaxa ◽  
2021 ◽  
Vol 4974 (2) ◽  
pp. 333-360
Author(s):  
KOJI TOJO ◽  
KEN MIYAIRI ◽  
YUTO KATO ◽  
AYANA SAKANO ◽  
TOMOYA SUZUKI
Keyword(s):  
Phylogenetic Analyses ◽  
Ribosomal Subunit ◽  
Nuclear Gene ◽  
Taxonomic Status ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Gene Sequences ◽  
Molecular Phylogenetic ◽  
Black Band ◽  
Relationship Of

A new mayfly species, Bleptus michinokuensis sp. nov. (Ephemeroptera: Heptageniidae) is described on the basis of specimens of male and female adults and mature nymphs collected at a seepage zone of a small freshwater branch of the ‘Tachiya-zawa-gawa’ River located amongst the northern foothills of Mt. Gassan (Shonai-machi Town, Yamagata Prefecture, Japan). This new Bleptus species is characterized by its clear fore and hind wings. That is, they neither exhibit the distinct black band on the fore wings, nor the characteristic darkened margins along the edges of both the fore and hind wings. Rather it has a blackish colored terminal half of its fore legs (i.e., tibial, tarsal and pretarsal segments). These features differ clearly when comparing them to the other known species, Bleptus fasciatus Eaton. The information and data describing the habitat and distribution range of this new species are also noted. We also examined and discussed the genetic relationship of two Bleptus mayflies to settle the taxonomic status, inferred from the partially sequenced cytochrome c oxidase subunit I (COI) and large mitochondrial ribosomal subunit (16S rRNA) genes, and also the nuclear internal transcribed spacer 2 (ITS2) gene sequences. Consequently, phenetic and molecular phylogenetic analyses agreed well in terms of clustering. 

scholarly journals Unraveling the Etiology of North American Grapevine Yellows (NAGY): Novel NAGY Phytoplasma Sequevars Related to ‘Candidatus Phytoplasma pruni’

Plant Disease ◽  
2015 ◽  
Vol 99 (8) ◽  
pp. 1087-1097 ◽  
Author(s):  
Robert E. Davis ◽  
Ellen L. Dally ◽  
Yan Zhao ◽  
Ing-Ming Lee ◽  
Wei Wei ◽  
...  
Keyword(s):  
16S Rdna ◽  
North American ◽  
Phylogenetic Analyses ◽  
New York State ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Vitis Vinifera L ◽  
Polymorphism Analysis ◽  
Ribosomal Protein Genes ◽  
Grapevine Yellows

North American grapevine yellows (NAGY) disease has sometimes been attributed to infection of Vitis vinifera L. by Prunus X-disease phytoplasma (‘Candidatus Phytoplasma pruni’) but this attribution may not be fully adequate. In this study, phytoplasma strains related to ‘Ca. Phytoplasma pruni’ were found in NAGY-diseased grapevines in Maryland, Pennsylvania, Virginia, Ohio, Missouri, and New York State. Based on restriction fragment length polymorphism analysis of 16S ribosomal RNA gene (16S rDNA) sequences, the strains (termed NAGYIII strains) were classified in group 16SrIII (X-disease group) but they contained a recognition site for the restriction endonuclease MseI that is not present in the 16S rDNA of ‘Ca. Phytoplasma pruni’. The 16S rDNA of the strains differed by three or four nucleotides from that of ‘Ca. Phytoplasma pruni’, indicating that they belonged to two novel 16S rDNA sequevars, designated NAGYIIIα and NAGYIIIβ. Both sequevars differed from ‘Ca. Phytoplasma pruni’ by a single base in each of three regions corresponding to species-unique (signature) sequences described for ‘Ca. Phytoplasma pruni’. Phylogenetic analyses of 16S rRNA genes and SecY proteins, and single-nucleotide polymorphism analyses of secY and ribosomal protein genes, further distinguished the two grapevine sequevar lineages from one another and from ‘Ca. Phytoplasma pruni’. The NAGYIIIα and NAGYIIIβ sequevars also differed from ‘Ca. Phytoplasma pruni’ in regions of the folded SecY protein that are predicted to be near or exposed at the outer surface of the phytoplasma membrane. No evidence indicated that diseased grapevines contained any phytoplasma strain conforming to ‘Ca. Phytoplasma pruni’ sensu stricto. Because the NAGYIII sequevars have not been reported in X-disease, a question is raised as to whether NAGYIII and Prunus X-disease are caused by different phytoplasma genotypes.

scholarly journals Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2320-2325 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
Cheng-Zhe Wen ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sea Urchins ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Moderate Amount ◽  
Polar Lipid Profile

A Gram-stain-negative, aerobic, rod-shaped, yellow-pigment-producing bacterium (designated strain CC-CZW007T) was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW007T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity to Vitellibacter vladivostokensis JCM 11732T (96.8 %), Vitellibacter soesokkakensis KCTC 32536T (96.4 %), Vitellibacter nionensis KCTC 32420T (95.8 %) and Vitellibacter aestuarii JCM 15496T (95.6 %) and lower sequence similarity to members of other genera. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW007T with respect to other species of the genus Vitellibacter. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, unidentified lipids and aminolipids; a moderate amount of aminophospholipid was also detected. The DNA G+C content was 34.7 mol%. The predominant quinone system was menaquinone (MK-6). On the basis of polyphasic taxonomic evidence presented here, strain CC-CZW007T is proposed to represent a novel species within the genus Vitellibacter, for which the name Vitellibacter echinoideorum sp. nov. is proposed. The type strain is CC-CZW007T ( = BCRC 80886T = JCM 30378T).

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