scholarly journals Diversity of active viral infections within the Sphagnum microbiome

2018 ◽  
Author(s):  
Joshua M.A. Stough ◽  
Max Kolton ◽  
Joel E. Kostka ◽  
David J. Weston ◽  
Dale A. Pelletier ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Viral Infections ◽  
Housekeeping Gene ◽  
Model Systems ◽  
Microbial Consortia ◽  
Soil Conditions ◽  
Marker Genes ◽  
Ecological Value ◽  
Metabolic Potential ◽  
Virus Diversity

AbstractSphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of 6 Sphagnum plants were obtained from a peatland in northern Minnesota and total RNA extracted and sequenced. Metatranscriptomes were assembled and contigs screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein, gp23, as a marker for phage diversity, we identified 33 contigs representing undocumented phage s that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) major capsid protein were used as markers for ssRNA viruses and NCLDV, respectively. In total 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent near-complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinto-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades, and suggest viruses may play a considerable role in the ecology of the Sphagnum microbiome.SignificanceSphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor its own growth over other plant species. This slows rates of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss’s growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome, and identifying new potential model systems to study virus-host interactions in the peatland ecosystem.

scholarly journals Diversity of Active Viral Infections within the Sphagnum Microbiome

2018 ◽  
Vol 84 (23) ◽  
Author(s):  
Joshua M. A. Stough ◽  
Max Kolton ◽  
Joel E. Kostka ◽  
David J. Weston ◽  
Dale A. Pelletier ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Viral Infections ◽  
Model Systems ◽  
Microbial Consortia ◽  
Soil Conditions ◽  
Marker Genes ◽  
Ecological Value ◽  
Metabolic Potential ◽  
Content Type ◽  
Virus Diversity

ABSTRACT Sphagnum-dominated peatlands play an important role in global carbon storage and represent significant sources of economic and ecological value. While recent efforts to describe microbial diversity and metabolic potential of the Sphagnum microbiome have demonstrated the importance of its microbial community, little is known about the viral constituents. We used metatranscriptomics to describe the diversity and activity of viruses infecting microbes within the Sphagnum peat bog. The vegetative portions of six Sphagnum plants were obtained from a peatland in northern Minnesota, and the total RNA was extracted and sequenced. Metatranscriptomes were assembled and contigs were screened for the presence of conserved virus marker genes. Using bacteriophage capsid protein gp23 as a marker for phage diversity, we identified 33 contigs representing undocumented phages that were active in the community at the time of sampling. Similarly, RNA-dependent RNA polymerase and the nucleocytoplasmic large DNA virus (NCLDV) major capsid protein were used as markers for single-stranded RNA (ssRNA) viruses and NCLDV, respectively. In total, 114 contigs were identified as originating from undescribed ssRNA viruses, 22 of which represent nearly complete genomes. An additional 64 contigs were identified as being from NCLDVs. Finally, 7 contigs were identified as putative virophage or polinton-like viruses. We developed co-occurrence networks with these markers in relation to the expression of potential-host housekeeping gene rpb1 to predict virus-host relationships, identifying 13 groups. Together, our approach offers new tools for the identification of virus diversity and interactions in understudied clades and suggests that viruses may play a considerable role in the ecology of the Sphagnum microbiome. IMPORTANCE Sphagnum-dominated peatlands play an important role in maintaining atmospheric carbon dioxide levels by modifying conditions in the surrounding soil to favor the growth of Sphagnum over that of other plant species. This lowers the rate of decomposition and facilitates the accumulation of fixed carbon in the form of partially decomposed biomass. The unique environment produced by Sphagnum enriches for the growth of a diverse microbial consortia that benefit from and support the moss's growth, while also maintaining the hostile soil conditions. While a growing body of research has begun to characterize the microbial groups that colonize Sphagnum, little is currently known about the ecological factors that constrain community structure and define ecosystem function. Top-down population control by viruses is almost completely undescribed. This study provides insight into the significant viral influence on the Sphagnum microbiome and identifies new potential model systems to study virus-host interactions in the peatland ecosystem.

scholarly journals Halotolerant Microbial Consortia for Sustainable Mitigation of Salinity Stress, Growth Promotion, and Mineral Uptake in Tomato Plants and Soil Nutrient Enrichment

2021 ◽  
Vol 13 (15) ◽  
pp. 8369
Author(s):  
Chintan Kapadia ◽  
R. Z. Sayyed ◽  
Hesham Ali El Enshasy ◽  
Harihar Vaidya ◽  
Deepshika Sharma ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salinity Stress ◽  
Dry Weight ◽  
Stress Factors ◽  
Microbial Consortia ◽  
Soil Conditions ◽  
Mineral Uptake ◽  
Shoot Height ◽  
Tomato Plants ◽  
Secondary Roots

Salinity significantly impacts the growth, development, and reproductive biology of various crops such as vegetables. The cultivable area is reduced due to the accumulation of salts and chemicals currently in use and is not amenable to a large extent to avoid such abiotic stress factors. The addition of microbes enriches the soil without any adverse effects. The effects of microbial consortia comprising Bacillus sp., Delftia sp., Enterobacter sp., Achromobacter sp., was evaluated on the growth and mineral uptake in tomatoes (Solanum Lycopersicum L.) under salt stress and normal soil conditions. Salinity treatments comprising Ec 0, 2, 5, and 8 dS/m were established by mixing soil with seawater until the desired Ec was achieved. The seedlings were transplanted in the pots of the respective pH and were inoculated with microbial consortia. After sufficient growth, these seedlings were transplanted in soil seedling trays. The measurement of soil minerals such as Na, K, Ca, Mg, Cu, Mn, and pH and the Ec were evaluated and compared with the control 0 days, 15 days, and 35 days after inoculation. The results were found to be non-significant for the soil parameters. In the uninoculated seedlings’ (control) seedling trays, salt treatment significantly affected leaf, shoot, root dry weight, shoot height, number of secondary roots, chlorophyll, and mineral contents. While bacterized seedlings sown under saline soil significantly increased leaf (105.17%), shoot (105.62%), root (109.06%) dry weight, leaf number (75.68%), shoot length (92.95%), root length (146.14%), secondary roots (91.23%), and chlorophyll content (−61.49%) as compared to the control (without consortia). The Na and K intake were higher even in the presence of the microbes, but the beneficial effect of the microbe helps plants sustain in the saline environment. The inoculation of microbial consortia produced more secondary roots, which accumulate more minerals and transport substances to the different parts of the plant; thus, it produced higher biomass and growth. Results of the present study revealed that the treatment with microbial consortia could alleviate the deleterious effects of salinity stress and improve the growth of tomato plants under salinity stress. Microbial consortia appear to be the best alternative and cost-effective and sustainable approach for managing soil salinity and improving plant growth under salt stress conditions.

scholarly journals Unravelling diversity and metabolic potential of microbial consortia at each stage of leather sewage treatment

RSC Advances ◽  
2017 ◽  
Vol 7 (66) ◽  
pp. 41727-41737 ◽  
Author(s):  
Hebin Liang ◽  
Dongdong Ye ◽  
Lixin Luo
Keyword(s):  
Wastewater Treatment ◽  
Activated Sludge ◽  
Treatment Process ◽  
Sewage Treatment ◽  
Microbial Consortia ◽  
Biological Wastewater Treatment ◽  
Metabolic Potential ◽  
Ecological Functions ◽  
Wastewater Treatment Process ◽  
System P

Activated sludge is essential for the biological wastewater treatment process and the identification of active microbes enlarges awareness of their ecological functions in this system.

scholarly journals Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Diego Javier Jiménez ◽  
Diego Chaves-Moreno ◽  
Jan Dirk van Elsas
Keyword(s):  
Wheat Straw ◽  
Microbial Consortia ◽  
Metabolic Potential

scholarly journals CANT-HYD: A curated database of phylogeny-derived Hidden Markov Models for annotation of marker genes involved in hydrocarbon degradation

2021 ◽  
Author(s):  
Varada Khot ◽  
Jackie Zorz ◽  
Daniel A Gittins ◽  
Anirban Chakraborty ◽  
Emma Bell ◽  
...  
Keyword(s):  
Markov Models ◽  
Hydrocarbon Degradation ◽  
Marker Genes ◽  
Degradation Pathways ◽  
Metabolic Potential ◽  
Accurate Identification ◽  
Isolation And Characterization ◽  
Anaerobic Hydrocarbon Degradation ◽  
Aliphatic And Aromatic Hydrocarbons

Discovery of microbial hydrocarbon degradation pathways has traditionally relied on laboratory isolation and characterization of microorganisms. Although many metabolic pathways for hydrocarbon degradation have been discovered, the absence of tools dedicated to their annotation makes it difficult to identify the relevant genes and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Furthermore, sequence homology between hydrocarbon degradation genes and genes with other functions often results in misannotation. A tool that systematically identifies hydrocarbon metabolic potential is therefore needed. We present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database containing HMMs of 37 marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we show that hydrocarbon metabolic potential is widespread in the tree of life and identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate scalability by analyzing large metagenomic datasets for the prediction of hydrocarbon utilization in diverse environments. To the best of our knowledge, CANT-HYD is the first comprehensive tool for robust and accurate identification of marker genes associated with aerobic and anaerobic hydrocarbon degradation.

scholarly journals Plasma MicroRNA-122 as a Biomarker for Viral-, Alcohol-, and Chemical-Related Hepatic Diseases

2010 ◽  
Vol 56 (12) ◽  
pp. 1830-1838 ◽  
Author(s):  
Yi Zhang ◽  
Yin Jia ◽  
Ruiying Zheng ◽  
Yingjun Guo ◽  
Yue Wang ◽  
...  
Keyword(s):  
Liver Injury ◽  
Viral Infections ◽  
Chemical Exposure ◽  
Organ Damage ◽  
Muscle Disease ◽  
Model Systems ◽  
Pcr Analysis ◽  
Large Set ◽  
Plasma Samples ◽  
Hepatic Diseases

BACKGROUND The liver is frequently subject to insult because of viral infection, alcohol abuse, or toxic chemical exposure. Extensive research has been conducted to identify blood markers that can better discern liver damage, but little progress has been achieved in clinical practice. Recently, circulating microRNAs (miRNAs) have been reported as potential biomarkers for the noninvasive diagnosis of cancer. In this study, we investigated whether plasma miRNAs have diagnostic utility in identifying liver disease. METHODS The study was divided into 2 phases: marker selection by real-time quantitative PCR analysis of a small set of plasma samples, and marker validation with a large set of plasma samples from 83 patients with chronic hepatitis B viral infections, 15 patients with skeletal muscle disease, and 40 healthy controls. Two mouse model systems, d-galactosamine- and alcohol-induced liver injury, were also developed to evaluate whether differences in miRNA concentration were associated with various liver diseases. RESULTS Among the miRNA candidates identified, miR-122 presented a disease severity–dependent change in plasma concentration in the patients and animal models. Compared with an increase in aminotransferase activity in the blood, the change in miR-122 concentration appeared earlier. Furthermore, this change was more specific for liver injury than for other organ damage and was more reliable, because the change was correlated with liver histologic stage. CONCLUSIONS Our findings suggest that circulating miR-122 has potential as a novel, predictive, and reliable blood marker for viral-, alcohol-, and chemical-induced liver injury.

scholarly journals Genomic Characterization of Orf Virus Strain D1701-V (Parapoxvirus) and Development of Novel Sites for Multiple Transgene Expression

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 127 ◽  
Author(s):  
Hanns-Joachim Rziha ◽  
Mathias Büttner ◽  
Melanie Müller ◽  
Ferdinand Salomon ◽  
Alena Reguzova ◽  
...  
Keyword(s):  
Viral Infections ◽  
Blot Hybridization ◽  
Insertion Site ◽  
Vero Cells ◽  
Orf Virus ◽  
Marker Genes ◽  
Promoter Strength ◽  
Fluorescent Marker ◽  
Genomic Changes ◽  
Specific Pcr

The Orf virus (ORFV; Parapoxvirus) strain D1701 with an attenuated phenotype and excellent immunogenic capacity is successfully used for the generation of recombinant vaccines against different viral infections. Adaption for growth in Vero cells was accompanied by additional major genomic changes resulting in ORFV strain variant D1701-V. In this study, restriction enzyme mapping, blot hybridization and DNA sequencing of the deleted region s (A, AT and D) in comparison to the predecessor strain D1701-B revealed the loss of 7 open reading frames (ORF008, ORF101, ORF102, ORF114, ORF115, ORF116, ORF117). The suitability of deletion site D for expression of foreign genes is demonstrated using novel synthetic early promoter eP1 and eP2. Comparison of promoter strength showed that the original vegf-e promoter Pv as well as promoter eP2 display an up to 11-fold stronger expression than promoter eP1, irrespective of the insertion site. Successful integration and expression of the fluorescent marker genes is demonstrated by gene- and insertion-site specific PCR assays, fluorescence microscopy and flow cytometry. For the first time ORFV recombinants are generated simultaneously expressing transgenes in two different insertion loci. That allows production of polyvalent vaccines containing several antigens against one or different pathogens in a single vectored ORFV vaccine.

scholarly journals Rapid expansion and long-term persistence of elevated NK cell numbers in humans infected with hantavirus

2010 ◽  
Vol 208 (1) ◽  
pp. 13-21 ◽  
Author(s):  
Niklas K. Björkström ◽  
Therese Lindgren ◽  
Malin Stoltz ◽  
Cyril Fauriat ◽  
Monika Braun ◽  
...  
Keyword(s):  
Nk Cells ◽  
Cell Activation ◽  
Viral Infections ◽  
Nk Cell ◽  
Killer Cell ◽  
Experimental Models ◽  
Rapid Expansion ◽  
Model Systems ◽  
Hantavirus Infection ◽  
Virus Infections

Natural killer (NK) cells are known to mount a rapid response to several virus infections. In experimental models of acute viral infection, this response has been characterized by prompt NK cell activation and expansion followed by rapid contraction. In contrast to experimental model systems, much less is known about NK cell responses to acute viral infections in humans. We demonstrate that NK cells can rapidly expand and persist at highly elevated levels for >60 d after human hantavirus infection. A large part of the expanding NK cells expressed the activating receptor NKG2C and were functional in terms of expressing a licensing inhibitory killer cell immunoglobulin-like receptor (KIR) and ability to respond to target cell stimulation. These results demonstrate that NK cells can expand and remain elevated in numbers for a prolonged period of time in humans after a virus infection. In time, this response extends far beyond what is considered normal for an innate immune response.

Colonization of carbapenem-resistant Klebsiella pneumoniae in a sink-drain model biofilm system

2020 ◽  
pp. 1-9
Author(s):  
Maria Burgos-Garay ◽  
Christine Ganim ◽  
Tom J.B. de Man ◽  
Terri Davy ◽  
Amy J. Mathers ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Community Analysis ◽  
Model System ◽  
Model Systems ◽  
Microbial Consortia ◽  
Healthcare Facilities ◽  
Biofilm Reactors ◽  
Carbapenem Resistant ◽  
Significant Difference ◽  
Biofilm Development

Abstract Background: Sink drains in healthcare facilities may provide an environment for antimicrobial-resistant microorganisms, including carbapenemase-producing Klebsiella pneumoniae (CPKP). Methods: We investigated the colonization of a biofilm consortia by CPKP in a model system simulating a sink-drain P-trap. Centers for Disease Control (CDC) biofilm reactors (CBRs) were inoculated with microbial consortia originally recovered from 2 P-traps collected from separate patient rooms (designated rooms A and B) in a hospital. Biofilms were grown on stainless steel (SS) or polyvinyl chloride (PVC) coupons in autoclaved municipal drinking water (ATW) for 7 or 28 days. Results: Microbial communities in model systems (designated CBR-A or CBR-B) were less diverse than communities in respective P-traps A and B, and they were primarily composed of β and γ Proteobacteria, as determined using 16S rRNA community analysis. Following biofilm development CBRs were inoculated with either K. pneumoniae ST45 (ie, strain CAV1016) or K. pneumoniae ST258 KPC+ (ie, strain 258), and samples were collected over 21 days. Under most conditions tested (CBR-A: SS, 7-day biofilm; CBR-A: PVC, 28-day biofilm; CBR-B: SS, 7-day and 28-day biofilm; CBR-B: PVC, 28-day biofilm) significantly higher numbers of CAV1016 were observed compared to 258. CAV1016 showed no significant difference in quantity or persistence based on biofilm age (7 days vs 28 days) or substratum type (SS vs PVC). However, counts of 258 were significantly higher on 28-day biofilms and on SS. Conclusions: These results suggest that CPKP persistence in P-trap biofilms may be strain specific or may be related to the type of P-trap material or age of the biofilm.

scholarly journals High numbers of IL-2-producing CD8+ T cells during viral infection: correlation with stable memory development

2002 ◽  
Vol 83 (9) ◽  
pp. 2123-2133 ◽  
Author(s):  
Nanna Ny Kristensen ◽  
Jan Pravsgaard Christensen ◽  
Allan Randrup Thomsen
Keyword(s):  
T Cells ◽  
T Cell ◽  
Mhc Class Ii ◽  
Viral Infections ◽  
Cell Subset ◽  
Lymphocytic Choriomeningitis ◽  
Model Systems ◽  
Loss Of Function ◽  
Ifn Γ ◽  
Lcmv Infection

Using infections with lymphocytic choriomeningitis virus (LCMV) and vesicular stomatitis virus in mice as model systems, we have investigated the ability of antigen-primed CD8+ T cells generated in the context of viral infections to produce IL-2. Our results indicate that acute immunizing infection normally leads to generation of high numbers of IL-2-producing antigen-specific CD8+ T cells. By costaining for IL-2 and IFN-γ intracellularly, we found that IL-2-producing cells predominantly constitute a subset of cells also producing IFN-γ. Comparison of the kinetics of generation revealed that IL-2-producing cells appear slightly delayed compared with the majority of IFN-γ producing cells, and the relative frequency of the IL-2-producing subset increases with transition into the memory phase. In contrast to acute immunizing infection, few IL-2-producing cells are generated during chronic LCMV infection. Furthermore, in MHC class II-deficient mice, which only transiently control LCMV infection, IL-2-producing CD8+ T cells are initially generated, but by 4 weeks after infection this subset has nearly disappeared. Eventually the capacity to produce IFN-γ also becomes impaired, while cell numbers are maintained at a level similar to those in wild-type mice controlling the infection. Taken together, these findings indicate that phenotyping of T cell populations based on capacity to produce cytokines, and especially IL-2, can provide important information as to the functional status of the analysed cell subset. Specifically, combined analysis of the capacity to produce IL-2 and IFN-γ can be used as a predictor for loss of function within the CD8+ T cell compartment.

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