scholarly journals Distribution of soil viruses across China and their potential role in phosphorous metabolism

2021 ◽  
Author(s):  
Li-Li Han ◽  
Dan-Ting Yu ◽  
Li Bi ◽  
Shuai Du ◽  
Cynthia Silveira ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Phylogenetic Analyses ◽  
Geographical Location ◽  
Global Scale ◽  
Ecological Functions ◽  
Nucleotide Synthesis ◽  
Viral Communities ◽  
Bacteria And Fungi ◽  
Biological Entities ◽  
Ssdna Viruses

Abstract Background: Viruses are the most abundant biological entities on the planet and drive biogeochemical cycling on a global scale. Our understanding of biogeography of soil viruses and their ecological functions lags significantly behind that of Bacteria and Fungi. Here, a viromic approach was used to investigate the distribution and ecological functions of viruses from 19 soils across China.Results: More than 60% of viral genome fragments could not be classified, representing potential new viruses. Among the 27 viral families identified, 15 families belonged to dsDNA viruses and 12 families belonged to ssDNA viruses. Soil samples clustered more significantly by geographical location than type of soil (agricultural and natural). Three clusters of viral communities were identified from North, Southeast and Southwest regions; these clusters differentiated using taxonomic as well as functional composition and were mainly driven by latitude. Phylogenetic analyses of the phoH gene showed a remarkable diversity and two new viral clades. Notably, five proteins involved in phosphorus (P) metabolism-related nucleotide synthesis functions, including dUTPase, MazG, PhoH, Thy1, and RNR, were mainly identified in agricultural soils. Conclusions: The present work revealed that soil viral communities and their functions were distributed across China according to geographical location, with latitude as the dominant driving factor. In addition, P metabolism genes encoded by these viruses probably drive the synthesis of nucleotides for their own genomes inside bacterial hosts, thereby affecting P cycling in the soil ecosystems.

scholarly journals Seasonal Variation Characteristics of Bacteria and Fungi in PM2.5 in Typical Basin Cities of Xi’an and Linfen, China

Atmosphere ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 809
Author(s):  
Sen Wang ◽  
Wanyu Liu ◽  
Jun Li ◽  
Haotian Sun ◽  
Yali Qian ◽  
...  
Keyword(s):  
Seasonal Variation ◽  
Relative Abundance ◽  
Pathogenic Bacteria ◽  
High Throughput Sequencing ◽  
Fine Particulate Matter ◽  
Ecological Functions ◽  
Factors Affecting ◽  
Bacterial Phyla ◽  
Variation Characteristics ◽  
Bacteria And Fungi

Microorganisms existing in airborne fine particulate matter (PM2.5) have key implications in biogeochemical cycling and human health. In this study, PM2.5 samples, collected in the typical basin cities of Xi’an and Linfen, China, were analyzed through high-throughput sequencing to understand microbial seasonal variation characteristics and ecological functions. For bacteria, the highest richness and diversity were identified in autumn. The bacterial phyla were dominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Metabolism was the most abundant pathway, with the highest relative abundance found in autumn. Pathogenic bacteria (Pseudomonas, Acinetobacter, Serratia, and Delftia) were positively correlated with most disease-related pathways. Besides, C cycling dominated in spring and summer, while N cycling dominated in autumn and winter. The relative abundance of S cycling was highest during winter in Linfen. For fungi, the highest richness was found in summer. Basidiomycota and Ascomycota mainly constituted the fungal phyla. Moreover, temperature (T) and sulfur dioxide (SO2) in Xi’an, and T, SO2, and nitrogen dioxide (NO2) in Linfen were the key factors affecting microbial community structures, which were associated with different pollution characteristics in Xi’an and Linfen. Overall, these results provide an important reference for the research into airborne microbial seasonal variations, along with their ecological functions and health impacts.

scholarly journals Loose Ends in the Cortinarius Phylogeny: Five New Myxotelamonoid Species Indicate a High Diversity of These Ectomycorrhizal Fungi with South American Nothofagaceae

Life ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 420
Author(s):  
María Eugenia Salgado Salomón ◽  
Carolina Barroetaveña ◽  
Tuula Niskanen ◽  
Kare Liimatainen ◽  
Matthew E. Smith ◽  
...  
Keyword(s):  
New Species ◽  
Current Knowledge ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Global Scale ◽  
South American ◽  
Edible Fungi ◽  
Rdna Its ◽  
Morphological And Molecular Data ◽  
High Diversity

This paper is a contribution to the current knowledge of taxonomy, ecology and distribution of South American Cortinarius (Pers.) Gray. Cortinarius is among the most widely distributed and species-rich basidiomycete genera occurring with South American Nothofagaceae and species are found in many distinct habitats, including shrublands and forests. Due to their ectomycorrhizal role, Cortinarius species are critical for nutrient cycling in forests, especially at higher latitudes. Some species have also been reported as edible fungi with high nutritional quality. Our aim is to unravel the taxonomy of selected Cortinarius belonging to phlegmacioid and myxotelamonioid species based on morphological and molecular data. After widely sampling Cortinarius specimens in Patagonian Nothofagaceae forests and comparing them to reference collections (including holotypes), we propose five new species of Cortinarius in this work. Phylogenetic analyses of concatenated rDNA ITS-LSU and RPB1 sequences failed to place these new species into known Cortinarius sections or lineages. These findings highlight our knowledge gaps regarding the fungal diversity of South American Nothofagaceae forests. Due to the high diversity of endemic Patagonian taxa, it is clear that the South American Cortinarius diversity needs to be discovered and described in order to understand the evolutionary history of Cortinarius on a global scale.

Morphological and molecular characterisation of Distolabrellus veechi (Rhabditida: Mesorhabditidae) from India

Nematology ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 439-452 ◽  
Author(s):  
Suman ◽  
Aashaq Hussain Bhat ◽  
Aasha ◽  
Ashok Kumar Chaubey ◽  
Joaquín Abolafia
Keyword(s):  
Phylogenetic Trees ◽  
Agricultural Soils ◽  
Phylogenetic Analyses ◽  
Uttar Pradesh ◽  
Sister Group ◽  
Molecular Characterisation ◽  
Soil Baiting ◽  
Its Rrna ◽  
First Time ◽  
Rrna Sequences

Summary A redescription of Distolabrellus veechi (Rhabditida: Mesorhabditidae) from agricultural soils in Uttarakhand and Uttar Pradesh, India, is provided. Specimens were extracted from soil using the Galleria soil baiting technique, with two strains of nematodes named JP1 and JP2 being obtained. Morphological and morphometric studies on the species agree well with previous records. Molecular analyses are provided using 18S, 28S and ITS rRNA sequences, the ITS sequences being obtained for the first time in this species. These analyses show that the material examined agrees well with previously studied populations. Phylogenetic analyses showed Distolabrellus to be the sister group of Crustorhabditis and Teratorhabditis, all having the male spicules fused for more than 50% of their length. Illustrations and phylogenetic trees based on 18S, 28S and ITS rRNA sequences are provided.

Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds

2018 ◽  
Vol 64 (10) ◽  
pp. 664-680 ◽  
Author(s):  
Maryanne Scott ◽  
Mamta Rani ◽  
Jamil Samsatly ◽  
Jean-Benoit Charron ◽  
Suha Jabaji
Keyword(s):  
Biochemical Characterization ◽  
Cannabis Sativa ◽  
Growth Promotion ◽  
Phylogenetic Analyses ◽  
Leaf Tissue ◽  
Cellulase Production ◽  
Culturable Bacteria ◽  
Fungal Strains ◽  
Bacteria And Fungi ◽  
Industrial Hemp

Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.

scholarly journals Viruses in the Built Environment (VIBE) meeting report

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Aaron J. Prussin ◽  
Jessica A. Belser ◽  
Werner Bischoff ◽  
Scott T. Kelley ◽  
Kaisen Lin ◽  
...  
Keyword(s):  
Built Environment ◽  
Temporal Dynamics ◽  
Virus Detection ◽  
Future Research ◽  
Meeting Report ◽  
Knowledge Gaps ◽  
Research Areas ◽  
Viral Communities ◽  
Bacteria And Fungi ◽  
Definition Of

Abstract Background During a period of rapid growth in our understanding of the microbiology of the built environment in recent years, the majority of research has focused on bacteria and fungi. Viruses, while probably as numerous, have received less attention. In response, the Alfred P. Sloan Foundation supported a workshop entitled “Viruses in the Built Environment (VIBE),” at which experts in environmental engineering, environmental microbiology, epidemiology, infection prevention, fluid dynamics, occupational health, metagenomics, and virology convened to synthesize recent advances and identify key research questions and knowledge gaps regarding viruses in the built environment. Results Four primary research areas and funding priorities were identified. First, a better understanding of viral communities in the built environment is needed, specifically which viruses are present and their sources, spatial and temporal dynamics, and interactions with bacteria. Second, more information is needed about viruses and health, including viral transmission in the built environment, the relationship between virus detection and exposure, and the definition of a healthy virome. The third research priority is to identify and evaluate interventions for controlling viruses and the virome in the built environment. This encompasses interactions among viruses, buildings, and occupants. Finally, to overcome the challenge of working with viruses, workshop participants emphasized that improved sampling methods, laboratory techniques, and bioinformatics approaches are needed to advance understanding of viruses in the built environment. Conclusions We hope that identifying these key questions and knowledge gaps will engage other investigators and funding agencies to spur future research on the highly interdisciplinary topic of viruses in the built environment. There are numerous opportunities to advance knowledge, as many topics remain underexplored compared to our understanding of bacteria and fungi.

scholarly journals Host Range of Verticillium isaacii and Verticillium klebahnii from Artichoke, Spinach, and Lettuce

Plant Disease ◽  
2015 ◽  
Vol 99 (7) ◽  
pp. 933-938 ◽  
Author(s):  
Suraj Gurung ◽  
Dylan P. G. Short ◽  
Xiaoping Hu ◽  
German V. Sandoya ◽  
Ryan J. Hayes ◽  
...  
Keyword(s):  
New Species ◽  
Host Range ◽  
Disease Severity ◽  
Verticillium Wilt ◽  
Agricultural Soils ◽  
Phylogenetic Analyses ◽  
Greenhouse Experiment ◽  
Vascular Wilt ◽  
Race 1 ◽  
Race 2

Verticillium is a genus that includes major vascular wilt pathogens. Recently, multilocus phylogenetic analyses of the genus identified five new species, including Verticillium isaacii and V. klebahnii, both of which occur in agricultural soils in coastal California and have been isolated from asymptomatic and diseased spinach and lettuce plants. Little data are available regarding their pathogenicity and virulence on a broader range of crops important to the region. Four isolates each of V. isaacii and V. klebahnii along with two reference isolates of V. dahliae races 1 and 2 were inoculated on eight crops (artichoke, cauliflower, eggplant, lettuce, pepper, tomato, spinach, and strawberry) in a greenhouse experiment. After 8 weeks, plants were assessed for disease severity to determine the relative host ranges of Verticillium isolates. Additionally, 13 lettuce lines resistant to race 1 and partially resistant to race 2 of V. dahliae were screened against V. isaacii and V. klebahnii to evaluate their responses. Three of four V. isaacii and four of four V. klebahnii isolates tested were nonpathogenic on all crops tested except those indicated below. One V. isaacii isolate caused wilt on artichoke and ‘Salinas’ lettuce and most isolates of both species caused varying degrees of Verticillium wilt on strawberry. Lettuce lines resistant to V. dahliae race 1 and partially resistant to V. dahliae race 2 also exhibited resistance to all of the isolates of V. isaacii and V. klebahnii. Thus, at least some isolates in the populations of V. isaacii and V. klebahnii have the potential to become significant pathogens of coastal California crops. However, resistance developed against V. dahliae also offers resistance to the pathogenic isolates of both species, at least in lettuce.

scholarly journals Co-Occurring Anammox, Denitrification, and Codenitrification in Agricultural Soils

2012 ◽  
Vol 79 (1) ◽  
pp. 168-176 ◽  
Author(s):  
Andrew Long ◽  
Joshua Heitman ◽  
Craig Tobias ◽  
Rebecca Philips ◽  
Bongkeun Song
Keyword(s):  
Agricultural Soils ◽  
The United States ◽  
Soil Samples ◽  
Soil Incubation ◽  
Production Rates ◽  
Content Type ◽  
The North ◽  
Incubation Experiments ◽  
Bacteria And Fungi ◽  
Isotope Analyses

ABSTRACTAnammox and denitrification mediated by bacteria are known to be the major microbial processes converting fixed N to N2gas in various ecosystems. Codenitrification and denitrification by fungi are additional pathways producing N2in soils. However, fungal codenitrification and denitrification have not been well investigated in agricultural soils. To evaluate bacterial and fungal processes contributing to N2production, molecular and15N isotope analyses were conducted with soil samples collected at six different agricultural fields in the United States. Denitrifying and anammox bacterial abundances were measured based on quantitative PCR (qPCR) of nitrous oxide reductase (nosZ) and hydrazine oxidase (hzo) genes, respectively, while the internal transcribed spacer (ITS) ofFusarium oxysporumwas quantified to estimate the abundance of codenitrifying and denitrifying fungi.15N tracer incubation experiments with15NO3−or15NH4+addition were conducted to measure the N2production rates from anammox, denitrification, and codenitrification. Soil incubation experiments with antibiotic treatments were also used to differentiate between fungal and bacterial N2production rates in soil samples. Denitrifying bacteria were found to be the most abundant, followed byF. oxysporumbased on the qPCR assays. The potential denitrification rates by bacteria and fungi ranged from 4.118 to 42.121 nmol N2-N g−1day−1, while the combined potential rates of anammox and codenitrification ranged from 2.796 to 147.711 nmol N2-N g−1day−1. Soil incubation experiments with antibiotics indicated that fungal codenitrification was the primary process contributing to N2production in the North Carolina soil. This study clearly demonstrates the importance of fungal processes in the agricultural N cycle.

scholarly journals Phytophthora Database 2.0: Update and Future Direction

2013 ◽  
Vol 103 (12) ◽  
pp. 1204-1208 ◽  
Author(s):  
Bongsoo Park ◽  
Frank Martin ◽  
David M. Geiser ◽  
Hye-Seon Kim ◽  
Michele A. Mansfield ◽  
...  
Keyword(s):  
Diagnostic Tool ◽  
Online Community ◽  
Phylogenetic Analyses ◽  
Global Scale ◽  
Rapid Identification ◽  
Tool Development ◽  
Sequence Alignments ◽  
Geographic Origins ◽  
Community Forum ◽  
Future Direction

The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for ≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD's future direction.

scholarly journals Phosphorus in agricultural soils: drivers of its distribution at the global scale

2017 ◽  
Vol 23 (8) ◽  
pp. 3418-3432 ◽  
Author(s):  
Bruno Ringeval ◽  
Laurent Augusto ◽  
Hervé Monod ◽  
Dirk van Apeldoorn ◽  
Lex Bouwman ◽  
...  
Keyword(s):  
Agricultural Soils ◽  
Global Scale

scholarly journals Soil viral communities are structured by pH at local and global scales

2021 ◽  
Author(s):  
Sungeun Lee ◽  
Jackson W Sorensen ◽  
Robin L Walker ◽  
Joanne B Emerson ◽  
Graeme W Nicol ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Ph ◽  
Environmental Gradients ◽  
Abiotic Factors ◽  
Global Scale ◽  
Community Structures ◽  
Viral Community ◽  
Viral Communities ◽  
Virus Communities

Viruses shape microbial community structures, impacting metabolic pathways and influencing biogeochemical cycles. Despite their importance, the influence of biotic and abiotic factors on viral community structures across environmental gradients in soil is relatively unknown compared to their prokaryotic hosts. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil virus communities. In this study, prokaryotic and viral communities were characterized in soils sampled from the extremes of a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations were compared to those in a variety of soil ecosystems ranging in pH (4.0 - 7.5). Prokaryotic and viral community structure were significantly influenced by soil pH at the local scale. Of 1,910 viral operational taxonomic units (vOTUs), 99% were restricted to pH 4.5 or 7.5 soil only. These were compared in gene sharing networks of populations from six other European and North American soil systems. A selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. Results indicate that as with prokaryotes, soil pH is a factor structuring viral communities at the local and global scale.

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