Qirong Shen

Bio: Qirong Shen is an academic researcher from Nanjing Agricultural University. The author has contributed to research in topics: Rhizosphere & Fusarium oxysporum. The author has an hindex of 74, co-authored 566 publications receiving 18528 citations.

Initial soil microbiome composition and functioning predetermine future plant health

Abstract: Plant-pathogen interactions are shaped by multiple environmental factors, making it difficult to predict disease dynamics even in relatively simple agricultural monocultures. Here, we explored how variation in the initial soil microbiome predicts future disease outcomes at the level of individual plants. We found that the composition and functioning of the initial soil microbiome predetermined whether the plants survived or succumbed to disease. Surviving plant microbiomes were associated with specific rare taxa, highly pathogen-suppressing Pseudomonas and Bacillus bacteria, and high abundance of genes encoding antimicrobial compounds. Microbiome-mediated plant protection could subsequently be transferred to the next plant generation via soil transplantation. Together, our results suggest that small initial variation in soil microbiome composition and functioning can determine the outcomes of plant-pathogen interactions under natural field conditions.

Root exudates drive the soil-borne legacy of aboveground pathogen infection

Abstract: Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure to foliar pathogens and if such responses might improve plant performance in the presence of the pathogen. Here, we conditioned soil by growing multiple generations (five) of Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) in the same soil. We then examined rhizosphere communities and plant performance in a subsequent generation (sixth) grown in pathogen-conditioned versus control-conditioned soil. Moreover, we assessed the role of altered root exudation profiles in shaping the root microbiome of infected plants. Plants grown in conditioned soil showed increased levels of jasmonic acid and improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both rhizosphere and bulk soil bacterial communities were altered by Pst infection. Infected plants exhibited significantly higher exudation of amino acids, nucleotides, and long-chain organic acids (LCOAs) (C > 6) and lower exudation levels for sugars, alcohols, and short-chain organic acids (SCOAs) (C ≤ 6). Interestingly, addition of exogenous amino acids and LCOA also elicited a disease-suppressive response. Collectively, our data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.

Antibiotics and antibiotic resistance from animal manures to soil: a review

Abstract: The overuse of veterinary antibiotics in animal production and the subsequent land applications of manures contribute to the elevated antibiotic resistance in the soil environment. To minimize the risk of antibiotic resistance, it is important to understand the fate of antibiotics and the spread of antibiotic resistance genes (ARGs) from animal production systems to soil. In this paper, we review recent studies on veterinary antibiotic use, the concentrations of antibiotics and the abundance and diversity of AGRs in animal manures and in soil that receives manures or manure composts. The mechanisms of ARG dissemination in the environment are also discussed. Although we focus on China where around 3 billion tons of animal manures are produced and more than 84 000 tons of antibiotics are consumed annually in animal production industries, the problem is worldwide. Approximately 58% of the veterinary antibiotics consumed are excreted into the environment, more than half of which end up in the soil. The abundance of ARGs in manures can reach up to 10−1 of the 16S rRNA genes. Applications of manures or manure composts can enrich soil ARGs in at least three ways: (i) by the direct introduction of manure-derived ARGs, (ii) by elevating the intrinsic soil ARGs and (iii) by imposing a selection of ARGs with the antibiotics in the manures. We also discuss the need for more stringent regulations on the use of veterinary antibiotics and future research directions on the mechanisms of antibiotic resistance and resistance management.

Role of silicon on plant-pathogen interactions.

Abstract: Although silicon (Si) is not recognized as an essential element for general higher plants, it has beneficial effects on the growth and production of a wide range of plant species. Si is known to effectively mitigate various environmental stresses and enhance plant resistance against both fungal and bacterial pathogens; however, the underlying mechanisms are largely unknown. In this review, the effects of Si on plant-pathogen interactions are discussedanalyzed, mainly from on physical, biochemical, and molecular aspects. In most cases, the Si-induced biochemical/molecular resistance during plant-pathogen interactions were dominated as joint resistance, involving activating defense-related enzymes activates, stimulating antimicrobial compound production, regulating the complex network of signal pathways, and activating of the expression of defense-related genes. The most previous studies described an independent process, however, the whole plant resistances were rarely considered, especially the interaction of different process in higher plants. Si can act as a modulator influencing plant defense responses and interacting with key components of plant stress signaling systems leading to induced resistance. Priming of plant defense responses, alterations in phytohormone homeostasis, and networking by defense signaling components are all potential mechanisms involved in Si-triggered resistance responses. This review summarizes the roles of Si in plant-microbe interactions, evaluates the potential for improving plant resistance by modifying Si fertilizer inputs, and highlights future research concerning the role of Si in agriculture.

Methods in Enzymology.

Abstract: I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Drought-Induced Reduction in Global Terrestrial Net Primary Production from 2000 Through 2009

Abstract: Terrestrial net primary production (NPP) quantifies the amount of atmospheric carbon fixed by plants and accumulated as biomass. Previous studies have shown that climate constraints were relaxing with increasing temperature and solar radiation, allowing an upward trend in NPP from 1982 through 1999. The past decade (2000 to 2009) has been the warmest since instrumental measurements began, which could imply continued increases in NPP; however, our estimates suggest a reduction in the global NPP of 0.55 petagrams of carbon. Large-scale droughts have reduced regional NPP, and a drying trend in the Southern Hemisphere has decreased NPP in that area, counteracting the increased NPP over the Northern Hemisphere. A continued decline in NPP would not only weaken the terrestrial carbon sink, but it would also intensify future competition between food demand and proposed biofuel production.