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Plant microbiome

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https://www.readbyqxmd.com/read/28430944/plant-microbial-diversity-is-suggested-as-the-key-to-future-biocontrol-and-health-trends
#1
Gabriele Berg, Martina Köberl, Daria Rybakova, Henry Müller, Rita Grosch, Kornelia Smalla
The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances in multi-omics tools are dramatically increasing access to the plant microbiome and consequently to the identification of its links with diseases and to the control of those diseases. Recent insights reveal a close, often symbiotic relationship between microorganisms and plants. Microorganisms can stimulate germination and plant growth, prevent diseases, and promote stress resistance and general fitness. Plants and their associated microorganisms form a holo-biont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal, and diverse eukaryotic species...
April 19, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28424249/lignocellulose-pretreatment-in-a-fungus-cultivating-termite
#2
Hongjie Li, Daniel J Yelle, Chang Li, Mengyi Yang, Jing Ke, Ruijuan Zhang, Yu Liu, Na Zhu, Shiyou Liang, Xiaochang Mo, John Ralph, Cameron R Currie, Jianchu Mo
Depolymerizing lignin, the complex phenolic polymer fortifying plant cell walls, is an essential but challenging starting point for the lignocellulosics industries. The variety of ether- and carbon-carbon interunit linkages produced via radical coupling during lignification limit chemical and biological depolymerization efficiency. In an ancient fungus-cultivating termite system, we reveal unprecedentedly rapid lignin depolymerization and degradation by combining laboratory feeding experiments, lignocellulosic compositional measurements, electron microscopy, 2D-NMR, and thermochemolysis...
April 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28421100/integrated-approach-of-agri-nanotechnology-challenges-and-future-trends
#3
REVIEW
Sandhya Mishra, Chetan Keswani, P C Abhilash, Leonardo F Fraceto, Harikesh Bahadur Singh
Nanotechnology representing a new frontier in modern agriculture is anticipated to become a major thrust in near future by offering potential applications. This integrating approach, i.e., agri-nanotechnology has great potential to cope with global challenges of food production/security, sustainability and climate change. However, despite the potential benefits of nanotechnology in agriculture so far, their relevance has not reached up to the field conditions. The elevating concerns about fate, transport, bioavailability, nanoparticles toxicity and inappropriateness of regulatory framework limit the complete acceptance and inclination to adopt nanotechnologies in agricultural sector...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28421041/metagenome-wide-association-study-and-machine-learning-prediction-of-bulk-soil-microbiome-and-crop-productivity
#4
Hao-Xun Chang, James S Haudenshield, Charles R Bowen, Glen L Hartman
Areas within an agricultural field in the same season often differ in crop productivity despite having the same cropping history, crop genotype, and management practices. One hypothesis is that abiotic or biotic factors in the soils differ between areas resulting in these productivity differences. In this study, bulk soil samples collected from a high and a low productivity area from within six agronomic fields in Illinois were quantified for abiotic and biotic characteristics. Extracted DNA from these bulk soil samples were shotgun sequenced...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28420074/natural-pathogen-control-chemistry-to-replace-toxic-treatment-of-microbes-and-biofilm-in-cooling-towers
#5
REVIEW
Lon Brouse, Richard Brouse, Daniel Brouse
Application of toxic antibacterial agents is considered necessary to control prevalent fresh water microorganisms that grow in evaporative cooling water systems, but can adversely affect the environment and human health. However, natural antibacterial water chemistry has been applied in industrial cooling water systems for over 10 years to inhibit microorganisms with excellent results. The water chemistry method concentrates natural minerals in highly-softened water to produce elevated pH and dissolved solids, while maintaining low calcium and magnesium content...
March 31, 2017: Pathogens
https://www.readbyqxmd.com/read/28412534/isolation-and-identification-of-culturable-bacteria-capable-of-heterotrophic-growth-from-rapid-sand-filters-of-drinking-water-treatment-plants
#6
Johanna Vandermaesen, Bart Lievens, Dirk Springael
The microbial community in sand filters (SFs) of drinking water treatment plants (DWTPs) likely contributes to SF functionalities, such as organic carbon removal through heterotrophic metabolism. However, the dynamics and functionality of the SF microbiome and microbial communities in oligotrophic environments, in general, are poorly understood. Therefore, the availability of bacterial cultures from these oligotrophic environments is of great interest, yet it is underrepresented in culture collections. Focusing on heterotrophic carbon metabolism, bacteria were isolated from SFs using conventional media and media that contained SF extracts to mimic the SF environment...
April 12, 2017: Research in Microbiology
https://www.readbyqxmd.com/read/28411219/global-scale-structure-of-the-eelgrass-microbiome
#7
Ashkaan K Fahimipour, Melissa R Kardish, Jenna M Lang, Jessica L Green, Jonathan A Eisen, John J Stachowicz
Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. Here we report results of a global-scale analysis of microbial communities associated with leaf and root surfaces of the marine eelgrass Zostera marina throughout its range in the Northern Hemisphere. By contrasting host microbiomes with those of surrounding seawater and sediment, we uncovered the structure, composition and variability of microbial communities associated with eelgrass...
April 14, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28402786/atractiella-rhizophila-sp-nov-an-endorrhizal-fungus-isolated-from-the-populus-root-microbiome
#8
Gregory Bonito, Khalid Hameed, Merje Toome-Heller, Rosanne Healy, Chantal Reid, Hui-Ling Liao, M Catherine Aime, Christopher Schadt, Rytas Vilgalys
Among fungi isolated from healthy root mycobiomes of Populus, we discovered a new endorrhizal fungal species belonging to the rust lineage Pucciniomycotina, described here as Atractiella rhizophila. We characterized this species by transmission electron microscopy (TEM), phylogenetic analysis, and plant bioassay experiments. Phylogenetic sequence analysis of isolates and available environmental and reference sequences indicates that this new species, A. rhizophila, has a broad geographic and host range. Atractiella rhizophila appears to be present in North America, Australia, Asia, and Africa and is associated with trees, orchids, and other agriculturally important species, including soybean, corn, and rice...
2017: Mycologia
https://www.readbyqxmd.com/read/28400755/comparative-evaluation-of-four-bacteria-specific-primer-pairs-for-16s-rrna-gene-surveys
#9
Sofie Thijs, Michiel Op De Beeck, Bram Beckers, Sascha Truyens, Vincent Stevens, Jonathan D Van Hamme, Nele Weyens, Jaco Vangronsveld
Bacterial taxonomic community analyses using PCR-amplification of the 16S rRNA gene and high-throughput sequencing has become a cornerstone in microbiology research. To reliably detect the members, or operational taxonomic units (OTUs), that make up bacterial communities, taxonomic surveys rely on the use of the most informative PCR primers to amplify the broad range of phylotypes present in up-to-date reference databases. However, primers specific for the domain Bacteria were often developed some time ago against database versions that are now out of date...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28399400/phr1-balances-between-nutrition-and-immunity-in-plants
#10
Hans Motte, Tom Beeckman
Plants assemble beneficial root-associated microbiomes to support growth, especially in nutrient-poor conditions. To do so, however, plants have to suppress their immune system. Reporting in Nature, Castrillo et al. (2017) identified PHOSPHATE STARVATION RESPONSE1 (PHR1) as a central regulator in this balance between nutrient stress response and immune regulation.
April 10, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28396926/comparison-of-microbial-community-shifts-in-two-parallel-multi-step-drinking-water-treatment-processes
#11
Jiajiong Xu, Wei Tang, Jun Ma, Hong Wang
Drinking water treatment processes remove undesirable chemicals and microorganisms from source water, which is vital to public health protection. The purpose of this study was to investigate the effects of treatment processes and configuration on the microbiome by comparing microbial community shifts in two series of different treatment processes operated in parallel within a full-scale drinking water treatment plant (DWTP) in Southeast China. Illumina sequencing of 16S rRNA genes of water samples demonstrated little effect of coagulation/sedimentation and pre-oxidation steps on bacterial communities, in contrast to dramatic and concurrent microbial community shifts during ozonation, granular activated carbon treatment, sand filtration, and disinfection for both series...
April 11, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28392403/matrix-metalloproteinases-outside-vertebrates
#12
Laura Marino-Puertas, Theodoros Goulas, F Xavier Gomis-Rüth
The matrix metalloproteinase (MMP) family belongs to the metzincin clan of zinc-dependent metallopeptidases. Due to their enormous implications in physiology and disease, MMPs have mainly been studied in vertebrates. They are engaged in extracellular protein processing and degradation, and present extensive paralogy, with 23 forms in humans. One characteristic of MMPs is a~165-residue catalytic domain (CD), which has been structurally studied for 14 MMPs from human, mouse, rat, pig and the oral-microbiome bacterium Tannerella forsythia...
April 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28390108/deciphering-conjugative-plasmid-permissiveness-dynamics-in-wastewater-microbiomes
#13
Samuel Jacquiod, Asker Brejnrod, Stefan M Morberg, Waleed Abu Al-Soud, Søren J Sørensen, Leise Riber
Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer (HGT) between bacteria via conjugative plasmids, leading to dissemination of potentially hazardous genetic material such as antimicrobial resistance genes (AMRGs). While current focus is on the threat of AMRGs spreading and environmental maintenance, conjugative plasmid transfer dynamics within and between bacterial communities still remains largely uncharted...
April 8, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28386769/relative-abundance-and-strain-diversity-in-the-bacterial-endosymbiont-community-of-a-sap-feeding-insect-across-its-native-and-introduced-geographic-range
#14
Caroline Fromont, Markus Riegler, James M Cook
Most insects are associated with bacterial symbionts. The bacterial diversity and community composition within hosts may play an important role in shaping insect population biology, ecology and evolution. We focussed on the bacterial microbiome of the Australian fig homotomid Mycopsylla fici (Hemiptera: Psylloidea), which can cause defoliation of its only host tree, Ficus macrophylla. This sap-feeding insect is native to mainland Australia and Lord Howe Island (LHI) but also occurs where its host has been planted, notably in New Zealand...
April 6, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28386252/caenorhabditis-elegans-as-a-model-for-microbiome-research
#15
Fan Zhang, Maureen Berg, Katja Dierking, Marie-Anne Félix, Michael Shapira, Buck S Samuel, Hinrich Schulenburg
The nematode Caenorhabditis elegans is used as a central model system across biological disciplines. Surprisingly, almost all research with this worm is performed in the absence of its native microbiome, possibly affecting generality of the obtained results. In fact, the C. elegans microbiome had been unknown until recently. This review brings together results from the first three studies on C. elegans microbiomes, all published in 2016. Meta-analysis of the data demonstrates a considerable conservation in the composition of the microbial communities, despite the distinct geographical sample origins, study approaches, labs involved and perturbations during worm processing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28383519/cassava-foliage-affects-the-microbial-diversity-of-chinese-indigenous-geese-caecum-using-16s-rrna-sequencing
#16
Mao Li, Hanlin Zhou, Xiangyu Pan, Tieshan Xu, Zhenwen Zhang, Xuejuan Zi, Yu Jiang
Geese are extremely adept in utilizing plant-derived roughage within their diet. However, the intestinal microbiome of geese remains limited, especially the dietary effect on microbial diversity. Cassava foliage was widely used in animal feed, but little information is available for geese. In this study, the geese were fed with control diet (CK), experimental diet supplemented with 5% cassava foliage (CF5) or 10% (CF10) for 42 days, respectively. The cecal samples were collected after animals were killed. High-throughput sequencing technology was used to investigate the microbial diversity in the caecum of geese with different dietary supplements...
April 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28362326/natural-pathogen-control-chemistry-to-replace-toxic-treatment-of-microbes-and-biofilm-in-cooling-towers
#17
REVIEW
Lon Brouse, Richard Brouse, Daniel Brouse
Application of toxic antibacterial agents is considered necessary to control prevalent fresh water microorganisms that grow in evaporative cooling water systems, but can adversely affect the environment and human health. However, natural antibacterial water chemistry has been applied in industrial cooling water systems for over 10 years to inhibit microorganisms with excellent results. The water chemistry method concentrates natural minerals in highly-softened water to produce elevated pH and dissolved solids, while maintaining low calcium and magnesium content...
March 31, 2017: Pathogens
https://www.readbyqxmd.com/read/28351950/papers-of-note-in-nature543-7646
#18
Annalisa M VanHook
This week's articles highlight synaptic organization in sociability, the interactions between a plant and its microbiome, and the role of RNA modification in the response to DNA damage.
March 28, 2017: Science Signaling
https://www.readbyqxmd.com/read/28350798/research-priorities-for-harnessing-plant-microbiomes-in-sustainable-agriculture
#19
Posy E Busby, Chinmay Soman, Maggie R Wagner, Maren L Friesen, James Kremer, Alison Bennett, Mustafa Morsy, Jonathan A Eisen, Jan E Leach, Jeffery L Dangl
Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One way to assist in achieving these goals is to integrate beneficial plant microbiomes-i.e., those enhancing plant growth, nutrient use efficiency, abiotic stress tolerance, and disease resistance-into agricultural production. This integration will require a large-scale effort among academic researchers, industry researchers, and farmers to understand and manage plant-microbiome interactions in the context of modern agricultural systems...
March 2017: PLoS Biology
https://www.readbyqxmd.com/read/28345666/members-of-gammaproteobacteria-as-indicator-species-of-healthy-banana-plants-on-fusarium-wilt-infested-fields-in-central-america
#20
Martina Köberl, Miguel Dita, Alfonso Martinuz, Charles Staver, Gabriele Berg
Culminating in the 1950's, bananas, the world's most extensive perennial monoculture, suffered one of the most devastating disease epidemics in history. In Latin America and the Caribbean, Fusarium wilt (FW) caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (FOC), forced the abandonment of the Gros Michel-based export banana industry. Comparative microbiome analyses performed between healthy and diseased Gros Michel plants on FW-infested farms in Nicaragua and Costa Rica revealed significant shifts in the gammaproteobacterial microbiome...
March 27, 2017: Scientific Reports
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