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Soil microbes

David M Aronoff, Powel H Kazanjian
Clostridium novyi is an anaerobic bacterium that resides in the soil in nature and that may cause severe clinical infections in humans. It is named after Frederick Novy, who incidentally discovered the anaerobic organism responsible for septicemia in rabbits. In this paper, we explore the circumstances surrounding the identification of the organism. In particular, we address who Novy was and what he was trying to do when he first described the organism in the 1890s. We then address what is known about the biological features of the organism today, as well as the clinical syndromes that are now recognized to be associated with the microbe...
February 19, 2018: Anaerobe
Michael T Guarnieri, Mary Ann Franden, Christopher W Johnson, Gregg T Beckham
The sugar dehydration products, furfural and 5-(hydroxymethyl)furfural (HMF), are commonly formed during high-temperature processing of lignocellulose, most often in thermochemical pretreatment, liquefaction, or pyrolysis. Typically, these two aldehydes are considered major inhibitors in microbial conversion processes. Many microbes can convert these compounds to their less toxic, dead-end alcohol counterparts, furfuryl alcohol and 5-(hydroxymethyl)furfuryl alcohol. Recently, the genes responsible for aerobic catabolism of furfural and HMF were discovered in Cupriavidus basilensis HMF14 to enable complete conversion of these compounds to the TCA cycle intermediate, 2-oxo-glutarate...
June 2017: Metabolic Engineering Communications
Joseph E Knelman, Emily B Graham, Janet S Prevéy, Michael S Robeson, Patrick Kelly, Eran Hood, Steve K Schmidt
Past research demonstrating the importance plant-microbe interactions as drivers of ecosystem succession has focused on how plants condition soil microbial communities, impacting subsequent plant performance and plant community assembly. These studies, however, largely treat microbial communities as a black box. In this study, we sought to examine how emblematic shifts from early successional Alnus viridus ssp. sinuata (Sitka alder) to late successional Picea sitchensis (Sitka spruce) in primary succession may be reflected in specific belowground changes in bacterial community structure and nitrogen cycling related to the interaction of these two plants...
2018: Frontiers in Microbiology
Eman M Khalaf, Manish N Raizada
The cucurbit vegetables, including cucumbers, melons and pumpkins, have been cultivated for thousands of years without fungicides. However, their seed germination stage is prone to be infected by soil-borne fungal and oomycete pathogens. Endophytes are symbionts that reside inside plant tissues including seeds. Seed endophytes are founders of the juvenile plant microbiome and can promote host defense at seed germination and later stages. We previously isolated 169 bacterial endophytes associated with seeds of diverse cultivated cucurbits...
2018: Frontiers in Microbiology
Akhilesh Kumar, Jay Prakash Verma
The biotic and abiotic stresses are major constraints for crop yield, food quality and global food security. A number of parameters such as physiological, biochemical, molecular of plants are affected under stress condition. Since the use of inorganic fertilizers and pesticides in agriculture practices cause degradation of soil fertility and environmental pollutions. Hence it is necessary to develop safer and sustainable means for agriculture production. The application of plant growth promoting microbes (PGPM) and mycorrhizal fungi enhance plant growth, under such conditions...
March 2018: Microbiological Research
Shatrupa Ray, Sandhya Mishra, Kartikay Bisen, Surendra Singh, Birinchi Kumar Sarma, Harikesh Bahadur Singh
Phenolics play a key role in communication between plants and microbes in the rhizosphere. In this study, shikimic, gallic, fumaric, ferulic, vanillic acid and quercetin in root exudates of Abelmoschus esculentus act as chemoattractants of endophytic Alcaligenes faecalis strains, BHU 12, BHU 16 and BHU M7. In vitro chemotaxis assay showed that BHU 12 expressed highest chemotactic movement (CFU ∼50×1012 ) towards A.esculentus root exudates followed by BHU 16 and BHU M7 (CFU∼ 9×1012 ), thereby confirming their ability to colonize the host rhizoplane region...
March 2018: Microbiological Research
Nidhi Arora, Sunil Kumar, N Satti, Asif Ali, Prasoon Gupta, Meenu Katoch
AIM: Exploration of microbes isolated from rhizospheric soil of Crataegus oxycantha for bioactive natural products. METHODS AND RESULTS: A strain of Streptomyces sp. (C-7) was isolated from rhizospheric soil of Crataegus oxycantha. The 16S rRNA gene sequence of strain C-7 displayed 99% sequence similarity with different Streptomyces species. The highest score was displayed for Streptomyces sp. strain Chy2-8 followed by Streptomyces violarus strain NBRC13104 and Streptomyces arenae strain ISP5293...
February 19, 2018: Journal of Applied Microbiology
Supratim Basu, Roel C Rabara, Sangeeta Negi, Pratyoosh Shukla
In light of extensive urbanization and deforestation, toxic wastes are being released into the atmosphere, causing increased air and soil pollution. Conventional methods of soil remediation are time consuming and labor and cost intensive, rendering them uneconomical to maintain sustainable agriculture. One solution is to use natural resources like plants and microbes for phytoremediation. A thorough systemic knowledge of plant-microbe interactions will allow the use of gene editing and gene manipulation techniques to increase the efficiency of plants in phytoremediation...
February 15, 2018: Trends in Biotechnology
Petra Bukovská, Michael Bonkowski, Tereza Konvalinková, Olena Beskid, Martina Hujslová, David Püschel, Veronika Řezáčová, María Semiramis Gutiérrez-Núñez, Milan Gryndler, Jan Jansa
Arbuscular mycorrhizal (AM) fungi can significantly contribute to plant nitrogen (N) uptake from complex organic sources, most likely in concert with activity of soil saprotrophs and other microbes releasing and transforming the N bound in organic forms. Here, we tested whether AM fungus (Rhizophagus irregularis) extraradical hyphal networks showed any preferences towards certain forms of organic N (chitin of fungal or crustacean origin, DNA, clover biomass, or albumin) administered in spatially discrete patches, and how the presence of AM fungal hyphae affected other microbes...
February 17, 2018: Mycorrhiza
Janet K Jansson, Kirsten S Hofmockel
Soil microorganisms carry out important processes, including support of plant growth and cycling of carbon and other nutrients. However, the majority of soil microbes have not yet been isolated and their functions are largely unknown. Although metagenomic sequencing reveals microbial identities and functional gene information, it includes DNA from microbes with vastly varying physiological states. Therefore, metagenomics is only predictive of community functional potential. We posit that the next frontier lies in understanding the metaphenome, the product of the combined genetic potential of the microbiome and available resources...
February 15, 2018: Current Opinion in Microbiology
Jia Zhao, Jiang Liu, Hong Liang, Jing Huang, Zhe Chen, Yuanjun Nie, Changbiao Wang, Yuguo Wang
Bio-organic fertilizers (BOFs) combine functional microbes with a suitable substrate and have been shown to effectively suppress soil-borne diseases and promote plant growth. Here, we developed a novel bio-organic fertilizer (BOF) by fermentation of a cow plus chicken manure (M) compost using Fen-liquor Daqu (FLD) as a fermentation starter and compared the compositions of bacterial and fungal communities in the rhizosphere soil of watermelon plants after treatment with different fertilizers. Further, we aimed to explore the mechanisms underlying plant-promoting and disease (Fusarium wilt)-suppressing activities of each rhizosphere microbial community...
2018: PloS One
Sondos Badran, Nathanael Morales, Phillip Schick, Brandon Jacoby, William Villella, Todd Lorenz
Bacillus spp. are ubiquitous Gram-positive microbes with many ecological and symbiotic interactions and can be pathogens. Phage Leo2 was found to infect a Bacillus pumilus strain isolated from soil. The sequence of phage Leo2 revealed 74 genes; 31% of the genes have associated functions, and 67% of coding regions are unidentified open reading frames.
February 15, 2018: Genome Announcements
Corina Diana Ceapă, Melissa Vázquez-Hernández, Stefany Daniela Rodríguez-Luna, Angélica Patricia Cruz Vázquez, Verónica Jiménez Suárez, Romina Rodríguez-Sanoja, Elena R Alvarez-Buylla, Sergio Sánchez
Endophytic bacteria are wide-spread and associated with plant physiological benefits, yet their genomes and secondary metabolites remain largely unidentified. In this study, we explored the genome of the endophyte Streptomyces scabrisporus NF3 for discovery of potential novel molecules as well as genes and metabolites involved in host interactions. The complete genomes of seven Streptomyces and three other more distantly related bacteria were used to define the functional landscape of this unique microbe. The S...
2018: PloS One
Gang Feng, Tian Xie, Xin Wang, Jiuyuan Bai, Lin Tang, Hai Zhao, Wei Wei, Maolin Wang, Yun Zhao
BACKGROUND: Soil contaminated with the heavy metal Cadmium (Cd) is a widespread problem in many parts of the world. Based on metagenomic analysis, we investigated the functional potential and structural diversity of the microbial community in Cd-contaminated and non-contaminated soil samples and we explored the associated metabolic pathway network in cluster of orthologous groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG). RESULTS: The results showed that microorganisms in these soils were quite abundant, and many of them possessed numerous physiological functions...
February 13, 2018: BMC Microbiology
Yu-Ping Yang, Hong-Mei Zhang, Hai-Yan Yuan, Gui-Lan Duan, De-Cai Jin, Fang-Jie Zhao, Yong-Guan Zhu
Arsenic (As) contamination is a global problem. Straw incorporation is widely performed in As contaminated paddy fields. To understand how straw and straw biochar incorporation affect As transformation and translocation in the soil-microbe-rice system, a pot experiment was carried out with different dosages of rice straw and straw biochar application. Results showed that both straw biochar and straw application significantly increased As mobility. Straw biochar mobilized As mainly through increasing soil pH and DOM content...
February 9, 2018: Environmental Pollution
Juejie Yang, Guanghe Li, Yi Qian, Yunfeng Yang, Fang Zhang
Linking microbial community structure to physiology and ecological processes is a critical focus of microbial ecology. To understand the microbial functional gene patterns related to soil greenhouse gas [carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)] emissions under oil contamination, we used functional gene array (GeoChip 5.0) analysis and network methods to investigate the feedback responses of soil microbial functional gene patterns and identify keystone genes in Shengli Oilfield, China. The microbial functional gene number, relative abundance and diversity involved in carbon degradation and nitrogen cycling decreased consistently with the reduced CO2 and N2O flux in oil contaminated soils, whereas the gene number and relative abundance of methane-production related genes increased with contamination...
February 8, 2018: Science of the Total Environment
Yajun Hu, Yinhang Xia, Qi Sun, Kunping Liu, Xiangbi Chen, Tida Ge, Baoli Zhu, Zhenke Zhu, Zhenhua Zhang, Yirong Su
Phosphorus (P) acquisition by plants from soil organic P mainly relies on microorganisms. Examining the community of functional microbes that encode phosphatases (e.g. PhoD) under different fertilization managements may provide valuable information for promoting soil organic P availability. Here, we investigated how the abundance and community diversity of phoD-harboring bacteria responded to long-term fertilization in Karst soils. Six fertilization treatments were designed as follows: non-fertilized control (CK), inorganic fertilization only (NPK), and inorganic fertilization combined with low- and high amounts of straw (LSNPK and HSNPK), or cattle manure (LMNPK and HMNPK)...
February 8, 2018: Science of the Total Environment
Weihui Xu, Yimin You, Zhigang Wang, Wenjing Chen, Jin Zeng, Xiaosong Zhao, Yunpeng Su
Dibutyl phthalate (DBP) is well known as a high-priority pollutant. This study explored the impacts of DBP on the metabolic pathways of microbes in black soils in the short term (20 days). The results showed that the microbial communities were changed in black soils with DBP. In nitrogen cycling, the abundances of the genes were elevated by DBP. DBP contamination facilitated 3'-phosphoadenosine-5'-phosphosulfate (PAPS) formation, and the gene flux of sulfate metabolism was increased. The total abundances of ABC transporters and the gene abundances of the monosaccharide-transporting ATPases MalK and MsmK were increased by DBP...
February 8, 2018: Scientific Reports
Huihui Du, Qiaoyun Huang, Ruijia Yang, Boqing Tie, Ming Lei
Microbe-associated aluminum (Al) hydroxides occur naturally in aquatic and geologic environments and they might play a crucial role in the sequestration of trace metals because these composite solids comprise both reactive mineral and organic surface, but how they do it still remains unknown. Here we replicate Al hydroxide organo-mineral composite formation in soil and sediments by synthesising composites using Pseudomonas putida cells, during coprecipitation with Al hydroxide. Morphological and ATR-FTIR analysis show closely attached nano-sized Al hydroxides on the bacterial surface...
January 29, 2018: Chemosphere
Peng Zhang, Hongwen Sun, Lujuan Min, Chao Ren
One interest of using biochar as soil amendment is to reduce pesticide adverse effects. In this paper, the sorption and degradation of thiacloprid (THI) in a black soil amended by various biochars were systematically investigated, and the mechanisms therein were explored by analyzing the changes in soil physicochemical properties, degrading enzymes and genes and microorganism community. Biochar amendment increased THI sorption in soil, which was associated with an increase in organic carbon and surface area and a decrease in H/C...
January 30, 2018: Environmental Pollution
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