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Soil microbes

Stijn van Gils, Giovanni Tamburini, Lorenzo Marini, Arjen Biere, Maaike van Agtmaal, Olaf Tyc, Martine Kos, David Kleijn, Wim H van der Putten
There is increasing evidence showing that microbes can influence plant-insect interactions. In addition, various studies have shown that aboveground pathogens can alter the interactions between plants and insects. However, little is known about the role of soil-borne pathogens in plant-insect interactions. It is also not known how environmental conditions, that steer the performance of soil-borne pathogens, might influence these microbe-plant-insect interactions. Here, we studied effects of the soil-borne pathogen Rhizoctonia solani on aphids (Sitobion avenae) using wheat (Triticum aestivum) as a host...
2017: PloS One
Muhammad Khalid, Danial Hassani, Muhammad Bilal, Fayaz Asad, Danfeng Huang
BACKGROUND: This study evaluates the influences of bio fertilizers containing mycorrhizal fungi (Glomus fasciculatum, Glomus mosseae) individually or in combination with N-fixer (Azotobacter chroococcum), K solubilizer (Bacillus mucilaginous) and P solubilizer (Bacillus megaterium) on soil fertility and phytochemical levels of spinach. RESULTS: Root colonization by mycorrhizal fungi was increased in the presence of bacterial inoculation in comparison to individual inoculation treatments...
August 16, 2017: Botanical Studies (Taipei, Taiwan)
Longfei Jiang, Zhineng Cheng, Dayi Zhang, Mengke Song, Yujie Wang, Chunling Luo, Hua Yin, Jun Li, Gan Zhang
Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e...
August 8, 2017: Environmental Pollution
Yunzeng Zhang, Jin Xu, Nadia Riera, Tao Jin, Jinyun Li, Nian Wang
BACKGROUND: Roots are the primary site for plant-microbe interactions. Among the three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), the rhizoplane is a key component serving a critical gating role that controls microbial entry into plant roots. The microbial communities colonizing the three layers are believed to be gradually enriched from the bulk soil inoculum. However, it is unknown how this enrichment process, particularly the rhizosphere to rhizoplane step, is affected by biotic stresses, such as disease...
August 10, 2017: Microbiome
Mohammad S Khan, Syed U Sadat, Asad Jan, Iqbal Munir
Transgenic Brassica napus harboring the synthetic chitinase (NiC) gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC) showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen...
2017: Frontiers in Plant Science
Xiaoli Song, Jianxing Zhu, Nianpeng He, Jianhui Huang, Jing Tian, Xiang Zhao, Yuan Liu, Changhui Wang
Rewetting after precipitation events plays an important role in regulating soil carbon (C) and nitrogen (N) turnover processes in arid and semiarid ecosystems. Here, we conducted a 48-h rewetting simulation experiment with measurements of soil C and N mineralization rates (R C and R N, respectively) and microbial biomass N (MBN) at high temporal resolution to explore the pulse responses of R C and R N. R C and R N responded strongly and rapidly to rewetting over the short term. The maximum R C value (because of pulse effects) ranged from 16...
August 8, 2017: Scientific Reports
Eric A Griffin, S Joseph Wright, Peter J Morin, Walter P Carson
Producing and retaining leaves underlie the performance and survivorship of seedlings in deeply shaded tropical forests. These habitats are characterized by conditions ideal for foliar bacteria, which can be potent plant pathogens. Leaf production, retention and susceptibility to enemies may ultimately depend upon interactions among soil nutrients and foliar microbes, yet this has never been tested. We experimentally evaluated the degree that foliar bacteria and soil resource supply mediate leaf dynamics for five common tree species (five different families) in a Panamanian forest...
August 7, 2017: New Phytologist
Sijing Chang, Gaosen Zhang, Ximing Chen, Haozhi Long, Yilin Wang, Tuo Chen, Guangxiu Liu
Pedobacter steynii DX4 was isolated from the soil of Tibetan Plateau and it can use crude oil as sole carbon and energy source at 15 °C. The genome of Pedobacter steynii DX4 has been sequenced and served as basis for analysis its metabolic mechanism. It is the first genome of crude oil degrading strain in Pedobacter genus. The 6.58 Mb genome has an average G + C content of 41.31% and encodes 5464 genes. In addition, annotation revealed that Pedobacter steynii DX4 has cold shock proteins, abundant response regulators for cell motility, and enzymes involved in energy conversion and fatty acid metabolism...
2017: Standards in Genomic Sciences
Andre A Pulschen, Amanda G Bendia, Ashwana D Fricker, Vivian H Pellizari, Douglas Galante, Fabio Rodrigues
Uncultured microorganisms comprise most of the microbial diversity existing on our planet. Despite advances in environmental sequencing and single-cell genomics, in-depth studies about bacterial metabolism and screening of novel bioproducts can only be assessed by culturing microbes in the laboratory. Here we report uncultured, or recalcitrant, microorganisms from an Antarctic soil sample, using relatively simple methods: oligotrophic media, extended incubation periods, observation under stereo microscopy, and selection of slow-growing bacteria...
2017: Frontiers in Microbiology
Briana Vecchio-Pagan, Sharon Bewick, Kumar Mainali, David K Karig, William F Fagan
Ecological stoichiometry (ES) uses organism-specific elemental content to explain differences in species life histories, species interactions, community organization, environmental constraints and even ecosystem function. Although ES has been successfully applied to a range of different organisms, most emphasis on microbial ecological stoichiometry focuses on lake, ocean, and soil communities. With the recent advances in human microbiome research, however, large amounts of data are being generated that describe differences in community composition across body sites and individuals...
2017: Frontiers in Microbiology
Shu-Hong Wu, Bing-Hong Huang, Chia-Lung Huang, Gang Li, Pei-Chun Liao
The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils...
August 1, 2017: Microbial Ecology
Chao Ju, Jun Xu, Xiaohu Wu, Fengshou Dong, Xingang Liu, Chunyan Tian, Yongquan Zheng
The ecological risks of widely used hexaconazole on soil microbes remain obscure. Thus, a 3-month-long experiment using two typical paddy soils in China (red soil and black soil) was conducted to assess the effects of hexaconazole (0.6 (T1) and 6 (T10) mgkg(-1) soil) on the overall microbial biomass, respiratory activity, bacterial abundance and community structure, and nitrogen transformations. Soil was sampled after 7, 15, 30, 60, and 90days of incubation. The half-lives of the two doses of hexaconazole varied from 122 to 135d in the black soil and from 270 to 845d in the red soil...
July 28, 2017: Science of the Total Environment
Qinglong Liu, Jingchun Tang, Xiaomei Liu, Benru Song, Meinan Zhen, Nicholas J Ashbolt
AIMS: Study the response of microbial communities and selected petroleum hydrocarbon (PH)-degrading genes on simulated PH spills in soils/sediments from different geographic locations. METHODS AND RESULTS: A microcosm experiment was conducted by spiking mixtures of petroleum hydrocarbons to soils/sediments collected from four different regions of China, including the Dagang Oilfield (DG), Sand of Bohai Sea (SS), Northeast China (NE), and Xiamen (XM). Changes in bacterial community and the abundance of PH-degrading genes (alkB, nah, and phe) were analyzed by denaturing gradient electrophoresis (DGGE) and qPCR, respectively...
August 1, 2017: Journal of Applied Microbiology
Venkadasamy Govindasamy, Priya George, Lalitkumar Aher, Shunmugiah V Ramesh, Arunachalam Thangasamy, Sivalingam Anandan, Susheel Kumar Raina, Mahesh Kumar, Jagadish Rane, Kannepalli Annapurna, Paramjit Singh Minhas
Symbiotic effectiveness of rhizobitoxine (Rtx)-producing strains of Bradyrhizobium spp. in soybean (cultivar NRC-37/Ahilya-4) under limited soil moisture conditions was evaluated using phenomics tools such as infrared(IR) thermal and visible imaging. Red, green and blue (RGB) colour pixels were standardized to analyse a total of 1017 IR thermal and 692 visible images. Plants inoculated with the Rtx-producing strains B. elkanii USDA-61 and USDA-94 and successive inoculation by B. diazoefficiens USDA-110 resulted in cooler canopy temperatures and increased canopy greenness...
July 31, 2017: Scientific Reports
Zhaoyu Kong, Bernard R Glick
Phytoremediation is a promising technology that uses plants and their associated microbes to clean up contaminants from the environment. In recent years, phytoremediation assisted by plant growth-promoting bacteria (PGPB) has been highly touted for cleaning up toxic metals from soil. PGPB include rhizospheric bacteria, endophytic bacteria and the bacteria that facilitate phytoremediation by other means. This review provides information about the traits and mechanisms possessed by PGPB that improve plant metal tolerance and growth, and illustrate mechanisms responsible for plant metal accumulation/translocation in plants...
2017: Advances in Microbial Physiology
Ana Pineda, Ian Kaplan, T Martijn Bezemer
Soil-borne microbes affect aboveground herbivorous insects through a cascade of molecular and chemical changes in the plant, but knowledge of these microbe-plant-insect interactions is mostly limited to one or a few microbial strains. Yet, the soil microbial community comprises thousands of unique taxa interacting in complex networks, the so-called 'microbiome', which provides plants with multiple beneficial functions. There has been little exploration of the role and management of whole microbiomes in plant-insect interactions, calling for the integration of this complexity in aboveground-belowground research...
July 27, 2017: Trends in Plant Science
Shantanu P Shukla, Heiko Vogel, David G Heckel, Andreas Vilcinskas, Martin Kaltenpoth
Necrophagous beetles utilize carrion, a highly nutritious resource that is susceptible to intense microbial competition, by treating it with antimicrobial anal and oral secretions. However, how this regulates the carcass microbiota remains unclear. Here, we show that carcasses prepared by the burying beetle Nicrophorus vespilloides undergo significant changes in their microbial communities subsequent to their burial and 'preparation'. Prepared carcasses hosted a microbial community that was more similar to that of beetles' anal and oral secretions than to the native carcass community or the surrounding soil, indicating that the beetles regulated the carcass microbiota...
July 27, 2017: Molecular Ecology
Casper N Kamutando, Surendra Vikram, Gilbert Kamgan-Nkuekam, Thulani P Makhalanyane, Michelle Greve, Johannes J Le Roux, David M Richardson, Don Cowan, Angel Valverde
Invasiveness and the impacts of introduced plants are known to be mediated by plant-microbe interactions. Yet, the microbial communities associated with invasive plants are generally poorly understood. Here we report on the first comprehensive investigation of the bacterial and fungal communities inhabiting the rhizosphere and the surrounding bulk soil of a widespread invasive tree, Acacia dealbata. Amplicon sequencing data indicated that rhizospheric microbial communities differed significantly in structure and composition from those of the bulk soil...
July 26, 2017: Scientific Reports
Lawrence G Oates, Harry W Read, Jessica L M Gutknecht, David S Duncan, Teri B Balser, Randall D Jackson
Microbial communities are important drivers and regulators of ecosystem processes. To understand how management of ecosystems may affect microbial communities, a relatively precise but effort-intensive technique to assay microbial community composition is phospholipid fatty acid (PLFA) analysis. PLFA was developed to analyze phospholipid biomarkers, which can be used as indicators of microbial biomass and the composition of broad functional groups of fungi and bacteria. It has commonly been used to compare soils under alternative plant communities, ecology, and management regimes...
July 16, 2017: Journal of Visualized Experiments: JoVE
Yulian Zhao, Faqin Dong, Qunwei Dai, Gang Li, Jie Ma
This paper aimed to investigate the variation of preserving organic matter bound in the interlayer space of montmorillonite (Mt) induced by a microbe metabolic process. We selected Bacillus pumilus as the common soil native bacteria. The alteration of d 001 value, functional group, and C,N organic matter contents caused by bacteria were analyzed by XRD, FTIR, and elementary analyzer, respectively. XRD results showed that the d 001 value of montmorillonite increased with the concentration decreasing and decreased with the culture time increasing after interacting with bacteria indicating the interlayer space of montmorillonite was connected with the organic matter...
July 25, 2017: Environmental Science and Pollution Research International
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