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Bo Cao, Ying Zhang, Ziyi Wang, Mengyuan Li, Feng Yang, Duo Jiang, Zhao Jiang
Although plants of the genus Pennisetum can accelerate the removal of atrazine from its rhizosphere, the roles played by this plant in adjusting the soil environment and soil microorganism properties that might contribute to pollutant removal are incompletely understood. We selected Pennisetum americanum (L.) K. Schum ( P. americanum ) as the test plant and investigated the interaction between P. americanum and atrazine-contaminated soil, focusing on the adjustment of the soil biochemical properties as well as bacterial functional and community diversity in the rhizosphere using Biolog EcoPlates and high-throughput sequencing of the 16S rRNA gene...
2018: Frontiers in Microbiology
Michael F Freeman
Cobalamin-dependent radical S-adenosylmethionine (rSAM) methyltransferases catalyze chemically challenging methylation reactions on diverse natural products at unactivated carbon centers. In vivo reconstitution and biosynthetic studies of natural product gene clusters encoding these enzymes are often severely limited by ineffective heterologous expression hosts, including the otherwise versatile Escherichia coli. In this chapter, we describe the use of rhizobia bacteria as effective expression hosts for cobalamin-dependent rSAM C-methyltransferases...
2018: Methods in Enzymology
Beate Thal, Hans-Peter Braun, Holger Eubel
Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins...
May 19, 2018: Plant Molecular Biology
Julio Guerrero-Castro, Luis Lozano, Christian Sohlenkamp
Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic and physiological basis of the tolerance to acidic conditions. To identify genes in R. tropici involved in pH stress response we combined two different approaches: (1) A Tn 5 mutant library of R...
2018: Frontiers in Microbiology
Daiane R B Belgini, Virgínia M Siqueira, Douglas M Oliveira, Samantha G Fonseca, Viviane Piccin-Santos, Roberto S Dias, Larissa Quartaroli, Rodrigo S Souza, Ana Paula R Torres, Maíra P Sousa, Cláudio M Silva, Cynthia C Silva, Sérgio O De Paula, Valéria M Oliveira
Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality...
April 13, 2018: Systematic and Applied Microbiology
Marzena Sujkowska-Rybkowska, Rafał Ważny
This present paper studies the response of Anthyllis vulneraria-Rhizobium symbiosis to heavy metal stress. The symbiotic rhizobium bacteria isolated from root nodules of A. vulneraria from zinc and lead wastes were examined in this project. Light microscopy (LM) and transmission electron microscopy (TEM) were used to analyze the nodule anatomy and ultrastructure and conduct a comparison with nonmetal-treated nodules. 16S ribosomal DNA sequence analysis of bacteria isolated from metal-treated nodules revealed the presence of Rhizobium metallidurans and Bradyrhizobium sp...
June 7, 2018: International Journal of Phytoremediation
Haifeng Li, Zhijian Li, Jianhang Qu, Hailong Tian, Xiaohong Yang
Simulation experiments were conducted using sediments collected from the Taihu Lake to determine the combined effects of submerged macrophytes Ceratophyllum demersum and phosphate-solubilizing bacteria (PSB) strain XMT-5 (Rhizobium sp.) on phosphorus (P) concentrations in overlying waters and sediments. After 30 days of experimental incubation, the total phosphorus (TP) and dissolved total phosphorus (DTP) concentrations of the overlying water subjected to AMB and AHMB treatments (both with the combined effects of PSB cells and submerged macrophytes) were generally lower than those of the AM (with individual effects of inoculated C...
May 2, 2018: Environmental Science and Pollution Research International
Dominika Thiem, Marcin Gołębiewski, Piotr Hulisz, Agnieszka Piernik, Katarzyna Hrynkiewicz
Black alder ( Alnus glutinosa Gaertn.) belongs to dual mycorrhizal trees, forming ectomycorrhizal (EM) and arbuscular (AM) root structures, as well as represents actinorrhizal plants that associate with nitrogen-fixing actinomycete Frankia sp. We hypothesized that the unique ternary structure of symbionts can influence community structure of other plant-associated microorganisms (bacterial and fungal endophytes), particularly under seasonally changing salinity in A. glutinosa roots. In our study we analyzed black alder root bacterial and fungal microbiome present at two forest test sites (saline and non-saline) in two different seasons (spring and fall)...
2018: Frontiers in Microbiology
Robin van Velzen, Rens Holmer, Fengjiao Bu, Luuk Rutten, Arjan van Zeijl, Wei Liu, Luca Santuari, Qingqin Cao, Trupti Sharma, Defeng Shen, Yuda Roswanjaya, Titis A K Wardhani, Maryam Seifi Kalhor, Joelle Jansen, Johan van den Hoogen, Berivan Güngör, Marijke Hartog, Jan Hontelez, Jan Verver, Wei-Cai Yang, Elio Schijlen, Rimi Repin, Menno Schilthuizen, M Eric Schranz, Renze Heidstra, Kana Miyata, Elena Fedorova, Wouter Kohlen, Ton Bisseling, Sandra Smit, Rene Geurts
Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium...
May 1, 2018: Proceedings of the National Academy of Sciences of the United States of America
A A Igolkina, Yu B Porozov, E P Chizhevskaya, E E Andronov
Sandwich-like docking configurations of the heterodimeric complex of NFR5 and K1 Vicia sativa receptor-like kinases together with the putative ligand, Nod factor (NF) of Rhizobium leguminosarum bv. viciae , were modeled and two of the most probable configurations were assessed through the analysis of the mutual polymorphisms and conservatism. We carried out this analysis based on the hypothesis that in a contact zone of two docked components (proteins or ligands) the population polymorphism or conservatism is mutual, i...
2018: Frontiers in Plant Science
Xinye Wang, Liang Zhao, Lu Zhang, Yuanyuan Wu, Minxia Chou, Gehong Wei
Rhizobial symbiotic plasmids play vital roles in mutualistic symbiosis with legume plants by executing the functions of nodulation and nitrogen fixation. To explore the gene composition and genetic constitution of rhizobial symbiotic plasmids, comparison analyses of 24 rhizobial symbiotic plasmids derived from four rhizobial genera was carried out. Results illustrated that rhizobial symbiotic plasmids had higher proportion of functional genes participating in amino acid transport and metabolism, replication; recombination and repair; carbohydrate transport and metabolism; energy production and conversion and transcription...
April 26, 2018: Letters in Applied Microbiology
Rachel M Wheatley, Philip S Poole
The attachment of bacteria to roots constitutes the first physical step in many plant-microbe interactions. These interactions exert both positive and negative influences on agricultural systems depending on whether a growth-promoting, symbiotic, or pathogenic relationship transpires. A common biphasic mechanism of root attachment exists across agriculturally important microbial species, including Rhizobium, Agrobacterium, Pseudomonas, Azospirillum and Salmonella. Attachment studies have revealed how plant-microbe interactions develop, and how to manipulate these relationships for agricultural benefit...
April 17, 2018: FEMS Microbiology Reviews
Matthew Nelson, Joseph Guhlin, Brendan Epstein, Peter Tiffin, Michael J Sadowsky
Ensifer meliloti (formerly Rhizobium meliloti and Sinorhizobium meliloti) is a model bacterium for understanding legume-rhizobial symbioses. The tripartite genome of E. meliloti consists of a chromosome, pSymA and pSymB, and in some instances strain-specific accessory plasmids. The majority of previous sequencing studies have relied on the use of assemblies generated from short read sequencing, which leads to gaps and assembly errors. Here we used PacBio-based, long-read assemblies and were able to assemble, de novo, complete circular replicons...
April 19, 2018: Microbial Genomics
Katarzyna Siegel-Hertz, Véronique Edel-Hermann, Emilie Chapelle, Sébastien Terrat, Jos M Raaijmakers, Christian Steinberg
Disease-suppressive soils are soils in which specific soil-borne plant pathogens cause only limited disease although the pathogen and susceptible host plants are both present. Suppressiveness is in most cases of microbial origin. We conducted a comparative metabarcoding analysis of the taxonomic diversity of fungal and bacterial communities from suppressive and non-suppressive (conducive) soils as regards Fusarium wilts sampled from the Châteaurenard region (France). Bioassays based on Fusarium wilt of flax confirmed that disease incidence was significantly lower in the suppressive soil than in the conducive soil...
2018: Frontiers in Microbiology
Yue Hu, Jian Jiao, Li Xue Liu, Yan Wei Sun, Wenfeng Chen, Xinhua Sui, Wenxin Chen, Chang Fu Tian
Phosphate homeostasis is tightly modulated in all organisms including bacteria, which harbor both high- and low-affinity transporters acting under conditions of fluctuating phosphate levels. It was thought that nitrogen-fixing rhizobia, named as bacteroids, inhabiting root nodules of legumes are not phosphate limited. Here we show that the high-affinity phosphate transporter PstSCAB other than the low-affinity phosphate transporter Pit is essential for effective nitrogen fixation of Sinorhizobium fredii in soybean nodules...
April 17, 2018: Molecular Plant-microbe Interactions: MPMI
Christina Birnbaum, Andrew Bissett, Francois P Teste, Etienne Laliberté
Long-term soil age gradients are useful model systems to study how changes in nutrient limitation shape communities of plant root mutualists because they represent strong natural gradients of nutrient availability, particularly of nitrogen (N) and phosphorus (P). Here, we investigated changes in the dinitrogen (N2 )-fixing bacterial community composition and diversity in nodules of a single host legume (Acacia rostellifera) across the Jurien Bay chronosequence, a retrogressive 2 million-year-old sequence of coastal dunes representing an exceptionally strong natural soil fertility gradient...
April 16, 2018: Microbial Ecology
Uliana Ya Stambulska, Maria M Bayliak, Volodymyr I Lushchak
Most legume species have the ability to establish a symbiotic relationship with soil nitrogen-fixing rhizobacteria that promote plant growth and productivity. There is an increasing evidence of reactive oxygen species (ROS) important role in formation of legume-rhizobium symbiosis and nodule functioning. Environmental pollutants such as chromium compounds can cause damage to rhizobia, legumes, and their symbiosis. In plants, toxic effects of chromium(VI) compounds are associated with the increased production of ROS and oxidative stress development as well as with inhibition of pigment synthesis and modification of virtually all cellular components...
2018: BioMed Research International
Brittney N Wyatt, Leggy A Arnold, Martin St Maurice
Pyruvate carboxylase (PC) catalyzes the conversion of pyruvate to oxaloacetate (OAA), an important metabolic reaction in a wide range of organisms. Small molecules directed against PC would enable detailed studies on the metabolic role of this enzyme and would have the potential to be developed into pharmacological agents. Currently, specific and potent small molecule regulators of PC are unavailable. To assist in efforts to find, develop, and characterize small molecule effectors of PC, a novel fixed-time assay has been developed based on the reaction of OAA with the diazonium salt, Fast Violet B (FVB), which produces a colored adduct with an absorbance maximum at 530 nm...
April 12, 2018: Analytical Biochemistry
Ryota Miyazaki, Tomohiko Yamazaki, Keiichi Yoshimatsu, Katsuhiro Kojima, Ryutaro Asano, Koji Sode, Wakako Tsugawa
Glucoside 3‑dehydrogenase (G3DH) is a flavin adenine dinucleotide (FAD)-containing oxidoreductase that catalyzes the oxidation of the hydroxy group on the C-3 position of pyranose and shows broad substrate specificity by oxidizing many saccharides. Due to unique site specificity and wide substrate specificity, G3DHs can be used for synthesis of sugar derivatives, anodic catalysis in biofuel cells, multi-sugar analysis using enzyme electrode, and for enzymatic detection of 1,5‑anhydro‑d‑glucitol, a clinical marker for diabetes...
March 7, 2018: Bioelectrochemistry
Clarissien Ramongolalaina, Masayoshi Teraishi, Yutaka Okumoto
Soybean plants establish symbiotic relationships with soil rhizobia which form nodules on the plant roots. Nodule formation starts when the plant roots exudate isoflavonoids that induce nod gene expression of a specific Bradyrhizobium. We examined the specific indigenous rhizobia that form nodules with the soybean cultivars Peking and Tamahomare in different soils. PCR-RFLP analysis targeted to the 16S-23S rRNA gene internal transcribed spacer (ITS) region of the bacterial type of each root nodule showed that Bradyrhizobium japonicum (USDA110-type) and Bradyrhizobium elkanii (USDA94-type) had high compatibility with the Tamahomare and Peking cultivars, respectively...
2018: PloS One
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