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Environmental Microbiology Reports

Otto X Cordero, Roman Stocker
No abstract text is available yet for this article.
October 19, 2016: Environmental Microbiology Reports
Edward A Bayer
No abstract text is available yet for this article.
October 18, 2016: Environmental Microbiology Reports
Cornelia U Welte, Olivia Rasigraf, Annika Vaksmaa, Wouter Versantvoort, Arslan Arshad, Huub J M Op den Camp, Mike S M Jetten, Claudia Lüke, Joachim Reimann
Microbial methane oxidation is an important process to reduce the emission of the greenhouse gas methane. Anaerobic microorganisms couple the oxidation of methane to the reduction of sulfate, nitrate and nitrite, and possibly oxidized iron and manganese minerals. In this article, we review the recent finding of the intriguing nitrate- and nitrite-dependent anaerobic oxidation of methane (AOM). Nitrate-dependent AOM is catalyzed by anaerobic archaea belonging to the ANME-2d clade closely related to Methanosarcina methanogens...
October 18, 2016: Environmental Microbiology Reports
Mónica Rouco, Sheean T Haley, Harriet Alexander, Samuel T Wilson, David M Karl, Sonya T Dyhrman
Populations of nitrogen-fixing cyanobacteria in the genus Trichodesmium are critical to ocean ecosystems, yet predicting patterns of Trichodesmium distribution and their role in ocean biogeochemistry is an ongoing challenge. This may, in part, be due to differences in the physiological ecology of Trichodesmium species, which are not typically considered independently in field studies. In this study, the abundance of the two dominant Trichodesmium clades (Clade I and Clade III) was investigated during a survey at Station ALOHA in the North Pacific Subtropical Gyre (NPSG) using a clade-specific qPCR approach...
October 18, 2016: Environmental Microbiology Reports
Irene L G Newton
No abstract text is available yet for this article.
October 7, 2016: Environmental Microbiology Reports
Tianle Xu, Stavros D Veresoglou, Yongliang Chen, Matthias C Rillig, Dan Xiang, Daniel Ondrej, Zhipeng Hao, Lei Liu, Ye Deng, Yajun Hu, Weiping Chen, Juntao Wang, Jizheng He, Baodong Chen
Arbuscular mycorrhizal fungi (AMF) are ubiquitous mutualists of terrestrial plants and play key roles in regulating various ecosystem processes, but little is known about AMF biogeography at regional scale. This study aims at exploring the key predictors of AMF communities across a 5000-km transect in northern China. We determined the soil AMF species richness and community composition at 47 sites representative of four vegetation types (meadow steppe, typical steppe, desert steppe and desert) and related them to plant community characteristics, abiotic factors and geographic distance...
October 7, 2016: Environmental Microbiology Reports
Xinhe Huang, Yuxing Li, Jingmei Pan, Ming Li, Yongqin Lai, Jie Gao, Xueru Li
The nonessential metal cadmium can cause cell toxicity and is associated with a range of human diseases including cardiovascular diseases, neurodegenerative diseases and cancers. In this study, cadmium-induced global gene expression profile of yeast was obtained using RNA Sequencing (RNA-Seq) and further analyzed by means of informatics and experiments. A total of 912 Differentially Expressed Genes (DEGs) (FDR of q<0.01), including 415 Cd-inducible and 497 Cd-repressed genes were identified. Based on the DEGs, 25 cadmium responsive Clusters of Orthologous Group (COG) and three types of cadmium-induced Gene Ontology (GO) including cellular components, molecular functions and biological processes were analyzed in details...
October 7, 2016: Environmental Microbiology Reports
Thi Phuong Nam Bui, Sudarshan Shetty, Ilias Lagkouvardos, Jarmo Ritari, Bhawani Chamlagain, Francois Douillard, Lars Paulin, Vieno Piironen, Thomas Clavel, Caroline M Plugge, Willem M de Vos
Intestinimonas is a newly described bacterial genus with representative strains present in the intestinal tract of human and other animals. Despite unique metabolic features including the production of butyrate from both sugars and amino acids, there is to date no data on their diversity, ecology, and physiology. Using a comprehensive phylogenetic approach, Intestinimomas was found to include at least 3 species that colonize primarily the human and mouse intestine. We focused on the most common and cultivable species of the genus, Intestinimonas butyriciproducens, and performed detailed genomic and physiological comparison of strains SRB521(T) and AF211, isolated from the mouse and human gut, respectively...
October 7, 2016: Environmental Microbiology Reports
Zhipeng Li, André-Denis G Wright, Huazhe Si, Xiaoxu Wang, Wenxi Qian, Zhigang Zhang, Guangyu Li
The rumen microbiota plays important roles in nutrient metabolism and absorption of the host. However, it is poorly understood how host genetic variation shapes the community structure of the rumen microbiota and its metabolic phenotype. Here, we used sika deer (Cervus nippon) and elk (Cervus elaphus) to produce the following two types of hybrid offspring: sika deer ♀ × elk ♂ (SEH) and elk ♀ × sika deer ♂ (ESH). Then, we examined the rumen microbiome and metabolites in the parents and their hybrid offspring...
October 7, 2016: Environmental Microbiology Reports
Colleen Hansel
No abstract text is available yet for this article.
October 4, 2016: Environmental Microbiology Reports
Yujie Xiao, Hailing Nie, Huizhong Liu, Wenli Chen, Qiaoyun Huang
Cyclic di-GMP (c-di-GMP), a ubiquitous bacterial second messenger that regulates diverse cellular processes, is synthesized by diguanylate cyclase (DGC) and degraded by phosphodiesterase (PDE). GcbA is a well conserved DGC among Pseudomonas species, and has been reported to influence biofilm formation and flagellar motility in Pseudomonas fluorescens and Pseudomonas aeruginosa. Here we confirm the function of GcbA in Pseudomonas putida and reveal that expression of GcbA is regulated by FleQ in response to c-di-GMP...
October 4, 2016: Environmental Microbiology Reports
Christopher T Lefèvre, Paul A Howse, Marian L Schmidt, Monique Sabaty, Nicolas Menguy, George W Luther, Dennis A Bazylinski
Although dissimilatory sulfate-reducing bacteria (SRB) are generally described as strictly anaerobic organisms with regard to growth, several reports have shown that some SRB, particularly Desulfovibrio species, are quite resistant to O2 . For example, SRB remain viable in many aerobic environments while some even reduce O2 to H2 O. However, reproducible aerobic growth of SRB has not been unequivocally documented. Desulfovibrio magneticus is a SRB that is also a magnetotactic bacterium (MTB). MTB biomineralize magnetosomes which are intracellular, membrane-bounded, magnetic iron mineral crystals...
October 4, 2016: Environmental Microbiology Reports
Geoffrey Michael Gadd
No abstract text is available yet for this article.
October 4, 2016: Environmental Microbiology Reports
Man-Young Jung, Jong-Geol Kim, Jaap S Sinninghe Damsté, W Irene C Rijpstra, Eugene L Madsen, So-Jeong Kim, Heeji Hong, Ok-Ja Si, Melina Kerou, Christa Schleper, Sung-Keun Rhee
A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically, strain MY3 falls in clade 'Nitrosocosmicus' of the thaumarchaeotal group I.1b. The cells of strain MY3 are large "walnut-like" cocci, divide by binary fission along a central cingulum, and form aggregates. Strain MY3 is mesophilic and neutrophilic...
October 4, 2016: Environmental Microbiology Reports
Lawrence P Wackett
No abstract text is available yet for this article.
September 27, 2016: Environmental Microbiology Reports
Xiaochen Yang, Sheila I Jensen, Tune Wulff, Scott J Harrison, Katherine S Long
Small proteins of 50 amino acids or less have been understudied due to difficulties that impede their annotation and detection. In order to obtain information on small open reading frames (sORFs) in Pseudomonas putida, bioinformatic and proteomic approaches were used to identify putative sORFs in the well-characterized strain KT2440. A plasmid-based system was established for sORF validation, enabling expression of C-terminal sequential peptide affinity tagged variants and their detection via protein immunoblotting...
September 22, 2016: Environmental Microbiology Reports
Michaela Hayer, Egbert Schwartz, Jane C Marks, Benjamin J Koch, Ember M Morrissey, Alexa A Schuettenberg, Bruce A Hungate
Identification of microorganisms that facilitate the cycling of nutrients in freshwater is paramount to understanding how these ecosystems function. Here, we identify growing aquatic bacteria using H218O quantitative stable isotope probing. During 8 day incubations in 97 atom % H218O, 54% of the taxa grew. The most abundant phyla among growing taxa were Proteobacteria (45%), Bacteroidetes (30%) and Firmicutes (10%). Taxa differed in isotopic enrichment, reflecting variation in DNA replication of bacterial populations...
September 22, 2016: Environmental Microbiology Reports
Nancy A Moran
No abstract text is available yet for this article.
September 8, 2016: Environmental Microbiology Reports
Zaenab A Fahad, Emile B Bolou-Bi, Stephan J Köhler, Roger D Finlay, Shahid Mahmood
Symbiotic ectomycorrhizal fungi mobilise nutrients from both organic and inorganic substrates and supply them to their host plants. Their role in mobilising base cations and phosphorus from mineral substrates through weathering has received increasing attention in recent years but the processes involved remain to be elucidated. We grew selected ectomycorrhizal and nonmycorrhizal fungi in axenic systems containing mineral and organic substrates and examined their capacity to fractionate and assimilate stable isotopes of magnesium...
September 2, 2016: Environmental Microbiology Reports
Massimiliano Marvasi, Marcos H de Moraes, Isai Salas-Gonzalez, Steffen Porwollik, Marcelo Farias, Michael McClelland, Max Teplitski
It is becoming clear that human enteric pathogens, like Salmonella, can efficiently colonize vegetative and reproductive organs of plants. Even though the bacterium's ability to proliferate within plant tissues has been linked to outbreaks of salmonellosis, little is known about regulatory and physiological adaptations of Salmonella, or other human pathogens, to their persistence in plants. A screen of Salmonella deletion mutants in tomatoes identified rcsA and rcsB genes as those under positive selection. In tomato fruits, populations of Salmonella rcsB mutants were as much as 100-fold lower than those of the wild type...
August 25, 2016: Environmental Microbiology Reports
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