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Environmental Microbiology

Zhibing Luo, Hui Ren, Jarrod J Mousa, Drauzio Rangel, Yongjun Zhang, Steven D Bruner, Nemat O Keyhani
The PacC transcription factor is an important component of the fungal ambient pH-responsive regulatory system. Loss of pacC in the insect pathogenic fungus Beauveria bassiana resulted in an alkaline pH-dependent decrease in growth and pH-dependent increased susceptibility to osmotic (salt, sorbitol) stress and SDS. Extreme susceptibility to Congo Red was noted irrespective of pH, and ΔBbpacC conidia showed subtle increases in UV susceptibility. The ΔBbPacC mutant showed a reduced ability to acidify media during growth due to failure to produce oxalic acid...
January 12, 2017: Environmental Microbiology
Roman A Barco, Colleen L Hoffman, Gustavo A Ramírez, Brandy M Toner, Katrina J Edwards, Jason B Sylvan
Sulfide mineral precipitation occurs at mid-ocean ridge (MOR) spreading centers, both in the form of plume particles and seafloor massive sulfide structures. A common constituent of MOR is the iron-bearing sulfide mineral pyrrhotite, which was chosen as a substrate for in-situ incubation studies in shallow waters of Catalina Island, CA to investigate the colonization of iron-oxidizing bacteria. Microbial community datasets were obtained from in-situ incubated pyrrhotite, allowing for direct comparison to microbial communities of iron-sulfides from active and inactive chimneys in deep-sea environments...
January 12, 2017: Environmental Microbiology
Carmen Astudillo-Garcia, James J Bell, Nicole S Webster, Bettina Glasl, Jamaluddin Jompa, Jose M Montoya, Michael W Taylor
The study of complex microbial communities poses unique conceptual and analytical challenges, with microbial species potentially numbering in the thousands. With transient or allochthonous microorganisms often adding to this complexity, a 'core' microbiota approach, focusing only on the stable and permanent members of the community, is becoming increasingly popular. Given the various ways of defining a core microbiota, it is prudent to examine whether the definition of the core impacts upon the results obtained...
January 12, 2017: Environmental Microbiology
Jing Liu, Zhi-Kang Wang, Huan-Huan Sun, Sheng-Hua Ying, Ming-Guang Feng
High-osmolarity glycerol (HOG) pathway required for yeast osmoregulation relies upon the mitogen-activated protein kinase (MAPK) Hog1 cascade that comprise the MAPKKKs Ssk2/Ssk22 and Ste11 converging on the MAPKK Pbs2. Here we show a Hog1 cascade with the unique MAPKKK Ssk2 acting in Beauveria bassiana. Hypersensitivity to high osmolarity and high resistance to fludioxonil fungicide appeared in Δssk2, Δpbs2 and Δhog1 mutants whereas the two hallmark phenotypes were reversed in Δste11. Increased sensitivity to heat shock and decreased sensitivity to cell wall perturbation also occurred in the three mutants but not in Δste11 although antioxidant phenotypes were different in all deletion mutants...
January 11, 2017: Environmental Microbiology
J Uehling, A Gryganskyi, K Hameed, T Tschaplinski, P K Misztal, S Wu, A Desirò, N Vande Pol, Z Du, A Zienkiewicz, K Zienkiewicz, E Morin, E Tisserant, R Splivallo, M Hainaut, B Henrissat, R Ohm, A Kuo, J Yan, A Lipzen, M Nolan, K LaButti, K Barry, A H Goldstein, J Labbé, C Schadt, G Tuskan, I Grigoriev, F Martin, R Vilgalys, G Bonito
Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants, and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within in a lineage of endofungal symbionts that are sister clade to Burkholderia...
January 11, 2017: Environmental Microbiology
Jeanne Doré, Annegret Kohler, Audrey Dubost, Hope Hundley, Vasanth Singan, Yi Peng, Alan Kuo, Igor V Grigoriev, Francis Martin, Roland Marmeisse, And Gilles Gay
To clarify the early molecular interaction between ectomycorrhizal partners, we performed a RNA-Seq study of transcriptome reprogramming of the basidiomycete Hebeloma cylindrosporum before symbiotic structure differentiation with Pinus pinaster. Mycorrhiza transcriptome was studied for comparison. By reference to asymbiotic mycelium, 47 and 46 genes were specifically up-regulated over five-fold (p≤0.05) upon rhizosphere colonization and root adhesion respectively. Other 45 were up-regulated throughout the symbiotic interaction, from rhizosphere colonization to differentiated mycorrhizas, whereas 274 were specifically up-regulated in mycorrhizas...
January 11, 2017: Environmental Microbiology
Tanja Shabarova, Vojtěch Kasalický, Karel Šimek, Jiří Nedoma, Petr Znachor, Thomas Posch, Jakob Pernthaler, Michaela M Salcher
The ecological relevance and factors shaping dynamics of Limnohabitans sp. have been largely studied by fluorescence in situ hybridisation (CARD-FISH) with a 16S rRNA probe targeting the R-BT group (lineages LimBCDE), but not lineage LimA. Consequently, ecology and distribution of LimA remained unknown. We developed a double hybridisation strategy using a novel 23S rRNA probe specifically targeting LimA and LimE that in combination with the existing R-BT probe can discriminate LimA populations. This technique was applied for more than 1000 samples from 46 freshwater sites including long-term data sets from oligomesotrophic Lake Zurich, CH and mesoeutrophic Římov reservoir, CZ...
January 7, 2017: Environmental Microbiology
Elena Colombi, Christina Straub, Sven Künzel, Matthew D Templeton, Honour C McCann, Paul B Rainey
Horizontal gene transfer can precipitate rapid evolutionary change. In 2010 the global pandemic of kiwifruit canker disease caused by Pseudomonas syringae pv. actinidiae (Psa) reached New Zealand. At the time of introduction, the single clone responsible for the outbreak was sensitive to copper, however, analysis of a sample of isolates taken in 2015 and 2016 showed that a quarter were copper resistant. Genome sequences of seven strains showed that copper resistance - comprising czc/cusABC and copABCD systems - along with resistance to arsenic and cadmium, was acquired via uptake of integrative conjugative elements (ICEs), but also plasmids...
January 7, 2017: Environmental Microbiology
Nan Hui, Ari Jumpponen, Gaia Francini, D Johan Kotze, Xinxin Liu, Martin Romantschuk, Rauni Strömmer, Heikki Setälä
Soil microbes play a key role in controlling ecosystem functions and providing ecosystem services. Yet, microbial communities in urban green space soils remain poorly characterized. Here we compared soil microbial communities in 41 urban parks of (i) divergent plant functional types (evergreen trees, deciduous trees, lawn) and (ii) different ages (constructed 10, ∼50, and >100 years ago). These microbial communities were also compared to those in 5 control forests in southern Finland. Our results indicate that, despite frequent disturbances in urban parks, urban soil microbes still followed the classic patterns typical of plant-microbe associations in natural environments: both bacterial and fungal communities in urban parks responded to plant functional groups, but fungi were under tighter control of plants than bacteria...
January 7, 2017: Environmental Microbiology
Allison H Kerwin, Spencer V Nyholm
Female Hawaiian bobtail squid, Euprymna scolopes, have an accessory nidamental gland (ANG) housing a bacterial consortium that is hypothesized to be environmentally transmitted and to function in the protection of eggs from fouling and infection. The composition, stability, and variability of the ANG and egg jelly coat (JC) communities were characterized and compared to the bacterial community composition of the surrounding environment using Illumina sequencing and transmission electron microscopy. The ANG bacterial community was conserved throughout hosts collected from the wild and was not affected by maintaining animals in the laboratory...
January 7, 2017: Environmental Microbiology
Marina Fomina, Andrew D Bowen, John M Charnock, Valentin S Podgorsky, Geoffrey M Gadd
This work elucidates spatio-temporal aspects of the biogeochemical transformation of copper mobilized from malachite (Cu2 (CO3 )(OH)2 ) and bioaccumulated within Aspergillus niger colonies when grown on different inorganic nitrogen sources. It was shown that the use of either ammonium or nitrate determined how copper was distributed within the colony and its microenvironment and the copper oxidation state and succession of copper coordinating ligands within the biomass. Nitrate-grown colonies yielded ∼1.7× more biomass, bioaccumulated ∼7× less copper, excreted ∼1...
January 7, 2017: Environmental Microbiology
Dirk de Beer, Miriam Weber, Arjun Chennu, Trinity Hamilton, Christian Lott, Jennifer Macalady, Judith Klatt
Oxygenic and anoxygenic photosynthesis were studied with microsensors in microbial mats found at 9-10 m depth in anoxic and sulfidic water in Little Salt Spring (Florida, USA). The lake sediments were covered with a 1-2 mm thick red mat dominated by filamentous Cyanobacteria, below which Green Sulfur Bacteria (GSB, Chlorobiaceae) were highly abundant. Within 4 mm inside the mats, the incident radiation was attenuated to undetectable levels. In situ microsensor data showed both oxygenic photosynthesis in the red surface layer and light-induced sulfide dynamics up to 1 cm depth...
December 30, 2016: Environmental Microbiology
Fátima C Pereira, David Berry
The composition and function of the mammalian gut microbiota has been the subject of much research in recent years, but the principles underlying the assembly and structure of this complex community remain incompletely understood. Processes that shape the gut microbiota are thought to be mostly niche-driven, with environmental factors such as the composition of available nutrients largely determining whether or not an organism can establish. The concept that the nutrient landscape dictates which organisms can successfully colonize and persist in the gut was first proposed in Rolf Freter's nutrient niche theory...
December 30, 2016: Environmental Microbiology
Chang-Hong Liu, Xin Huang, Tian-Ning Xie, Ning Duan, Ya-Rong Xue, Tan-Xi Zhao, Mark A Lever, Kai-Uwe Hinrichs, Fumio Inagaki
Although subseafloor sediments are known to harbour a vast number of microbial cells, the distribution, diversity, and origins of fungal populations remain largely unexplored. In this study, we cultivated fungi from 34 of 47 deep coal-associated sediment samples collected at depths ranging from 1,289 to 2,457 meters below the seafloor (mbsf) off the Shimokita Peninsula, Japan (1,118 m water depth). We obtained a total of 69 fungal isolates under strict contamination controls, representing 61 Ascomycota (14 genera, 23 species) and 8 Basidiomycota (4 genera, 4 species)...
December 28, 2016: Environmental Microbiology
Uri Gophna, Tom Konikoff, Henrik Bjørn Nielsen
Oscillospira is an under-studied anaerobic bacterial genus from Clostridial cluster IV that has resisted cultivation for over a decade since the first time it was observed. In recent years its 16S rRNA gene was identified in several human gut microbiota studies where it was often associated with interesting traits, especially leanness. However, very little is known about its metabolism or physiology. Here we use nearly complete genomes derived from shot-gun metagenomic data from the human gut to analyze Oscillospira and related bacteria...
December 28, 2016: Environmental Microbiology
Johanna Rytioja, Kristiina Hildén, Marcos Di Falco, Miaomiao Zhou, Maria Victoria Aguilar-Pontes, Outi-Maaria Sietiö, Adrian Tsang, Ronald P de Vries, Miia R Mäkelä
The ability to obtain carbon and energy is a major requirement to exist in any environment. For several ascomycete fungi (post-)genomic analyses have shown that species that occupy a large variety of habitats possess a diverse enzymatic machinery, while species with a specific habitat have a more focused enzyme repertoire that is well-adapted to the prevailing substrate. White-rot basidiomycete fungi also live in a specific habitat, as they are found exclusively in wood. In this study, we evaluated how well the enzymatic machinery of the white-rot fungus Dichomitus squalens is tailored to degrade its natural wood substrate...
December 28, 2016: Environmental Microbiology
Lifeng Xiong, Ying Yang, Yuan-Nong Ye, Jade L L Teng, Elaine Chan, Rory M Watt, Feng-Biao Guo, Susanna K P Lau, Patrick C Y Woo
Laribacter hongkongensis is a fish-borne pathogen associated with invasive infections and gastroenteritis. Its adaptive mechanisms to oxygen-limiting conditions in various environmental niches remain unclear. In this study, we compared the transcriptional profiles of L. hongkongensis under aerobic and anaerobic conditions using RNA-sequencing. Expression of genes involved in arginine metabolism significantly increased under anoxic conditions. Arginine was exploited as the sole energy source in L. hongkongensis for anaerobic respiration via the arginine catabolism pathway: specifically via the arginine deiminase (ADI) pathway...
December 28, 2016: Environmental Microbiology
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...
December 28, 2016: Environmental Microbiology
Zunyong Liu, Sisi Wu, Yun Chen, Xinyue Han, Qin Gu, Yanni Yin, Zhonghua Ma
In yeasts, the end-binding protein 1 (EB1) homologs regulate microtubule dynamics, cell polarization, and chromosome stability. However, functions of EB1 orthologs in plant pathogenic fungi have not been characterized yet. Here, we observed that the FgEB1 deletion mutant (ΔFgEB1) of Fusarium graminearum exhibits twisted hyphae, increased hyphal branching and curved conidia, indicating that FgEB1 is involved in the regulation of cellular polarity. Microscopic examination further showed that the microtubules of ΔFgEB1 exhibited less organized in comparison with those of the wild type...
December 28, 2016: Environmental Microbiology
Markus V Lindh, Johanna Sjöstedt, Börje Ekstam, Michele Casini, Daniel Lundin, Luisa W Hugerth, Yue O O Hu, Anders F Andersson, Agneta Andersson, Catherine Legrand, Jarone Pinhassi
Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations...
December 28, 2016: Environmental Microbiology
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