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Environmental Microbiology

Hanaka Mera, David G Bourne
Rapidly changing climate regimes combined with other anthropogenic pressures are implicated in increased disease epizootics among reef building corals, resulting in changing habitat structure. These accumulated stressors directly contribute to disease outbreaks by compromising the coral host immune system, modulating virulence of microbial pathogens, and/or disrupting the balance within the microbiome of the holobiont. Disentangling coral disease causation has been challenging, and while progress has been made for certain diseases in terms of the roles the associated microorganisms play, it is evident that like in other marine or terrestrial systems, compromised host health cannot always be attributed to a single causative agent...
October 13, 2017: Environmental Microbiology
Joanna E Kowalczyk, Claire Khosravi, Samuel Purvine, Alice Dohnalkova, William B Chrisler, Galya Orr, Errol Robinson, Erika Zink, Ad Wiebenga, Mao Peng, Evy Battaglia, Scott Baker, Ronald P de Vries
In A. niger, two transcription factors, AraR and XlnR, regulate the production of enzymes involved in degradation of arabinoxylan and catabolism of the released L-arabinose and D-xylose. Deletion of both araR and xlnR in leads to reduced production of (hemi)cellulolytic enzymes and reduced growth on arabinan, arabinogalactan and xylan. In this study we investigated the colonization and degradation of wheat bran by the A. niger reference strain CBS 137562 and araR/xlnR regulatory mutants using high-resolution microscopy and exo-proteomics...
October 13, 2017: Environmental Microbiology
Craig Baker-Austin, James D Oliver
Vibrio vulnificus is a Gram-negative aquatic bacterium first isolated by the United States (US) Centers for Disease Control and Prevention (CDC) in 1964. This bacterium is part of the normal microbiota of estuarine waters and occurs in high numbers in molluscan shellfish around the world, particularly in warmer months. Infections in humans are derived from consumption of seafood produce and from water exposure. V. vulnificus is a striking and enigmatic human pathogen, yet many aspects related to its biology, genomics, virulence capabilities and epidemiology remain elusive and poorly understood...
October 13, 2017: Environmental Microbiology
Ruben Props, Marian L Schmidt, Jasmine Heyse, Henry A Vanderploeg, Nico Boon, Vincent J Denef
Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within one hour of feeding, and a total diversity loss of 11.6 ± 4.1 % after 3h...
October 13, 2017: Environmental Microbiology
Patricia Bernal, María A Llamas, Alain Filloux
The type VI secretion system (T6SS) is a bacterial nanomachine used to inject effectors into prokaryotic or eukaryotic cells and is thus involved in both host manipulation and inter-bacterial competition. The T6SS is widespread among Gram-negative bacteria, mostly within the Proteobacterium Phylum. This secretion system is commonly found in commensal and pathogenic plant-associated bacteria. Phylogenetic analysis of phytobacterial T6SS clusters shows that they are distributed in the five main clades previously described (group 1 to 5)...
October 13, 2017: Environmental Microbiology
Jonathan Rosenberg, KahYen C Yeak, Fabian M Commichau
Pyridoxal 5'-phosphate (PLP), the most important form of vitamin B6 serves as a cofactor for many proteins. Two alternative pathways for de novo PLP biosynthesis are known: the short deoxy-xylulose-5-phosphate (DXP)-independent pathway, which is present in the Gram-positive model bacterium Bacillus subtilis and the longer DXP-dependent pathway, which has been intensively studied in the Gram-negative model bacterium Escherichia coli. Previous studies revealed that bacteria contain many promiscuous enzymes causing a so-called "underground metabolism", which can be important for the evolution of novel pathways...
October 13, 2017: Environmental Microbiology
Roey Angel, Christopher Panhölzl, Raphael Gabriel, Craig Herbold, Wolfgang Wanek, Andreas Richter, Stephanie A Eichorst, Dagmar Woebken
Investigating active participants in the fixation of dinitrogen gas is vital as N is often a limiting factor for primary production. Biological nitrogen fixation (BNF) is performed by a diverse guild of bacteria and archaea (diazotrophs), which can be free-living or symbionts. Free-living diazotrophs are widely distributed in the environment, yet our knowledge about their identity and ecophysiology is still limited. A major challenge in investigating this guild is inferring activity from genetic data as this process is highly regulated...
October 13, 2017: Environmental Microbiology
Lucas Dantas Lopes, Edward W Davis, Michele de C Pereira E Silva, Alexandra J Weisberg, Luana Bresciani, Jeff H Chang, Joyce E Loper, Fernando D Andreote
Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isolates in the P. fluorescens (57) and P. putida (19) groups. Among the isolates in the P. fluorescens group, most (37) were classified in the P. koreensis subgroup and two in the P...
October 13, 2017: Environmental Microbiology
Margot Tragin, Adriana Zingone, Daniel Vaulot
We compared the composition of eukaryotic communities using two genetic markers (18S rRNA V4 and V9 regions) at 27 sites sampled during Ocean Sampling Day 2014, with a focus on photosynthetic groups and, more specifically green algae (Chlorophyta). Globally, the V4 and V9 regions of the 18S rRNA gene provided similar images of alpha diversity and ecological patterns. However, V9 provided 20% more OTUs built at 97% identity than V4 and 39% and 56% of the genera were found only in one dataset, respectively V4 and V9...
October 6, 2017: Environmental Microbiology
Melanie Sapp, Sebastian Ploch, Anna Maria Fiore-Donno, Michael Bonkowski, Laura E Rose
Although protists occupy a vast range of habitats and are known to interact with plants among other things via disease suppression, competition or growth stimulation, their contributions to the "phytobiome" are not well described. To contribute to a more comprehensive picture of the plant holobiont, we examined cercozoan and oomycete taxa living in association with the model plant Arabidopsis thaliana grown in two different soils. Soil, roots, leaves and wooden toothpicks were analyzed before and after surface sterilization...
October 2, 2017: Environmental Microbiology
Simone Rampelli, Silvia Turroni, Stephanie L Schnorr, Matteo Soverini, Sara Quercia, Monica Barone, Andrea Castagnetti, Elena Biagi, Giorgio Gallinella, Patrizia Brigidi, Marco Candela
It is a matter of fact that the human gut microbiome also includes a non-bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome datasets from human populations with different geographical origin and lifestyle. In particular, such datasets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter-gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre-agricultural tribe (Tunapuco from Peru)...
October 2, 2017: Environmental Microbiology
Fernanda Fazion, Stéphane Perchat, Christophe Buisson, Gislayne Vilas-Bôas, Didier Lereclus
The entomopathogen Bacillus thuringiensis specie harbours numerous plasmids essentially studied for their involvement in pathogenicity, as Cry-plasmids. The lifecycle of B. thuringiensis in the insect host is regulated by the sequential activation of quorum sensing systems to kill, survive and sporulate. In this study, we characterize a new quorum sensing system belonging to the Rap-Phr family. The Rap8-Phr8 system is borne by the pHT8_1 plasmid, a small cryptic plasmid from the B. thuringiensis var. kurstaki HD73 strain...
October 2, 2017: Environmental Microbiology
Chiara Ferrario, Giulia Alessandri, Leonardo Mancabelli, Eben Gering, Marta Mangifesta, Christian Milani, Gabriele Andrea Lugli, Alice Viappiani, Sabrina Duranti, Francesca Turroni, Maria Cristina Ossiprandi, Ricardo Hiyashi, Roderick Mackie, Douwe van Sinderen, Marco Ventura
Different factors may modulate the gut microbiota of animals. In any particular environment, diet, genetic factors and human influences can shape the bacterial communities residing in the gastrointestinal tract. Metagenomic approaches have significantly expanded our knowledge on microbiota dynamics inside hosts, yet cultivation and isolation of bacterial members of these complex ecosystems may still be necessary to fully understand interactions between bacterial communities and their host. A dual approach, involving culture-independent and -dependent techniques, was used here to decipher the microbiota communities that inhabit the gastro intestinal tract of free-range, broiler and feral chickens...
October 2, 2017: Environmental Microbiology
Srisailam Marupakula, Shahid Mahmood, Johanna Jernberg, Srivathsa Nallanchakravarthula, Zaenab A Fahad, Roger D Finlay
Plant roots select non-random communities of fungi and bacteria from the surrounding soil that have effects on their health and growth, but we know little about the factors influencing their composition. We profiled bacterial microbiomes associated with individual ectomycorrhizal Pinus sylvestris roots colonised by different fungi and analysed differences in microbiome structure related to soils from distinct podzol horizons and effects of short term additions of N, a growth-limiting nutrient commonly applied as a fertiliser, but known to influence patterns of carbon allocation to roots...
October 2, 2017: Environmental Microbiology
Daniele De Corte, Abhishek Srivastava, Marja Koski, Juan Antonio L Garcia, Yoshihiro Takaki, Taichi Yokokawa, Takuro Nunoura, Nathalie H Elisabeth, Eva Sintes, Gerhard J Herndl
Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater...
October 2, 2017: Environmental Microbiology
Marc Garcia-Garcera, Marie Touchon, Sylvain Brisse, Eduardo Pc Rochaa
Most bacteria have poorly characterized environmental reservoirs and unknown closely-related species. This hampers the study of bacterial evolutionary ecology because both the environment and the genetic background of ancestral lineages are unknown. We combined metagenomics, comparative genomics, and phylogenomics to overcome this limitation, to identify novel taxa, and to propose environments where they can be isolated. We applied this method to characterize the ecological distribution of known and novel lineages of Acinetobacter spp...
October 2, 2017: Environmental Microbiology
Gao Chen, Sara Kleindienst, Daniel R Griffiths, E Erin Mack, Edward S Seger, Frank E Löffler
The microbial mixed culture RM grows with dichloromethane (DCM) as the sole energy source generating acetate, methane, chloride and biomass as products. Chloromethane (CM) was not an intermediate during DCM utilization consistent with the observation that CM could not replace DCM as a growth substrate. Interestingly, cultures that received DCM and CM together degraded both compounds concomitantly. Transient hydrogen (H2 ) formation reaching a maximum concentration of 205 ± 13 ppmv was observed in cultures growing with DCM, and the addition of exogenous H2 at concentrations exceeding 3000 ppmv impeded DCM degradation...
October 2, 2017: Environmental Microbiology
Li Xue Liu, Qin Qin Li, Yun Zeng Zhang, Yue Hu, Jian Jiao, Hui Juan Guo, Xing Xing Zhang, Biliang Zhang, Wen Xin Chen, Chang Fu Tian
Receiving nodulation and nitrogen fixation genes does not guarantee rhizobia an effective symbiosis with legumes. Here, variations in gene content were determined for three Sinorhizobium species showing contrasting symbiotic efficiency on soybeans. A nitrate-reduction gene cluster absent in S. sojae was found to be essential for symbiotic adaptations of S. fredii and S. sp. III. In S. fredii, the deletion mutation of the nap (nitrate reductase), instead of nir (nitrite reductase) and nor (nitric oxide reductase), led to defects in nitrogen-fixation (Fix(-) )...
October 2, 2017: Environmental Microbiology
Sen-Miao Tong, An-Xue Zhang, Chong-Tao Guo, Sheng-Hua Ying, Ming-Guang Feng
The fungal insect pathogen Beauveria bassiana has the blue-light photoreceptor VIVID (VVD) but lacks a pigmentation pattern to trace its light responses. Here we show that the fungal vvd is transcriptionally expressed, and linked to other blue/red photoreceptor genes, in a daylight length-dependent manner. GFP-tagged VVD fusion protein was localized to periphery, cytoplasm and vacuoles of hyphal cells in light/dark (L:D) cycles of 24:0 and 16:8 and aggregated in cytoplasm with shortening daylight until transfer into nuclei in full darkness...
October 2, 2017: Environmental Microbiology
Anyi Hu, Feng Ju, Liyuan Hou, Jiangwei Li, Xiaoyong Yang, Hongjie Wang, Sikandar I Mulla, Qian Sun, Helmut Bürgmann, Chang-Ping Yu
Although the health of rivers is threatened by multiple anthropogenic stressors with increasing frequency, it remains an open question how riverine microbial communities respond to emerging micropollutants. Here, by using 16S rDNA amplicon sequencing of 60 water samples collected during different hydrological seasons, we investigated the spatio-temporal variation and the co-occurrence patterns of microbial communities in the anthropogenically impacted Jiulong River in China. The results indicated that the riverine microbial co-occurrence network had a non-random, modular structure, which was mainly shaped by the taxonomic relatedness of co-occurring species...
October 2, 2017: Environmental Microbiology
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