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Environmental Microbiology Reports

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https://www.readbyqxmd.com/read/30246498/vibrio-responses-to-extracytoplasmic-stress
#1
REVIEW
Cara M DeAngelis, Jessica Saul-McBeth, Jyl S Matson
A critical factor for bacterial survival in any environment is the ability to sense and respond appropriately to any stresses encountered. This is especially important for bacteria that inhabit environments that are constantly changing, or for those that inhabit more than one biological niche. Vibrio species are unique in that they are aquatic organisms, and must adapt to ever-changing temperatures, salinity levels, and nutrient concentrations. In addition, many species of Vibrio colonize other organisms, and must also deal with components of the host immune response...
September 24, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30246474/marine-biofilms-diversity-of-communities-and-of-chemical-cues
#2
REVIEW
Jorge Antunes, Pedro Leão, Vitor Vasconcelos
Surfaces immersed in seawater are rapidly colonized by various microorganisms, resulting in the formation of heterogenic marine biofilms. These communities are known to influence the settlement of algae spores and invertebrate larvae, triggering a succession of fouling events, with significant environmental and economic impacts. This review covers recent research regarding the differences in composition of biofilms isolated from different artificial surface types and the influence of environmental factors on their formation...
September 24, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30246414/prokaryotic-niche-partitioning-between-suspended-and-sinking-marine-particles
#3
Manon T Duret, Richard S Lampitt, Phyllis Lam
Suspended particles are major organic carbon substrates for heterotrophic microorganisms in the mesopelagic ocean (100-1000m). Nonetheless, communities associated with these particles have been overlooked compared to sinking particles, the latter generally considered as main carbon transporters to the deep ocean. This study is the first to differentiate prokaryotic communities associated with suspended and sinking particles, collected with a marine snow catcher at four environmentally distinct stations in the Scotia Sea...
September 24, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30246403/analysis-of-microbial-communities-in-natural-halite-springs-reveals-a-domain-dependent-relationship-of-species-diversity-to-osmotic-stress
#4
Ilona A Ruhl, Stephen E Grasby, Evan S Haupt, Peter F Dunfield
Microbial species diversity may peak at certain optimal environmental conditions, and decrease towards more extreme conditions. Indeed, bell shaped relationships of species diversity against pH and temperature have been demonstrated, but diversity patterns across other environmental conditions are less well reported. In this study, we investigated the impact of salinity on the diversity of microorganisms from all three Domains in a large set of natural springs with salinities ranging from freshwater to halite-saturated...
September 24, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30230256/recovering-cellular-biomass-from-fluids-using-chemical-flocculation
#5
Paul A Kenward, Rachel L Simister, Connor Morgan-Lang, Niko Finke, Arne Sturm, Steven J Hallam, Sean A Crowe
We developed an efficient, scalable, and inexpensive method for recovering cellular biomass from complex fluid matrices that cannot be processed using conventional filtration methods. The method uses chemical flocculation with iron oxyhydroxides, is capable of recovering >90% of cellular biomass from fluids with more than 103 cells ml-1 , and was validated using both mock communities and field samples. High quality DNA can be readily extracted from iron flocs using standard soil extraction kits. We applied chemical flocculation to fracing fluids from British Columbia, Canada, and recovered a diversity of microbial taxa including abundant members of the Epsilon- and Deltaproteobacteria previously recovered from shale gas operations in the United States...
September 19, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30136425/co-occurrence-network-analysis-reveals-thermodynamics-driven-microbial-interactions-in-methanogenic-bioreactors
#6
Takashi Narihiro, Masaru K Nobu, Ben T W Bocher, Ran Mei, Wen-Tso Liu
Methanogenic bioreactors have been applied to treat purified terephthalic acid (PTA) wastewater containing complex aromatic compounds, such as terephthalic acid, para-toluic acid, and benzoic acid. This study characterized the interaction of microbial populations in 42 samples obtained from 10 PTA-degrading methanogenic bioreactors. Approximately, 54 dominant populations (11 methanogens, 8 syntrophs, and 35 functionally unknown clades) that represented 73.9% of total 16S rRNA gene iTag sequence reads were identified...
August 22, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30126050/the-nitrogen-regulator-pipx-acts-in-cis-to-prevent-operon-polarity
#7
Raquel Cantos, Jose I Labella, Javier Espinosa, Asunción Contreras
Cyanobacteria, phototrophic organisms performing oxygenic photosynthesis, must adapt their metabolic processes to important environmental challenges, like those imposed by the succession of days and nights. Not surprisingly, certain regulatory proteins are found exclusively in this phylum. One of these unique factors, PipX, provides a mechanistic link between signals of carbon/nitrogen and of energy, transduced by the signalling protein PII, and the control of gene expression by the global nitrogen regulator NtcA...
August 20, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30094953/coral-microbiome-database-integration-of-sequences-reveals-high-diversity-and-relatedness-of-coral-associated-microbes
#8
Megan J Huggett, Amy Apprill
Coral-associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding of specific coral-microbial interactions are lacking. In order to create a framework to examine coral-microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger-produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database...
August 9, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30066495/two-nad-independent-l-lactate-dehydrogenases-drive-l-lactate-utilization-in-pseudomonas-aeruginosa-pao1
#9
Yujiao Wang, Dan Xiao, Qiuyuan Liu, Yipeng Zhang, Chunxia Hu, Jinkai Sun, Chunyu Yang, Ping Xu, Cuiqing Ma, Chao Gao
Pseudomonas aeruginosa often establishes a chronic infection in the airways of patients with cystic fibrosis (CF). l-Lactate is the most abundant carbon source in the CF sputum, and l-lactate utilization may be important for P. aeruginosa to survive in the lungs of CF patients. In this study, the key enzymes involved in l-lactate utilization by P. aeruginosa PAO1 were characterized using the synthetic CF sputum medium (SCFM). A highly conserved membrane-bound NAD-independent l-lactate dehydrogenase (l-iLDH) encoded by lldD (PA4771) and a novel flavin-containing membrane-bound l-iLDH encoded by lldA (PA2382) were both found to contribute to l-lactate utilization by P...
August 1, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30066486/the-ph-regulator-pacc-a-host-dependent-virulence-factor-in-botrytis-cinerea
#10
Christine Rascle, Cindy Dieryckx, Jean William Dupuy, Laetitia Muszkieta, Eytham Souibgui, Michel Droux, Christophe Bruel, Vincent Girard, Nathalie Poussereau
The phytopathogenic fungus Botrytis cinerea is able to infect a wide variety of plants and plant tissues with differing chemical compositions. During its interaction with the host, this pathogen modulates its ambient pH by secreting acids or ammonia. In this work, we examined the Pal/Pac pathway, the fungal ambient pH-responsive signalling circuit, and investigated the role of the PacC transcription factor. Characterization of the BcpacC deletion mutant revealed an alteration of both fungal growth and virulence depending on the pH of the culture medium or of the host tissue...
August 1, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30066470/a-prokaryotic-eukaryotic-relation-in-the-fat-body-of-bombus-terrestris
#11
Anneleen Parmentier, Annelies Billiet, Guy Smagghe, Peter Vandamme, Dieter Deforce, Filip Van Nieuwerburgh, Ivan Meeus
The interaction between the insect host and its microbiota plays a central role in insect health and is mostly studied in relation to the digestive system. Nonetheless, there are numerous microorganisms occupying multiple habitats in and on insects. We studied microbial communities in the gut and fat body of bumblebees (Bombus terrestris) using the V4 region of the 16S rRNA gene on the Illumina MiSeq platform. In one of the two study locations, the fat body microbial composition was marked by the dominant presence of Arsenophonus sp...
August 1, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30058291/newly-designed-16s-rrna-metabarcoding-primers-amplify-diverse-and-novel-archaeal-taxa-from-the-environment
#12
Mohammad Bahram, Sten Anslan, Falk Hildebrand, Peer Bork, Leho Tedersoo
High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low due to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes...
July 30, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30058121/rna-seq-based-monitoring-of-gene-expression-changes-of-viable-but-non-culturable-state-of-vibrio-cholerae-induced-by-cold-seawater
#13
Tingting Xu, Hengchun Cao, Wei Zhu, Min Wang, Yuhui Du, Zhiqiu Yin, Min Chen, Yutao Liu, Bin Yang, Bin Liu
Vibrio cholerae O1 is a natural inhabitant of aquatic environments and causes the acute diarrheal disease cholera. Entry into a viable but non-culturable (VBNC) state is a survival strategy by which V. cholerae withstands natural stresses and is important for the transition between the aquatic and host environments during the V. cholerae life cycle. In this study, the formation of VBNC V. cholerae induced by cold seawater exposure was investigated using RNA sequencing (RNA-seq). The analysis revealed that the expression of 1420 genes was changed on VBNC state formation...
July 30, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30047254/faecal-bacterial-communities-from-mediterranean-loggerhead-sea-turtles-caretta-caretta
#14
Elena Biagi, Federica D'Amico, Matteo Soverini, Valeria Angelini, Monica Barone, Silvia Turroni, Simone Rampelli, Sauro Pari, Patrizia Brigidi, Marco Candela
The loggerhead sea turtle (Caretta caretta) is the most widespread sea turtle species in the Mediterranean Sea and a relevant pollution 'flagship species'. Here, we profiled the faecal microbiota from 29 C. caretta from a rescue centre, and explored the impact of several variables linked to both the animal itself and the environment (i.e., tank water ecosystem). We show that loggerhead turtles share more gut microbiota features with carnivorous marine mammals, than with phylogenetically close, but herbivorous, turtles, as a confirmation of the gut microbiota adaptive function to diet and environment...
July 25, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30047246/extracellular-aminopeptidase-modulates-biofilm-development-of-pseudomonas-aeruginosa-by-affecting-matrix-exopolysaccharide-and-bacterial-cell-death
#15
Tianhu Zhao, Yuhuan Zhang, Huijun Wu, Di Wang, Yihua Chen, Mei-Jun Zhu, Luyan Z Ma
Biofilm bacteria are embedded within a self-secreted extracellular matrix that contains a considerable amount of proteins including many extracellular enzymes. However, little is known about the roles of such enzymes in biofilm development. Here, we studied Pseudomonas aeruginosa aminopeptidase (PaAP, encoded by PA2939 that we named the gene as paaP in this study), a quorum-sensing-regulated enzyme and one of the most abundant extracellular proteins in the biofilm matrix of this opportunistic pathogen and environmental bacterium...
July 25, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30043505/contrasting-community-composition-of-endospores-and-vegetative-firmicutes-in-a-marine-sediment-suggests-both-endo-and-exogenous-sources-of-endospore-accumulation
#16
Carina Cupit, Bente Aagaard Lomstein, Kasper Urup Kjeldsen
Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column...
July 24, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30043488/long-term-carriage-and-rapid-transmission-of-extended-spectrum-beta-lactamase-producing-e-coli-within-a-flock-of-mallards-in-the-absence-of-antibiotic-selection
#17
Linus Sandegren, Johan Stedt, Ulrika Lustig, Jonas Bonnedahl, Dan I Andersson, Josef D Järhult
Wild birds have been suggested as transmitters and reservoirs for antibiotic resistant bacteria. We performed an experimental study investigating carriage time and interindividual transmission of extended spectrum beta-lactamase- (ESBL-)producing Escherichia coli in Mallards (Anas platyrhynchos) to assess if the birds carry the bacteria long enough to transfer them geographically during migration. Mallards were inoculated intraoesophageally with four different strains of ESBL-producing E. coli and kept together in a flock...
July 24, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30028082/microbial-diversity-and-biogeography-in-arctic-soils
#18
REVIEW
Lucie A Malard, David A Pearce
Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and, thus, have the potential to generate positive feedback within the climate system...
July 20, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/30014579/electron-donor-driven-bacterial-and-archaeal-community-patterns-along-forest-ring-edges-in-ontario-canada
#19
Konstantin von Gunten, Stewart M Hamilton, Cheng Zhong, Camilla Nesbø, Jiaying Li, Karlis Muehlenbachs, Kurt O Konhauser, Daniel S Alessi
Forest rings are 50-1600 m diameter circular structures found in boreal forests around the globe. They are believed to be chemically reducing chimney features, having an accumulation of reduced species in the middle of the ring and oxidation processes occurring at the ring's edges. It has been suggested that microorganisms could be responsible for charge transfer from the inside to the outside of the ring. To explore this, we focused on the changes in bacterial and archaeal communities in the ring edges of two forest rings, the 'Bean' and the 'Thorn North' ring, in proximity to each other in Ontario, Canada...
July 16, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29992728/first-report-of-foregut-microbial-community-in-proboscis-monkeys-are-diverse-forests-a-reservoir-for-diverse-microbiomes
#20
Takashi Hayakawa, Senthilvel K S S Nathan, Danica J Stark, Diana A Ramirez Saldivar, Rosa Sipangkui, Benoit Goossens, Augustine Tuuga, Marcus Clauss, Akiko Sawada, Shinji Fukuda, Hiroo Imai, Ikki Matsuda
Foregut fermentation is well known to occur in a wide range of mammalian species and in a single bird species. Yet, the foregut microbial community of free-ranging, foregut-fermenting monkeys, i.e., colobines, has not been investigated so far. We analyzed the foregut microbiomes in four free-ranging proboscis monkeys (Nasalis larvatus) from two different tropical habitats with varying plant diversity (mangrove and riverine forests), in an individual from a semi-free-ranging setting with supplemental feeding, and in an individual from captivity, using high-throughput sequencing based on 16S ribosomal RNA genes...
July 11, 2018: Environmental Microbiology Reports
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