In today’s Digest you can read about: soil microbes regulating forest succession by H. Liao, sinking particles in the ocean microbiome by M. Mestre, ecology and evolution of seafloor and subseafloor microbial communities by W. D. Orsi, biotechnological potentials of marine bacteria by A. K. Farha, differentiation of Candida species Raman spectroscopy by A. Silge. Enjoy your summer read!
General microbiome
Signatures of ecological processes in microbial community time series – Karoline Faust – Microbiome
Review: Metabolic reprogramming for cancer cells and their microenvironment: Beyond the Warburg Effect – Linchong Sun – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer
Oral microbiota
Microbial similarity and preference for specific sites in healthy oral cavity and esophagus – Li Dong – Frontiers in Microbiology / Microbial Symbioses
Human gut microbiome
Altered Gut Microbiota: A Link Between Diet and the Metabolic Syndrome – Velasquez Manuel T. – Metabolic Syndrome and Related Disorders
The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut – Whitman B. Schofield – Cell Host & Microbe
Plant, root, and soil microbiome
Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession – Patrick J. Kearns – The ISME Journal
Links among warming, carbon and microbial dynamics mediated by soil mineral weathering – S. Doetterl – Nature Geoscience
In Planta Bacterial Transcriptomics Predict Plant Disease Outcomes – Stephen P.Cohen – Trends in Plant Science
Hymenobacter jeollabukensis sp. nov., isolated from soil – Leonid N. Ten -Journal of Microbiology
Ruegeria kandeliae sp. nov., isolated from the rhizosphere soil of a mangrove plant Kandelia candel – Lv Zhang – International Journal of Systematic and Evolutionary Microbiology
Soil microbes regulate forest succession in a subtropical ecosystem in China: evidence from a mesocosm experiment – Huixuan Liao – Plant and Soil
Solubilization of insoluble zinc compounds by zinc solubilizing bacteria (ZSB) and optimization of their growth conditions – Mohammad Yaghoubi Khanghahi – Environmental Science and Pollution Research
Soil microbial communities differ according to fertiliser regimes and cabbage (Brassica oleracea var. capitata L.) growth, but not aphid herbivory – Flora J. O’Brien – Frontiers in Microbiology / Terrestrial Microbiology
Paenibacillus elymi sp. nov., isolated from the rhizosphere of Elymus tsukushiensis, a plant native to the Dokdo Islands, Republic of Korea – Ye-Ji Hwang – International Journal of Systematic and Evolutionary Microbiology
Changes in rhizosphere microbial communities in potted cucumber seedlings treated with syringic acid – Zhilin Wang – PLOS One
Crop Rotation and Straw Application Impact Microbial Communities in Italian and Philippine Soils and the Rhizosphere of Zea mays – Sarah A. Maarastawi – Frontiers in Microbiology / Terrestrial Microbiology
Isolation of Pseudomonas putida from Harir/Erbil soil and screening for the presence of phosphate solubilizing genes – Aras Mohammed Khudhur – Polytechnic Journal
Environmental controls on soil microbial communities in a seasonally dry tropical forest – Silvia Pajaresa – Applied and Environmental Microbiology
Temperature effects on structure and function of the methanogenic microbial communities in two paddy soils and one desert soil – Pengfei Liu – Soil Biology and Biochemistry
Soil microbial communities differ according to fertiliser regimes and cabbage (Brassica oleracea var. capitata L.) growth, but not aphid herbivory – Flora J. O’Brien – Frontiers in Microbiology
Natural forests maintain a greater soil microbial diversity than that in rubber plantations in Southwest China – Jutamart Monkai – Agriculture, Ecosystems & Environment
Water and extremophile microbiome
Sinking particles promote vertical connectivity in the ocean microbiome – Mireia Mestre – PNAS
Filtering artefacts in bacterial community composition can affect the outcome of dissolved organic matter biolability assays – Joshua F. Dean – Biogeosciences
Review: Ecology and evolution of seafloor and subseafloor microbial communities – William D. Orsi – Nature Reviews Microbiology
The unexpected diversity of microbial communities associated with black corals revealed by high-throughput Illumina sequencing – Yong-Chun Liu – FEMS Microbiology Letters
Effect of spatial origin and hydrocarbon composition on bacterial consortia community structure and hydrocarbon biodegradation rates – Lloyd D Potts – FEMS Microbiology Ecology
Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments – Patricia M Valdespino-Castillo – FEMS Microbiology Ecology
Cultivation and characterization of Candidatus Nitrosotenuis aquariensis, an ammonia-oxidizing archaeon from a freshwater aquarium biofilter – Laura A. Sauder – Applied and Environmental Microbiology
Biofilm and planktonic bacterial communities in a drinking water distribution system supplied with untreated groundwater – Jianfei Chen – Archives of Microbiology
Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern Gulf of Mexico to light Louisiana sweet crude oil – Hernando P. Bacosa – The ISME Journal
A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales – Connor B.Driscoll – Harmful Algae
Review: Recent developments in synthetic biology and metabolic engineering in microalgae towards biofuel production – Sheeja Jagadevan – Biotechnology for Biofuels
Phylogenetic diversity and biotechnological potentials of marine bacteria from continental slope of eastern Arabian Sea – Arakkaveettil Kabeer Farha – Journal of Genetic Engineering and Biotechnology
Biochemical methane potential of microalgae biomass using different microbial inocula – Cristina Gonzalez-Fernandez – Biotechnology for Biofuels
Quorum sensing in thermophiles: prevalence of autoinducer-2 system – Amandeep Kaur – BMC Microbiology
Molecular Cloning and Characterization of a Novel α-Amylase from Antarctic Sea Ice Bacterium Pseudoalteromonas sp. M175 and Its Primary Application in Detergent – Xiaofei Wang – BioMed Research International
Low-temperature sulfidic-ice microbial communities, Borup Fiord Pass, Canadian high Arctic – Christopher B. Trivedi – Frontiers in Microbiology / Extreme Microbiology
Phages and viruses
Beyond members of the Flaviviridae family, sofosbuvir also inhibits chikungunya virus replication – Andre Ferreira – bioRxiv
Evaluation of bias induced by viral enrichment and random amplification protocols in metagenomic surveys of saliva DNA viruses – Marcos Parras-Moltó – Microbiome
Immuno-metabolic changes in herpes virus infection – Debprasa Chattopadhyay – Cytokine
Emergence of a Virulent Genotype VIIi of Newcastle Disease Virus in Iran – Arash Ghalyanchilangeroudi – Avian Pathology
Techniques
High-throughput microfluidic sorting of live magnetotactic bacteria – Andy Tay – Applied and Environmental Microbiology
The application of UV resonance Raman spectroscopy for the differentiation of clinically relevant Candida species – Anja Silge – Analytical and Bioanalytical Chemistry