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The Ecology and Evolution of Microbial Competition [PDF]

Trends in Microbiology, 2016
Microbes are typically surrounded by different strains and species with whom they compete for scarce nutrients and limited space. Given such challenging living conditions, microbes have evolved many phenotypes with which they can outcompete and displace their neighbours: secretions to harvest resources, loss of costly genes whose products can be ...
Ghoul Melanie, Mitri Sara
openaire   +4 more sources

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia

Microbiome, 2019
Background Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.
Juan E. Pérez-Jaramillo, Mattias de Hollander, Camilo A. Ramírez, Rodrigo Mendes, Jos M. Raaijmakers, Víctor J. Carrión   +5 more
doaj   +1 more source

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems

Microbiome, 2021
Background Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown.
Xun Qian, Santosh Gunturu, Jiarong Guo, Benli Chai, James R. Cole, Jie Gu, James M. Tiedje   +6 more
doaj   +1 more source

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer

Microbiome, 2020
Background Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments.
Ohana Y. A. Costa, Mattias de Hollander, Agata Pijl, Binbin Liu, Eiko E. Kuramae   +4 more
doaj   +1 more source

Current Challenges and Pitfalls in Soil Metagenomics

Microorganisms, 2022
Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity.
Marcio F. A. Leite, Sarah W. E. B. van den Broek, Eiko E. Kuramae   +2 more
doaj   +1 more source

The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots

Metabolites, 2021
Plants are faced with various biotic and abiotic stresses during their life cycle. To withstand these stresses, plants have evolved adaptive strategies including the production of a wide array of primary and secondary metabolites.
Muhammad Syamsu Rizaludin, Nejc Stopnisek, Jos M. Raaijmakers, Paolina Garbeva   +3 more
doaj   +1 more source

PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

Microorganisms, 2022
The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a ...
Ohana Y. A. Costa, Mattias de Hollander, Eiko E. Kuramae, Paul L. E. Bodelier   +3 more
doaj   +1 more source

A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting

BMC Evolutionary Biology, 2018
Background Due to the DNA triplet code, it is possible that the sequences of two or more protein-coding genes overlap to a large degree. However, such non-trivial overlaps are usually excluded by genome annotation pipelines and, thus, only a few ...
Sarah M. Hücker, Sonja Vanderhaeghen, Isabel Abellan-Schneyder, Romy Wecko, Svenja Simon, Siegfried Scherer, Klaus Neuhaus   +6 more
doaj   +1 more source

MICROBIAL ECOLOGY OF PITINA

Italian Journal of Food Safety, 2009
The aim of the study was to investigate the microbiological properties of Pitina, a typical fermented meat product, to evaluate its attributes and safety.
Osualdini M., IACUMIN, Lucilla, Boscolo D., BOVOLENTA, Stefano, COMI, Giuseppe   +4 more
openaire   +6 more sources

Safeguarding the microbial water quality from source to tap

npj Clean Water, 2021
Anthropogenic activities and climate change can deteriorate the freshwater quality and stress its availability. This stress can, in turn, have an impact on the biostability of drinking water.
Jorien Favere, Raquel G. Barbosa, Tom Sleutels, Willy Verstraete, Bart De Gusseme, Nico Boon   +5 more
doaj   +1 more source