Special Issue "Towards Integrated Multi-omics Analyses of Environmental Microbiota"

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: 31 July 2019.

Special Issue Editors

Guest Editor
Prof. Dr. Martin Von Bergen

Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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Fax: +49 (0)341 235 1786
Interests: microbial ecology; biodegradation of pollutants; metaproteomics; microbial physiology
Guest Editor
Dr. Dirk Benndorf

Bioprocess Engineering, Otto von Guericke University MagdeburgMagdeburg, Germany
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Guest Editor
Dr. Nico Jehmlich

Department of Molecular Systems Biology, UFZ-Helmholtz Centre for Environmental Research , 04318 Leipzig, Germany
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Phone: +493412354767
Interests: Metaproteomics, Protein-Stable Isotope Probing, Microbiome Biology, Environmental Microbiology

Special Issue Information

Dear Colleagues,

Microbial communities are responsible for energy and nutrient cycling and are massively involved in the planet’s sustainability. Microbes are directly involved in the dynamics of climate change via their impact on the destabilization, mineralization, and sequestration of organic matter. The facets of microbial diversity consist of morphological, structural, metabolic, ecological or evolutionary diversity; however, the central question in microbial ecology is “who eats what, where and when?” means how is the key player in the community to perform the most meaningful activity. To answer this, one major task is to identify the relationships between the composition of the microbial community and the functional processes.

For this Special Issue of Microorganisms, we invite you to send contributions concerning any aspects relating to microorganisms utilized in environmental applications, including to ecology, diversity, physiology, detection methods and processes. The Special Issue will be devoted to topics microbial communities including the multi-omics technologies and cross-disciplinary studies dedicated to basic and/or applied research.

Prof. Dr. Martin von Bergen
Dr. Dirk Benndorf
Dr. Nico Jehmlich
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Microbial community structure
  • Metagenomics
  • Metatranscriptomics
  • Metaproteomics
  • Metabolomics
  • Degradation
  • Biogeochemical processes
  • Microbial diversity
  • Climate change

Published Papers (2 papers)

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Research

Open AccessArticle
Response of Microbial Communities and Their Metabolic Functions to Drying–Rewetting Stress in a Temperate Forest Soil
Microorganisms 2019, 7(5), 129; https://doi.org/10.3390/microorganisms7050129
Received: 25 March 2019 / Revised: 5 May 2019 / Accepted: 6 May 2019 / Published: 13 May 2019
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Abstract
Global climate change is predicted to alter drought–precipitation patterns, which will likely affect soil microbial communities and their functions, ultimately shifting microbially-mediated biogeochemical cycles. The present study aims to investigate the simultaneous variation of microbial community compositions and functions in response to drought [...] Read more.
Global climate change is predicted to alter drought–precipitation patterns, which will likely affect soil microbial communities and their functions, ultimately shifting microbially-mediated biogeochemical cycles. The present study aims to investigate the simultaneous variation of microbial community compositions and functions in response to drought and following rewetting events, using a soil metaproteomics approach. For this, an established field experiment located in an Austrian forest with two levels (moderate and severe stress) of precipitation manipulation was evaluated. The results showed that fungi were more strongly influenced by drying and rewetting (DRW) than bacteria, and that there was a drastic shift in the fungal community towards a more Ascomycota-dominated community. In terms of functional responses, a larger number of proteins and a higher functional diversity were observed in both moderate and severe DRW treatments compared to the control. Furthermore, in both DRW treatments a rise in proteins assigned to “translation, ribosomal structure, and biogenesis” and “protein synthesis” suggests a boost in microbial cell growth after rewetting. We also found that the changes within intracellular functions were associated to specific phyla, indicating that responses of microbial communities to DRW primarily shifted microbial functions. Microbial communities seem to respond to different levels of DRW stress by changing their functional potential, which may feed back to biogeochemical cycles. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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Open AccessArticle
Systematic Affiliation and Genome Analysis of Subtercola vilae DB165T with Particular Emphasis on Cold Adaptation of an Isolate from a High-Altitude Cold Volcano Lake
Microorganisms 2019, 7(4), 107; https://doi.org/10.3390/microorganisms7040107
Received: 4 April 2019 / Revised: 17 April 2019 / Accepted: 18 April 2019 / Published: 23 April 2019
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Abstract
Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number [...] Read more.
Among the Microbacteriaceae the species of Subtercola and Agreia form closely associated clusters. Phylogenetic analysis demonstrated three major phylogenetic branches of these species. One of these branches contains the two psychrophilic species Subtercola frigoramans and Subtercola vilae, together with a larger number of isolates from various cold environments. Genomic evidence supports the separation of Agreia and Subtercola species. In order to gain insight into the ability of S. vilae to adapt to life in this extreme environment, we analyzed the genome with a particular focus on properties related to possible adaptation to a cold environment. General properties of the genome are presented, including carbon and energy metabolism, as well as secondary metabolite production. The repertoire of genes in the genome of S. vilae DB165T linked to adaptations to the harsh conditions found in Llullaillaco Volcano Lake includes several mechanisms to transcribe proteins under low temperatures, such as a high number of tRNAs and cold shock proteins. In addition, S. vilae DB165T is capable of producing a number of proteins to cope with oxidative stress, which is of particular relevance at low temperature environments, in which reactive oxygen species are more abundant. Most important, it obtains capacities to produce cryo-protectants, and to combat against ice crystal formation, it produces ice-binding proteins. Two new ice-binding proteins were identified which are unique to S. vilae DB165T. These results indicate that S. vilae has the capacity to employ different mechanisms to live under the extreme and cold conditions prevalent in Llullaillaco Volcano Lake. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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