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Microorganisms
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Towards Integrated Multi-omics Analyses of Environmental Microbiota
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Towards Integrated Multi-omics Analyses of Environmental Microbiota

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

Deadline for manuscript submissions: closed (31 January 2020) | Viewed by 56361

Special Issue Editors

Prof. Dr. Martin Von Bergen

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Guest Editor
Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research—UFZ, Permoserstr. 15, 04318 Leipzig, Germany
Interests: microbial ecology; biodegradation of pollutants; metaproteomics; microbial physiology
Special Issues, Collections and Topics in MDPI journals
Dr. Dirk Benndorf

E-Mail Website
Guest Editor
Bioprocess Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
Interests: microbial communities in natural environments; metaproteomics; mass spectrometry and bioinformatics; microbial metabolisms
Dr. Nico Jehmlich

E-Mail Website
Guest Editor
Department of Molecular Systems Biology, UFZ-Helmholtz Centre for Environmental Research, 04318 Leipzig, Germany
Interests: metaproteomics; protein-stable isotope probing; microbiome biology; environmental microbiology
Special Issues, Collections and Topics in MDPI journals

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 submissions that pass pre-check are 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 2700 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 (7 papers)

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Research

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14 pages, 1309 KiB  
Article
Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation
by Luz Breton-Deval, Ayixon Sanchez-Reyes, Alejandro Sanchez-Flores, Katy Juárez, Ilse Salinas-Peralta and Patricia Mussali-Galante
Microorganisms 2020, 8(4), 554; https://doi.org/10.3390/microorganisms8040554 - 12 Apr 2020
Cited by 9 | Viewed by 4300
Abstract
The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. [...] Read more.
The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1–S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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27 pages, 3340 KiB  
Article
Influence of Human Activities on Broad-Scale Estuarine-Marine Habitats Using Omics-Based Approaches Applied to Marine Sediments
by Rohan M. Shah, Joseph Crosswell, Suzanne S. Metcalfe, Geoffrey Carlin, Paul D. Morrison, Avinash V. Karpe, Enzo A. Palombo, Andy D.L. Steven and David J. Beale
Microorganisms 2019, 7(10), 419; https://doi.org/10.3390/microorganisms7100419 - 04 Oct 2019
Cited by 10 | Viewed by 3008
Abstract
Rapid urban expansion and increased human activities have led to the progressive deterioration of many marine ecosystems. The diverse microbial communities that inhabit these ecosystems are believed to influence large-scale geochemical processes and, as such, analyzing their composition and functional metabolism can be [...] Read more.
Rapid urban expansion and increased human activities have led to the progressive deterioration of many marine ecosystems. The diverse microbial communities that inhabit these ecosystems are believed to influence large-scale geochemical processes and, as such, analyzing their composition and functional metabolism can be a means to assessing an ecosystem’s resilience to physical and chemical perturbations, or at the very least provide baseline information and insight into future research needs. Here we show the utilization of organic and inorganic contaminant screening coupled with metabolomics and bacterial 16S rRNA gene sequencing to assess the microbial community structure of marine sediments and their functional metabolic output. The sediments collected from Moreton Bay (Queensland, Australia) contained low levels of organic and inorganic contaminants, typically below guideline levels. The sequencing dataset suggest that sulfur and nitrite reduction, dehalogenation, ammonia oxidation, and xylan degradation were the major metabolic functions. The community metabolites suggest a level of functional homogeneity down the 40-cm core depth sampled, with sediment habitat identified as a significant driver for metabolic differences. The communities present in river and sandy channel samples were found to be the most active, with the river habitats likely to be dominated by photoheterotrophs that utilized carbohydrates, fatty acids and alcohols as well as reduce nitrates to release atmospheric nitrogen and oxidize sulfur. Bioturbated mud habitats showed overlapping faunal activity between riverine and sandy ecosystems. Nitrogen-fixing bacteria and lignin-degrading bacteria were most abundant in the sandy channel and bioturbated mud, respectively. The use of omics-based approaches provide greater insight into the functional metabolism of these impacted habitats, extending beyond discrete monitoring to encompassing whole community profiling that represents true phenotypical outputs. Ongoing omics-based monitoring that focuses on more targeted pathway analyses is recommended in order to quantify the flux changes within these systems and establish variations from these baseline measurements. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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13 pages, 1217 KiB  
Article
Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome
by Oskar Hickl, Anna Heintz-Buschart, Anke Trautwein-Schult, Rajna Hercog, Peer Bork, Paul Wilmes and Dörte Becher
Microorganisms 2019, 7(9), 367; https://doi.org/10.3390/microorganisms7090367 - 19 Sep 2019
Cited by 27 | Viewed by 4583
Abstract
With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible [...] Read more.
With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at −80 °C should be chosen wherever possible. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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13 pages, 4036 KiB  
Article
Response of Microbial Communities and Their Metabolic Functions to Drying–Rewetting Stress in a Temperate Forest Soil
by Dong Liu, Katharina M. Keiblinger, Sonja Leitner, Uwe Wegner, Michael Zimmermann, Stephan Fuchs, Christian Lassek, Katharina Riedel and Sophie Zechmeister-Boltenstern
Microorganisms 2019, 7(5), 129; https://doi.org/10.3390/microorganisms7050129 - 13 May 2019
Cited by 32 | Viewed by 5131
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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13 pages, 1834 KiB  
Article
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
by Alvaro S. Villalobos, Jutta Wiese, Johannes F. Imhoff, Cristina Dorador, Alexander Keller and Ute Hentschel
Microorganisms 2019, 7(4), 107; https://doi.org/10.3390/microorganisms7040107 - 23 Apr 2019
Cited by 4 | Viewed by 3477
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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Review

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16 pages, 590 KiB  
Review
Does Soil Contribute to the Human Gut Microbiome?
by Winfried E.H. Blum, Sophie Zechmeister-Boltenstern and Katharina M. Keiblinger
Microorganisms 2019, 7(9), 287; https://doi.org/10.3390/microorganisms7090287 - 23 Aug 2019
Cited by 85 | Viewed by 30845
Abstract
Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with the modern lifestyle. We tracked relationships between the soil microbiome and the human [...] Read more.
Soil and the human gut contain approximately the same number of active microorganisms, while human gut microbiome diversity is only 10% that of soil biodiversity and has decreased dramatically with the modern lifestyle. We tracked relationships between the soil microbiome and the human intestinal microbiome. We propose a novel environmental microbiome hypothesis, which implies that a close linkage between the soil microbiome and the human intestinal microbiome has evolved during evolution and is still developing. From hunter-gatherers to an urbanized society, the human gut has lost alpha diversity. Interestingly, beta diversity has increased, meaning that people in urban areas have more differentiated individual microbiomes. On top of little contact with soil and feces, hygienic measures, antibiotics and a low fiber diet of processed food have led to a loss of beneficial microbes. At the same time, loss of soil biodiversity is observed in many rural areas. The increasing use of agrochemicals, low plant biodiversity and rigorous soil management practices have a negative effect on the biodiversity of crop epiphytes and endophytes. These developments concur with an increase in lifestyle diseases related to the human intestinal microbiome. We point out the interference with the microbial cycle of urban human environments versus pre-industrial rural environments. In order to correct these interferences, it may be useful to adopt a different perspective and to consider the human intestinal microbiome as well as the soil/root microbiome as ‘superorganisms’ which, by close contact, replenish each other with inoculants, genes and growth-sustaining molecules. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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Other

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17 pages, 4217 KiB  
Protocol
Metagenomic Evaluation of Bacterial and Fungal Assemblages Enriched within Diffusion Chambers and Microbial Traps Containing Uraniferous Soils
by Rajneesh Jaswal, Ashish Pathak and Ashvini Chauhan
Microorganisms 2019, 7(9), 324; https://doi.org/10.3390/microorganisms7090324 - 06 Sep 2019
Cited by 17 | Viewed by 4003
Abstract
Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such [...] Read more.
Despite significant technological advancements in the field of microbial ecology, cultivation and subsequent isolation of the vast majority of environmental microorganisms continues to pose challenges. Isolation of the environmental microbiomes is prerequisite to better understand a myriad of ecosystem services they provide, such as bioremediation of contaminants. Towards this end, in this culturomics study, we evaluated the colonization of soil bacterial and fungal communities within diffusion chambers (DC) and microbial traps (MT) established using uraniferous soils collected from a historically contaminated soil from Aiken, USA. Microbial assemblages were compared between the DC and MT relative to the native soils using amplicon based metagenomic and bioinformatic analysis. The overall rationale of this study is that DC and MT growth chambers provide the optimum conditions under which desired microbiota, identified in a previous study to serve as the “core” microbiomes, will proliferate, leading to their successful isolation. Specifically, the core microbiomes consisted of assemblages of bacteria (Burkholderia spp.) and fungi (Penicillium spp.), respectively. The findings from this study further supported previous data such that the abundance and diversity of the desired “core” microbiomes significantly increased as a function of enrichments over three consecutive generations of DC and MT, respectively. Metagenomic analysis of the DC/MT generations also revealed that enrichment and stable populations of the desired “core” bacterial and fungal microbiomes develop within the first 20 days of incubation and the practice of subsequent transfers for second and third generations, as is standard in previous studies, may be unnecessary. As a cost and time cutting measure, this study recommends running the DC/MT chambers for only a 20-day time period, as opposed to previous studies, which were run for months. In summation, it was concluded that, using the diffusion chamber-based enrichment techniques, growth of desired microbiota possessing environmentally relevant functions can be achieved in a much shorter time frame than has been previously shown. Full article
(This article belongs to the Special Issue Towards Integrated Multi-omics Analyses of Environmental Microbiota)
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