Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
6.4
4.5
Journals
Microorganisms
Special Issues
Molecular Ecology and Genetic Diversity of Marine Microorganisms
share announcement

Molecular Ecology and Genetic Diversity of Marine Microorganisms

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

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 15004

Special Issue Editors

Dr. Bernd Wemheuer

E-Mail Website
Guest Editor
Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, D-37077 Göttingen, Germany
Interests: environmental microbiology; next-generation sequencing; transcriptomics; bioinformatics and computational biology; RNA; DNA extraction; cell culture; molecular cloning; RNA extraction; microbial ecology
Prof. Dr. Rolf Daniel

E-Mail Website
Guest Editor
Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, D-37077 Göttingen, Germany
Interests: functional genomics; RNA-seq; molecular microbial ecology; Pseudomonas aeruginosa; genome annotation; transcriptome sequencing; microbial genomics; marine microbiology; pyrosequencing; microbiome; marine microbial ecology; annotation; gene annotation; functional annotation; environmental genomics; microbial evolution
Dr. Franziska Wemheuer

E-Mail Website
Guest Editor
Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, D-37077 Göttingen, Germany
Interests: applied microbiology; environmental microbiology; microbial ecology; bacteria; microbial diversity; sequence analysis; metagenomics; rhizosphere; microbial genomics; marine microbiology; gut microbiology; denaturing gradient gel electrophoresis; archaea; rRNA genes; extremophiles; rRNA

Special Issue Information

Dear Colleagues,

Microorganisms are an integral component of marine ecosystems. They are essential to ecosystem stability and functioning. Marine microbes are key drivers of important nutrient cycles and support higher food-webs. Marine environments vary in an array of parameters such as temperature, salinity, and wind patterns. Despite the increasing number of studies, our knowledge of microbial community assembly under various environmental conditions and their interactions with each other and with their environment remains limited.

With this Special Issue, we seek to improve our understanding of the molecular ecology and genetic diversity of marine microorganisms. As this can only be achieved by gathering information from different perspectives, we encourage marine biologists around the world to submit research articles, review articles, and short communications related to the various aspects of microbial life in marine ecosystems. Special emphasis will be placed on coastal marine ecosystems because these areas are constantly threatened by several abiotic and biotic factors, such as pollution. As new interdisciplinary techniques, such as modeling approaches, are needed to bridge the gap between omics and earth system sciences, we especially welcome both environmental and laboratory studies, particularly those with a cross-disciplinary strategy that combines molecular, physiological, and chemical methods.

Dr. Bernd Wemheuer
Prof. Dr. Rolf Daniel
Dr. Franziska Wemheuer
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 ecology
  • marine microorganisms
  • bacteria
  • archaea
  • microeukaryoytes

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Other

14 pages, 2605 KiB  
Article
The Influence of pCO2-Driven Ocean Acidification on Open Ocean Bacterial Communities during A Short-Term Microcosm Experiment in the Eastern Tropical South Pacific (ETSP) off Northern Chile
by Paulina Aguayo, Víctor L. Campos, Carlos Henríquez, Francisca Olivares, Rodrigo De Ia Iglesia, Osvaldo Ulloa and Cristian A. Vargas
Microorganisms 2020, 8(12), 1924; https://doi.org/10.3390/microorganisms8121924 - 04 Dec 2020
Cited by 7 | Viewed by 2585
Abstract
Due to the increasing anthropogenic CO2 emissions, Ocean Acidification (OA) is progressing rapidly around the world. Despite the major role that microorganisms play on the marine biogeochemical cycling and ecosystem functioning, the response of bacterial communities upon OA scenarios is still not [...] Read more.
Due to the increasing anthropogenic CO2 emissions, Ocean Acidification (OA) is progressing rapidly around the world. Despite the major role that microorganisms play on the marine biogeochemical cycling and ecosystem functioning, the response of bacterial communities upon OA scenarios is still not well understood. Here, we have conducted a detailed characterization of the composition and relative abundance of bacterial communities in the water column of an open-ocean station in the Eastern Tropical South Pacific (ETSP) off northern Chile and their interactions with environmental factors. In addition, through a short-term microcosm experiment, we have assessed the effect of low pH/high pCO2 conditions over the abundance and genetic diversity of bacterial communities. Our results evidence a clear partitioning of community composition that could be attributed mostly to dissolved oxygen. However, our experimental approach demonstrated that low pH/high pCO2 conditions might modify the structure of the bacterial community, evidencing that small changes in pH may impact significantly the abundance and diversity of key microorganisms. This study constitutes a first step aiming to provide insight about the influence of changing carbonate chemistry conditions on natural bacterial communities and to shed light on the potential impact of OA in biogeochemical cycles on the ETSP region. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Marine Microorganisms)
►▼ Show Figures

Figure 1

17 pages, 3190 KiB  
Article
An Optimized Metabarcoding Method for Mimiviridae
by Florian Prodinger, Hisashi Endo, Yasuhiro Gotoh, Yanze Li, Daichi Morimoto, Kimiho Omae, Kento Tominaga, Romain Blanc-Mathieu, Yoshihito Takano, Tetsuya Hayashi, Keizo Nagasaki, Takashi Yoshida and Hiroyuki Ogata
Microorganisms 2020, 8(4), 506; https://doi.org/10.3390/microorganisms8040506 - 02 Apr 2020
Cited by 5 | Viewed by 4116
Abstract
Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological profiling of Mimiviridae, we previously proposed a meta-barcoding [...] Read more.
Mimiviridae is a group of viruses with large genomes and virions. Ecological relevance of Mimiviridae in marine environments has been increasingly recognized through the discoveries of novel isolates and metagenomic studies. To facilitate ecological profiling of Mimiviridae, we previously proposed a meta-barcoding approach based on 82 degenerate primer pairs (i.e., MEGAPRIMER) targeting the DNA polymerase gene of Mimiviridae. The method detected a larger number of operational taxonomic units (OTUs) in environmental samples than previous methods. However, it required large quantities of DNA and was laborious due to the use of individual primer pairs. Here, we examined coastal seawater samples using varying PCR conditions and purification protocols to streamline the MEGAPRIMER method. Mixing primer pairs in “cocktails” reduced the required amount of environmental DNA by 90%, while reproducing the results obtained by the original protocol. We compared the results obtained by the meta-barcoding approach with quantifications using qPCR for selected OTUs. This revealed possible amplification biases among different OTUs, but the frequency profiles for individual OTUs across multiple samples were similar to those obtained by qPCR. We anticipate that the newly developed MEGAPRIMER protocols will be useful for ecological investigation of Mimiviridae in a larger set of environmental samples. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Marine Microorganisms)
►▼ Show Figures

Figure 1

15 pages, 2330 KiB  
Article
Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas
by Huilong Ou, Mingyu Li, Shufei Wu, Linli Jia, Russell T. Hill and Jing Zhao
Microorganisms 2020, 8(1), 63; https://doi.org/10.3390/microorganisms8010063 - 30 Dec 2019
Cited by 6 | Viewed by 3034 | Correction
Abstract
Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts [...] Read more.
Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments. Massive polyP granules were observed under confocal microscopy in samples from very low DIP environments. The composition of sponge symbiotic microbes was analyzed by high-throughput sequencing and the corresponding polyphosphate kinase (ppk) genes were detected. Sequence analysis revealed that in the low DIP environment, those sponges with higher polyP content and enrichment rates had relatively higher abundances of cyanobacteria. Mantel tests and canonical correspondence analysis (CCA) examined that the polyP enrichment rate was most strongly correlated with the structure of microbial communities, including genera Synechococcus, Rhodopirellula, Blastopirellula, and Rubripirellula. About 50% of ppk genes obtained from the total DNA of sponge holobionts, had above 80% amino acid sequence similarities to those sequences from Synechococcus. In general, it suggested that sponges employed differentiated strategies towards the use of phosphorus in different nutrient environments and the symbiotic Synechococcus could play a key role in accumulating polyP. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Marine Microorganisms)
►▼ Show Figures

Graphical abstract

15 pages, 3235 KiB  
Article
Environmental Filtering Drives the Assembly of Habitat Generalists and Specialists in the Coastal Sand Microbial Communities of Southern China
by Anyi Hu, Hongjie Wang, Meixian Cao, Azhar Rashid, Mingfeng Li and Chang-Ping Yu
Microorganisms 2019, 7(12), 598; https://doi.org/10.3390/microorganisms7120598 - 21 Nov 2019
Cited by 26 | Viewed by 3464
Abstract
Coastal sands harbor diverse microbial assemblages that play a critical role in the biogeochemical cycling of beach ecosystems. However, little is known about the relative importance of the different ecological processes underlying the assembly of communities of sand microbiota. Here, we employed 16S [...] Read more.
Coastal sands harbor diverse microbial assemblages that play a critical role in the biogeochemical cycling of beach ecosystems. However, little is known about the relative importance of the different ecological processes underlying the assembly of communities of sand microbiota. Here, we employed 16S rDNA amplicon sequencing to investigate the sand microbiota of two coastal beaches, in southern China. The results showed that sand microbial assemblages at intertidal and supratidal zones exhibited contrasting compositions that can be attributed to environmental filtering by electric conductivity. A consistent pattern of habitat generalists and specialists of sand microbiota was observed among different beach zones. Null and neutral model analyses indicated that the environmental filtering was mainly responsible for supratidal microbial communities, while the neutral processes could partially influence the assembly of intertidal communities. Moreover, environmental filtering was found to shape the habitat specialists, while random dispersal played a major role in shaping generalists. The neutral model analysis revealed that the habitat generalists exceeding the neutral prediction harbored a relatively higher proportion of microbial taxa than the specialist counterparts. An opposite pattern was observed for taxa falling below the neutral prediction. Collectively, these findings offer a novel insight into the assembly mechanisms of coastal sand microbiota. Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Marine Microorganisms)
►▼ Show Figures

Figure 1

Other

Jump to: Research

1 pages, 158 KiB  
Correction
Correction: Ou et al. Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas. Microorganisms 2020, 8, 63
by Huilong Ou, Mingyu Li, Shufei Wu, Linli Jia, Russell T. Hill and Jing Zhao
Microorganisms 2021, 9(9), 1826; https://doi.org/10.3390/microorganisms9091826 - 27 Aug 2021
Viewed by 1228
Abstract
The authors wish to make the following corrections to this paper [...] Full article
(This article belongs to the Special Issue Molecular Ecology and Genetic Diversity of Marine Microorganisms)
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop