Special Issue "Diversity and Dynamics of Marine Microbial Communities"

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

Deadline for manuscript submissions: closed (29 February 2016)

Special Issue Editor

Guest Editor
Prof. Dr. Johannes F. Imhoff

Marine Mikrobiologie, Helmholtz Centre for Ocean Research GEOMAR, Düsternbrooker Weg 20, D-24105 Kiel, Germany
E-Mail
Fax: +0431-600-4452
Interests: microbiology, microbial diversity, marine biotechnology, bioactive compounds, marine microbiology, marine natural products, algae microbe interactions, marine microbial resources, marine fungi

Special Issue Information

Dear Colleagues,

Powerful tools have been developed in recent years, not only to study the diversity of microbial communities in marine habitats, but also to follow up their dynamic changes using different genomic and genetic approaches. Although information is available on a few functional groups, such as sulfate reducers, nitrifyers, and methane oxidizers, others have received less attention and only a little information is available on their dynamic changes. The marine realm includes such different habitats as marine coastal waters and sediments, the surfaces of marine algae and animals, the deep sea (including deep subsurface habitats, hot vents and polar ice habitats), which all harbor specifically adapted microbial communities. Such studies may include marine fungi, actinobacteria, phototrophic bacteria or algae and a wide range of other groups of microorganisms. Also, studies on the functional microbial diversity of marine habitats and their dynamic changes, which apply metagenomic approaches on the basis of functional genes, are highly welcome for this Special Issue.

Prof. Dr. Johannes F. Imhoff
Guest Editor

Manuscript Submission Information

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Keywords

  • functional genes
  • dynamic changes
  • functional genetic groups
  • Metagenomic approaches
  • marine environmental biodiversity
  • adaptation of functional microbial groups
  • diversity changes along environmental gradients
  • impact of environmental changes on community composition and diversity of marine bacteria and archaea

Published Papers (5 papers)

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Research

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Open AccessArticle Phylogenetic Characterization of Marine Benthic Archaea in Organic-Poor Sediments of the Eastern Equatorial Pacific Ocean (ODP Site 1225)
Microorganisms 2016, 4(3), 32; https://doi.org/10.3390/microorganisms4030032
Received: 20 April 2016 / Revised: 16 July 2016 / Accepted: 22 August 2016 / Published: 6 September 2016
Cited by 8 | PDF Full-text (1254 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Sequencing surveys of microbial communities in marine subsurface sediments have focused on organic-rich, continental margins; the database for organic-lean deep-sea sediments from mid-ocean regions is underdeveloped. The archaeal community in subsurface sediments of ODP Site 1225 in the eastern equatorial Pacific (3760 m [...] Read more.
Sequencing surveys of microbial communities in marine subsurface sediments have focused on organic-rich, continental margins; the database for organic-lean deep-sea sediments from mid-ocean regions is underdeveloped. The archaeal community in subsurface sediments of ODP Site 1225 in the eastern equatorial Pacific (3760 m water depth; 1.1 and 7.8 m sediment depth) was analyzed by PCR, cloning and sequencing, and by denaturant gradient gel electrophoresis (DGGE) of 16S rRNA genes. Three uncultured archaeal lineages with different depth distributions were found: Marine Group I (MG-I) within the Thaumarchaeota, its sister lineage Marine Benthic Group A (MBG-A), the phylum-level archaeal lineage Marine Benthic Group B (also known as Deep-Sea Archaeal Group or Lokiarchaeota), and the Deep-Sea Euryarchaeotal Group 3. The MG-I phylotypes included representatives of sediment clusters that are distinct from the pelagic members of this phylum. On the scale from fully oxidized, extremely organic carbon-depleted sediments (for example, those the South Pacific Gyre) to fully reduced, organic carbon-rich marine subsurface sediments (such as those of the Peru Margin), Ocean Drilling Program (ODP) Site 1225 falls into the non-extreme organic carbon-lean category, and harbors archaeal communities from both ends of the spectrum. Full article
(This article belongs to the Special Issue Diversity and Dynamics of Marine Microbial Communities)
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Open AccessArticle Enrichment of Fusobacteria in Sea Surface Oil Slicks from the Deepwater Horizon Oil Spill
Microorganisms 2016, 4(3), 24; https://doi.org/10.3390/microorganisms4030024
Received: 15 April 2016 / Revised: 14 July 2016 / Accepted: 20 July 2016 / Published: 27 July 2016
Cited by 4 | PDF Full-text (1327 KB) | HTML Full-text | XML Full-text
Abstract
The Deepwater Horizon (DWH) oil spill led to rapid microbial community shifts in the Gulf of Mexico, including the formation of unprecedented quantities of marine oil snow (MOS) and of a massive subsurface oil plume. The major taxa that bloomed in sea surface [...] Read more.
The Deepwater Horizon (DWH) oil spill led to rapid microbial community shifts in the Gulf of Mexico, including the formation of unprecedented quantities of marine oil snow (MOS) and of a massive subsurface oil plume. The major taxa that bloomed in sea surface oil slicks during the spill included Cycloclasticus, and to a lesser extent Halomonas, Alteromonas, and Pseudoalteromonas—organisms that grow and degrade oil hydrocarbons aerobically. Here, we show that sea surface oil slicks at DWH contained obligate and facultative anaerobic taxa, including members of the obligate anaerobic phylum Fusobacteria that are commonly found in marine sediment environments. Pyrosequencing analysis revealed that Fusobacteria were strongly selected for when sea surface oil slicks were allowed to develop anaerobically. These organisms have been found in oil-contaminated sediments in the Gulf of Mexico, in deep marine oil reservoirs, and other oil-contaminated sites, suggesting they have putative hydrocarbon-degrading qualities. The occurrence and strong selection for Fusobacteria in a lab-based incubation of a sea surface oil slick sample collected during the spill suggests that these organisms may have become enriched in anaerobic zones of suspended particulates, such as MOS. Whilst the formation and rapid sinking of MOS is recognised as an important mechanism by which a proportion of the Macondo oil had been transported to the sea floor, its role in potentially transporting microorganisms, including oil-degraders, from the upper reaches of the water column to the seafloor should be considered. The presence of Fusobacteria on the sea surface—a highly oxygenated environment—is intriguing, and may be explained by the vertical upsurge of oil that provided a carrier to transport these organisms from anaerobic/micro-aerophilic zones in the oil plume or seabed to the upper reaches of the water column. We also propose that the formation of rapidly-sinking MOS may have re-transported these, and other microbial taxa, to the sediment in the Gulf of Mexico. Full article
(This article belongs to the Special Issue Diversity and Dynamics of Marine Microbial Communities)
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Open AccessArticle Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae
Microorganisms 2016, 4(3), 23; https://doi.org/10.3390/microorganisms4030023
Received: 7 March 2016 / Revised: 1 June 2016 / Accepted: 23 June 2016 / Published: 5 July 2016
Cited by 9 | PDF Full-text (2254 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding [...] Read more.
Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome. Full article
(This article belongs to the Special Issue Diversity and Dynamics of Marine Microbial Communities)
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Open AccessArticle In Silico Analysis of a Novel Plasmid from the Coral Pathogen Vibrio coralliilyticus Reveals Two Potential “Ecological Islands”
Microorganisms 2016, 4(1), 3; https://doi.org/10.3390/microorganisms4010003
Received: 30 October 2015 / Revised: 1 December 2015 / Accepted: 10 December 2015 / Published: 4 January 2016
Cited by 1 | PDF Full-text (1416 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
As virulence often correlates with the presence of plasmid replicons in several Vibrio spp., this study investigated whether non-chromosomal DNA could be found in the coral pathogen, Vibrio coralliilyticus BAA-450. A circular plasmid, 26,631 bp in size, was identified. DNA sequence analysis indicated [...] Read more.
As virulence often correlates with the presence of plasmid replicons in several Vibrio spp., this study investigated whether non-chromosomal DNA could be found in the coral pathogen, Vibrio coralliilyticus BAA-450. A circular plasmid, 26,631 bp in size, was identified. DNA sequence analysis indicated that the plasmid contained 30 open reading frames, six tRNA genes, 12 inverted repeats, three direct repeats and presented no continuous sequence identity to other replicons within the database. Consequently, these findings indicate that this is a novel, previously unidentified, plasmid. Two putative “ecological islands” were also identified and are predicted to encode for various factors that would facilitate growth and survival under different ecological conditions. In addition, two open reading frames may encode proteins that contribute to the pathogenicity of the organism. Functional cooperativity is also indicated between several plasmid- and chromosomally-encoded proteins, which, in a single instance, would allow a fully functioning nutrient uptake system to be established. Full article
(This article belongs to the Special Issue Diversity and Dynamics of Marine Microbial Communities)
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Review

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Open AccessReview New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment
Microorganisms 2016, 4(2), 19; https://doi.org/10.3390/microorganisms4020019
Received: 8 March 2016 / Revised: 20 May 2016 / Accepted: 20 May 2016 / Published: 24 May 2016
Cited by 5 | PDF Full-text (3929 KB) | HTML Full-text | XML Full-text
Abstract
During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step [...] Read more.
During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane monooxygenase (pmoA) for methane oxidizing bacteria. Full article
(This article belongs to the Special Issue Diversity and Dynamics of Marine Microbial Communities)
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Graphical abstract

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