Special Issue "Response of Microbial Communities to Environmental Changes"

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

Deadline for manuscript submissions: closed (31 January 2018)

Special Issue Editor

Guest Editor
Dr. Ulrich (Uli) Stingl

Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Florida Research and Education Center, Davie, FL, USA
Website | E-Mail
Interests: marine microbiology; microbial ecology; microbiome; holobiont; marine bacteria; SAR11; microbes and climate change; microbial community structure; aquatic microbiology; bacterial cultivation

Special Issue Information

Dear Colleagues,

Microbes are an integral and essential part of all food webs. Microbial communities are extremely complex, containing thousands of species (or Operational Taxonomic Units, OTUs), and the exact function of most species, in and for a given environment, is unknown. Adding to this complexity, microbial communities respond quickly to alterations in physico-chemical parameters of their habitat (e.g., temperature, nutrient concentrations, pH, salinity), but the physiological consequences of these changes for higher trophic levels and for the respective ecosystem are mostly unknown. Changes in microbial community structure and function can happen in predictable seasonal patterns or more suddenly through disturbance events. This Special Issue will publish papers that address: (1) analyses of microbial community structure in relation to changes in physico-chemical parameters; (2) analyses of gene content (metagenomes) or gene expression (metatranscriptomes) of microbial communities in relation to changes in physico-chemical parameters; (3) physiological analyses of microbial communities, enrichment cultures, or pure cultures of key species in relation to changes in physico-chemical parameters; and (4) analyses and modeling of potential consequences of changes in microbial community structure or function for higher trophic levels in a given habitat.

Dr. Ulrich (Uli) Stingl
Guest Editor

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 1000 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

  • Climate change
  • Seasonal patterns
  • Disturbance events
  • Adaptation
  • Metagenomes
  • Metatranscriptomes
  • Physiological studies
  • Microbial community structure

Published Papers (8 papers)

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Editorial

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Open AccessEditorial Special Issue: Response of Microbial Communities to Environmental Changes
Microorganisms 2018, 6(2), 29; https://doi.org/10.3390/microorganisms6020029
Received: 21 March 2018 / Revised: 21 March 2018 / Accepted: 28 March 2018 / Published: 30 March 2018
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Abstract
Environmental issues such as eutrophication, ocean acidification, sea level rise, saltwater intrusion, increase in carbon dioxide levels, or rise of average global temperatures, among many others, are impacting and changing whole ecosystems [...]
Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)

Research

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Open AccessArticle Responses of Salt Marsh Plant Rhizosphere Diazotroph Assemblages to Drought
Microorganisms 2018, 6(1), 27; https://doi.org/10.3390/microorganisms6010027
Received: 1 February 2018 / Revised: 3 March 2018 / Accepted: 9 March 2018 / Published: 15 March 2018
Cited by 2 | PDF Full-text (6194 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Drought has many consequences in the tidally dominated Spartina sp. salt marshes of the southeastern US; including major dieback events, changes in sediment chemistry and obvious changes in the landscape. These coastal systems tend to be highly productive, yet many salt marshes are [...] Read more.
Drought has many consequences in the tidally dominated Spartina sp. salt marshes of the southeastern US; including major dieback events, changes in sediment chemistry and obvious changes in the landscape. These coastal systems tend to be highly productive, yet many salt marshes are also nitrogen limited and depend on plant associated diazotrophs as their source of ‘new’ nitrogen. A 4-year study was conducted to investigate the structure and composition of the rhizosphere diazotroph assemblages associated with 5 distinct plant zones in one such salt marsh. A period of greatly restricted tidal inundation and precipitation, as well as two periods of drought (June–July 2004, and May 2007) occurred during the study. DGGE of nifH PCR amplicons from rhizosphere samples, Principal Components Analysis of the resulting banding patterns, and unconstrained ordination analysis of taxonomic data and environmental parameters were conducted. Diazotroph assemblages were organized into 5 distinct groups (R2 = 0.41, p value < 0.001) whose presence varied with the environmental conditions of the marsh. Diazotroph assemblage group detection differed during and after the drought event, indicating that persistent diazotrophs maintained populations that provided reduced supplies of new nitrogen for vegetation during the periods of drought. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessArticle Responses of an Agricultural Soil Microbiome to Flooding with Seawater after Managed Coastal Realignment
Microorganisms 2018, 6(1), 12; https://doi.org/10.3390/microorganisms6010012
Received: 7 December 2017 / Revised: 12 January 2018 / Accepted: 18 January 2018 / Published: 26 January 2018
Cited by 1 | PDF Full-text (4036 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Coastal areas have become more prone to flooding with seawater due to climate-change-induced sea-level rise and intensified storm surges. One way to cope with this issue is by “managed coastal realignment”, where low-lying coastal areas are no longer protected and instead flooded with [...] Read more.
Coastal areas have become more prone to flooding with seawater due to climate-change-induced sea-level rise and intensified storm surges. One way to cope with this issue is by “managed coastal realignment”, where low-lying coastal areas are no longer protected and instead flooded with seawater. How flooding with seawater impacts soil microbiomes and the biogeochemical cycling of elements is poorly understood. To address this, we conducted a microcosm experiment using soil cores collected at the nature restoration project site Gyldensteen Strand (Denmark), which were flooded with seawater and monitored over six months. Throughout the experiment, biogeochemical analyses, microbial community fingerprinting and the quantification of marker genes documented clear shifts in microbiome composition and activity. The flooding with seawater initially resulted in accelerated heterotrophic activity that entailed high ammonium production and net removal of nitrogen from the system, also demonstrated by a concurrent increase in the abundances of marker genes for ammonium oxidation and denitrification. Due to the depletion of labile soil organic matter, microbial activity decreased after approximately four months. The event of flooding caused the largest shifts in microbiome composition with the availability of labile organic matter subsequently being the most important driver for the succession in microbiome composition in soils flooded with seawater. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessArticle Increase of Salt Tolerance in Carbon-Starved Cells of Rhodopseudomonas palustris Depending on Photosynthesis or Respiration
Microorganisms 2018, 6(1), 4; https://doi.org/10.3390/microorganisms6010004
Received: 1 December 2017 / Revised: 22 December 2017 / Accepted: 3 January 2018 / Published: 6 January 2018
Cited by 2 | PDF Full-text (806 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after [...] Read more.
Bacteria in natural environments are frequently exposed to nutrient starvation and survive against environmental stresses under non-growing conditions. In order to determine the energetic influence on survivability during starvation, changes in salt tolerance were investigated using the purple photosynthetic bacterium Rhodopseudomonas palustris after carbon starvation under photosynthetic conditions in comparison with anaerobic and aerobic dark conditions. Tolerance to a treatment with high concentration of salt (2.5 M NaCl for 1 h) was largely increased after starvation under anaerobically light and aerobically dark conditions. The starved cells under the conditions of photosynthesis or aerobic respiration contained high levels of cellular ATP, but starvation under the anaerobic dark conditions resulted in a decrease of cellular ATP contents. To observe the large increase of the salt tolerance, incubation of starved cells for more than 18 h under illumination was needed. These results suggest that the ATP-dependent rearrangement of cells induced salt tolerance. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessArticle Linking Compositional and Functional Predictions to Decipher the Biogeochemical Significance in DFAA Turnover of Abundant Bacterioplankton Lineages in the North Sea
Microorganisms 2017, 5(4), 68; https://doi.org/10.3390/microorganisms5040068
Received: 17 September 2017 / Revised: 1 November 2017 / Accepted: 2 November 2017 / Published: 5 November 2017
Cited by 4 | PDF Full-text (3094 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated [...] Read more.
Deciphering the ecological traits of abundant marine bacteria is a major challenge in marine microbial ecology. In the current study, we linked compositional and functional predictions to elucidate such traits for abundant bacterioplankton lineages in the North Sea. For this purpose, we investigated entire and active bacterioplankton composition along a transect ranging from the German Bight to the northern North Sea by pyrotag sequencing of bacterial 16S rRNA genes and transcripts. Functional profiles were inferred from 16S rRNA data using Tax4Fun. Bacterioplankton communities were dominated by well-known marine lineages including clusters/genera that are affiliated with the Roseobacter group and the Flavobacteria. Variations in community composition and function were significantly explained by measured environmental and microbial properties. Turnover of dissolved free amino acids (DFAA) showed the strongest correlation to community composition and function. We applied multinomial models, which enabled us to identify bacterial lineages involved in DFAA turnover. For instance, the genus Planktomarina was more abundant at higher DFAA turnover rates, suggesting its vital role in amino acid degradation. Functional predictions further indicated that Planktomarina is involved in leucine and isoleucine degradation. Overall, our results provide novel insights into the biogeochemical significance of abundant bacterioplankton lineages in the North Sea. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessArticle Effect of Environmental Factors on Intra-Specific Inhibitory Activity of Carnobacterium maltaromaticum
Microorganisms 2017, 5(3), 59; https://doi.org/10.3390/microorganisms5030059
Received: 26 June 2017 / Revised: 6 September 2017 / Accepted: 7 September 2017 / Published: 14 September 2017
Cited by 1 | PDF Full-text (1549 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Carnobacterium maltaromaticum is frequently associated with foods having extended shelf-life due to its inhibitory activity to other bacteria. The quantification of such inhibition interactions affected by various environmental factors is limited. This study investigated the effect of environmental factors relevant to vacuum-packaged beef [...] Read more.
Carnobacterium maltaromaticum is frequently associated with foods having extended shelf-life due to its inhibitory activity to other bacteria. The quantification of such inhibition interactions affected by various environmental factors is limited. This study investigated the effect of environmental factors relevant to vacuum-packaged beef on inhibition between two model isolates of C. maltaromaticum, D0h and D8c, specifically D8c sensitivity to D0h inhibition and D0h inhibitor production. The effects of temperature (−1, 7, 15, 25 °C), atmosphere (aerobic and anaerobic), pH (5.5, 6, 6.5), lactic acid (0, 25, 50 mM) and glucose (0, 0.56, 5.55 mM) on D8c sensitivity (diameter of an inhibition zone) were measured. The effects of pH, glucose, lactic acid and atmosphere on D0h inhibitor production were measured at 25 °C. Sensitivity of D8c was the highest at 15 °C, under aerobic atmosphere, at higher concentrations of undissociated lactic acid and glucose, and at pH 5.5 (p < 0.001). pH significantly affected D0h inhibitor production (p < 0.001), which was the highest at pH 6.5. The effect of lactic acid depended upon pH level; at relatively low pH (5.5), lactic acid decreased the production rate (arbitrary inhibition unit (AU)/mL/h). This study provides a quantitative description of intra-species interactions, studied in in vitro environments that are relevant to vacuum-packaged beef. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Review

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Open AccessReview What Kills the Hindgut Flagellates of Lower Termites during the Host Molting Cycle?
Microorganisms 2017, 5(4), 82; https://doi.org/10.3390/microorganisms5040082
Received: 3 November 2017 / Revised: 7 December 2017 / Accepted: 9 December 2017 / Published: 18 December 2017
Cited by 3 | PDF Full-text (1734 KB) | HTML Full-text | XML Full-text
Abstract
Subsocial wood feeding cockroaches in the genus Cryptocercus, the sister group of termites, retain their symbiotic gut flagellates during the host molting cycle, but in lower termites, closely related flagellates die prior to host ecdysis. Although the prevalent view is that termite [...] Read more.
Subsocial wood feeding cockroaches in the genus Cryptocercus, the sister group of termites, retain their symbiotic gut flagellates during the host molting cycle, but in lower termites, closely related flagellates die prior to host ecdysis. Although the prevalent view is that termite flagellates die because of conditions of starvation and desiccation in the gut during the host molting cycle, the work of L.R. Cleveland in the 1930s through the 1960s provides a strong alternate hypothesis: it was the changed hormonal environment associated with the origin of eusociality and its concomitant shift in termite developmental ontogeny that instigates the death of the flagellates in termites. Although the research on termite gut microbial communities has exploded since the advent of modern molecular techniques, the role of the host hormonal environment on the life cycle of its gut flagellates has been neglected. Here Cleveland’s studies are revisited to provide a basis for re-examination of the problem, and the results framed in the context of two alternate hypotheses: the flagellate symbionts are victims of the change in host social status, or the flagellates have become incorporated into the life cycle of the eusocial termite colony. Recent work on parasitic protists suggests clear paths for exploring these hypotheses and for resolving long standing issues regarding sexual-encystment cycles in flagellates of the Cryptocercus-termite lineage using molecular methodologies, bringing the problem into the modern era. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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Open AccessReview The Seagrass Holobiont and Its Microbiome
Microorganisms 2017, 5(4), 81; https://doi.org/10.3390/microorganisms5040081
Received: 2 November 2017 / Revised: 4 December 2017 / Accepted: 5 December 2017 / Published: 15 December 2017
Cited by 6 | PDF Full-text (3911 KB) | HTML Full-text | XML Full-text
Abstract
Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on [...] Read more.
Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on the shorelines. A global assessment reported that 29% of the known areal extent of seagrasses has disappeared since seagrass areas were initially recorded in 1879. Several factors such as direct and indirect human activity contribute to the demise of seagrasses. One of the main reasons for seagrass die-offs all over the world is increased sulfide concentrations in the sediment that result from the activity of sulfate-reducing prokaryotes, which perform the last step of the anaerobic food chain in marine sediments and reduce sulfate to H2S. Recent seagrass die-offs, e.g., in the Florida and Biscayne Bays, were caused by an increase in pore-water sulfide concentrations in the sediment, which were the combined result of unfavorable environmental conditions and the activities of various groups of heterotrophic bacteria in the sulfate-rich water-column and sediment that are stimulated through increased nutrient concentrations. Under normal circumstances, seagrasses are able to withstand low levels of sulfide, probably partly due to microbial symbionts, which detoxify sulfide by oxidizing it to sulfur or sulfate. Novel studies are beginning to give greater insights into the interactions of microbes and seagrasses, not only in the sulfur cycle. Here, we review the literature on the basic ecology and biology of seagrasses and focus on studies describing their microbiome. Full article
(This article belongs to the Special Issue Response of Microbial Communities to Environmental Changes)
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