Microorganisms

Research

14 pages, 1347 KiB

Open AccessArticle

Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale

by Sonia S. Valencia-Agami, Daniel Cerqueda-García, Sébastien Putzeys, María Magdalena Uribe-Flores, Norberto Ulises García-Cruz, Daniel Pech, Jorge Herrera-Silveira, M. Leopoldina Aguirre-Macedo and José Q. García-Maldonado

Microorganisms 2019, 7(10), 441; https://doi.org/10.3390/microorganisms7100441 - 11 Oct 2019

Cited by 23 | Viewed by 4022

Abstract

The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The [...] Read more.

The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r² = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r² = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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22 pages, 4323 KiB

Open AccessArticle

Effects of Vertical Water Mass Segregation on Bacterial Community Structure in the Beaufort Sea

by Yunyun Fu, Richard B. Rivkin and Andrew S. Lang

Microorganisms 2019, 7(10), 385; https://doi.org/10.3390/microorganisms7100385 - 24 Sep 2019

Cited by 5 | Viewed by 2479

Abstract

The Arctic Ocean is one of the least well-studied marine microbial ecosystems. Its low-temperature and low-salinity conditions are expected to result in distinct bacterial communities, in comparison to lower latitude oceans. However, this is an ocean currently in flux, with climate change exerting [...] Read more.

The Arctic Ocean is one of the least well-studied marine microbial ecosystems. Its low-temperature and low-salinity conditions are expected to result in distinct bacterial communities, in comparison to lower latitude oceans. However, this is an ocean currently in flux, with climate change exerting pronounced effects on sea-ice coverage and freshwater inputs. How such changes will affect this ecosystem are poorly constrained. In this study, we characterized the bacterial community compositions at different depths in both coastal, freshwater-influenced, and pelagic, sea-ice-covered locations in the Beaufort Sea in the western Canadian Arctic Ocean. The environmental factors controlling the bacterial community composition and diversity were investigated. Alphaproteobacteria dominated the bacterial communities in samples from all depths and stations. The Pelagibacterales and Rhodobacterales groups were the predominant taxonomic representatives within the Alphaproteobacteria. Bacterial communities in coastal and offshore samples differed significantly, and vertical water mass segregation was the controlling factor of community composition among the offshore samples, regardless of the taxonomic level considered. These data provide an important baseline view of the bacterial community in this ocean system that will be of value for future studies investigating possible changes in the Arctic Ocean in response to global change and/or anthropogenic disturbance. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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15 pages, 1217 KiB

Open AccessArticle

Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System

by Moonsuk Hur and Soo-Je Park

Microorganisms 2019, 7(9), 357; https://doi.org/10.3390/microorganisms7090357 - 16 Sep 2019

Cited by 23 | Viewed by 5015

Abstract

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio [...] Read more.

Heavy metal pollution is a serious environmental problem as it adversely affects crop production and human activity. In addition, the microbial community structure and composition are altered in heavy-metal-contaminated soils. In this study, using full-length 16S rRNA gene sequences obtained by a PacBio RS II system, we determined the microbial diversity and community structure in heavy-metal-contaminated soil. Furthermore, we investigated the microbial distribution, inferred their putative functional traits, and analyzed the environmental effects on the microbial compositions. The soil samples selected in this study were heavily and continuously contaminated with various heavy metals due to closed mines. We found that certain microorganisms (e.g., sulfur or iron oxidizers) play an important role in the biogeochemical cycle. Using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis, we predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) functional categories from abundances of microbial communities and revealed a high proportion belonging to transport, energy metabolism, and xenobiotic degradation in the studied sites. In addition, through full-length analysis, Conexibacter-like sequences, commonly identified by environmental metagenomics among the rare biosphere, were detected. In addition to microbial composition, we confirmed that environmental factors, including heavy metals, affect the microbial communities. Unexpectedly, among these environmental parameters, electrical conductivity (EC) might have more importance than other factors in a community description analysis. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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11 pages, 1487 KiB

Open AccessArticle

Unveiling of Concealed Processes for the Degradation of Pharmaceutical Compounds by Neopestalotiopsis sp.

by Bo Ram Kang, Min Sung Kim and Tae Kwon Lee

Microorganisms 2019, 7(8), 264; https://doi.org/10.3390/microorganisms7080264 - 16 Aug 2019

Cited by 8 | Viewed by 3476

Abstract

The presence of pharmaceutical products has raised emerging biorisks in aquatic environments. Fungi have been considered in sustainable approaches for the degradation of pharmaceutical compounds from aquatic environments. Soft rot fungi of the Ascomycota phylum are the most widely distributed among fungi, but [...] Read more.

The presence of pharmaceutical products has raised emerging biorisks in aquatic environments. Fungi have been considered in sustainable approaches for the degradation of pharmaceutical compounds from aquatic environments. Soft rot fungi of the Ascomycota phylum are the most widely distributed among fungi, but their ability to biodegrade pharmaceuticals has not been studied as much as that of white rot fungi of the Basidiomycota phylum. Herein, we evaluated the capacity of the soft rot fungus Neopestalotiopsis sp. B2B to degrade pharmaceuticals under treatment of woody and nonwoody lignocellulosic biomasses. Nonwoody rice straw induced laccase activity fivefold compared with that in YSM medium containing polysaccharide. But B2B preferentially degraded polysaccharide over lignin regions in woody sources, leading to high concentrations of sugar. Hence, intermediate products from saccharification may inhibit laccase activity and thereby halt the biodegradation of pharmaceutical compounds. These results provide fundamental insights into the unique characteristics of pharmaceutical degradation by soft rot fungus Neopestalotiopsis sp. in the presence of preferred substrates during delignification. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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18 pages, 1047 KiB

Open AccessArticle

The Form of N Supply Determines Plant Growth Promotion by P-Solubilizing Microorganisms in Maize

by Isaac Kwadwo Mpanga, Peteh Mehdi Nkebiwe, Mira Kuhlmann, Vincenza Cozzolino, Alessandro Piccolo, Jörg Geistlinger, Nils Berger, Uwe Ludewig and Günter Neumann

Microorganisms 2019, 7(2), 38; https://doi.org/10.3390/microorganisms7020038 - 29 Jan 2019

Cited by 49 | Viewed by 6707

Abstract

Phosphate-(P)-solubilizing microorganisms (PSM) are important drivers of P cycling in natural and agro-ecosystems. Their use as plant inoculants to improve P acquisition of crops has been investigated for decades. However, limited reproducibility of the expected effects, particularly under field conditions, remains a major [...] Read more.

Phosphate-(P)-solubilizing microorganisms (PSM) are important drivers of P cycling in natural and agro-ecosystems. Their use as plant inoculants to improve P acquisition of crops has been investigated for decades. However, limited reproducibility of the expected effects, particularly under field conditions, remains a major challenge. This study demonstrates that the form of nitrogen fertilization has a significant impact on the performance of various fungal and bacterial PSM inoculants in maize grown on neutral to alkaline soils with limited P availability. Under these conditions, a high soil pH-buffering capacity frequently limits the efficiency of nutrient mobilization, mediated by plant roots and microorganisms via rhizosphere acidification. In a soil pH range between 7.0 and 8.0, nitrate fertilization promoting rhizosphere alkalinisation further aggravates this problem. Accordingly, in greenhouse experiments, six strains of Pseudomonas, Bacillus, Paenibacillus, Streptomyces, and Penicillium with proven P-solubilizing potential, completely failed to promote P acquisition in maize grown on a calcareous Loess sub-soil pH 7.6 with nitrate fertilization and rock phosphate (Rock-P) as a sparingly soluble P source. However, after replacement of nitrate fertilization by ammonium, stabilized with the nitrification inhibitor 3,4-dimethylpyrazole-phosphate (DMPP), five out of seven investigated PSM inoculants (comprising 12 fungal and bacterial PSM strains) exerted beneficial effects on plant growth and reached up to 88% of the shoot biomass production of a control supplied with soluble triple-superphosphate (TSP). Stabilized ammonium combined with PSM-inoculants improved P acquisition (Trichoderma harzianum T22, Pseudomonas sp. DMSZ 13134), while other strains particularly stimulated root growth (T. harzianum OMG16, Bacillus amyloliquefaciens FZB42), which promoted the acquisition also of other mineral nutrients, such as N, K, and Mn. A similar effect was recorded under field conditions on an alkaline clay-loam soil pH 8.6. The combination of stabilized ammonium with a range of consortium products based on T. harzianum OMG16, B. amyloliquefaciens, micronutrients, and humic acids completely compensated the effect of a TSP fertilization on field establishment, nutrient acquisition, and yield formation in maize, while non-stabilized urea-di-ammonium phosphate fertilization was largely ineffective. These findings suggest that the efficiency of PSM-plant interactions can be influenced by the form of N fertilization, offering promising perspectives for synergistic effects with stabilized ammonium fertilizers. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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Review

Jump to: Research, Other

24 pages, 850 KiB

Open AccessReview

Antibiotic Pollution in the Environment: From Microbial Ecology to Public Policy

by Susanne A. Kraemer, Arthi Ramachandran and Gabriel G. Perron

Microorganisms 2019, 7(6), 180; https://doi.org/10.3390/microorganisms7060180 - 22 Jun 2019

Cited by 647 | Viewed by 28773

Abstract

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address [...] Read more.

The ability to fight bacterial infections with antibiotics has been a longstanding cornerstone of modern medicine. However, wide-spread overuse and misuse of antibiotics has led to unintended consequences, which in turn require large-scale changes of policy for mitigation. In this review, we address two broad classes of corollaries of antibiotics overuse and misuse. Firstly, we discuss the spread of antibiotic resistance from hotspots of resistance evolution to the environment, with special concerns given to potential vectors of resistance transmission. Secondly, we outline the effects of antibiotic pollution independent of resistance evolution on natural microbial populations, as well as invertebrates and vertebrates. We close with an overview of current regional policies tasked with curbing the effects of antibiotics pollution and outline areas in which such policies are still under development. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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14 pages, 1167 KiB

Open AccessReview

Microbial Eukaryotes in Oil Sands Environments: Heterotrophs in the Spotlight

by Elisabeth Richardson and Joel B. Dacks

Microorganisms 2019, 7(6), 178; https://doi.org/10.3390/microorganisms7060178 - 19 Jun 2019

Cited by 5 | Viewed by 4979

Abstract

Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial [...] Read more.

Hydrocarbon extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world’s largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region. Full article

(This article belongs to the Special Issue The Response of Microorganisms to Anthropogenic Disturbance and Global Change)

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