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13 pages, 1691 KiB

Open AccessArticle

Microcystin-LR, a Cyanobacterial Toxin, Induces Changes in the Organization of Membrane Compartments in Arabidopsis

by Gabriella Petra Juhász, Sándor Kéki, Anita Dékány-Adamoczky, Csongor Freytag, Gábor Vasas, Csaba Máthé and Tamás Garda

Microorganisms 2023, 11(3), 586; https://doi.org/10.3390/microorganisms11030586 - 25 Feb 2023

Cited by 2 | Viewed by 1856

Abstract

To evaluate the effects of the cyanobacterial toxin microcystin-LR (MCY-LR, a protein phosphatase inhibitor) and diquat (DQ, an oxidative stress inducer) on the organization of tonoplast, the effect of MCY-LR on plastid stromule formation and on mitochondria was investigated in wild-type Arabidopsis. Tonoplast [...] Read more.

To evaluate the effects of the cyanobacterial toxin microcystin-LR (MCY-LR, a protein phosphatase inhibitor) and diquat (DQ, an oxidative stress inducer) on the organization of tonoplast, the effect of MCY-LR on plastid stromule formation and on mitochondria was investigated in wild-type Arabidopsis. Tonoplast was also studied in PP2A catalytic (c3c4) and regulatory subunit mutants (fass-5 and fass-15). These novel studies were performed by CLSM microscopy. MCY-LR is produced during cyanobacterial blooms. The organization of tonoplast of PP2A mutants of Arabidopsis is much more sensitive to MCY-LR and DQ treatments than that of wild type. In c3c4, fass-5 and fass-15, control and treated plants showed increased vacuole fragmentation that was the strongest when the fass-5 mutant was treated with MCY-LR. It is assumed that both PP2A/C and B” subunits play an important role in normal formation and function of the tonoplast. In wild-type plants, MCY-LR affects mitochondria. Under the influence of MCY-LR, small, round-shaped mitochondria appeared, while long/fused mitochondria were typical in control plants. Presumably, MCY-LR either inhibits the fusion of mitochondria or induces fission. Consequently, PP2A also plays an important role in the fusion of mitochondria. MCY-LR also increased the frequency of stromules appearing on chloroplasts after 1 h treatments. Along the stromules, signals can be transported between plastids and endoplasmic reticulum. It is probable that they promote a faster response to stress. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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16 pages, 2083 KiB

Open AccessArticle

Development of A Rapid, Low-Cost Portable Detection Assay for Enterococci in Wastewater and Environmental Waters

by Alka Rani Batra, Darren Cottam, Muriel Lepesteur, Carina Dexter, Kelly Zuccala, Caroline Martino, Leadin Khudur, Vivek Daniel, Andrew S. Ball and Sarvesh Kumar Soni

Microorganisms 2023, 11(2), 381; https://doi.org/10.3390/microorganisms11020381 - 2 Feb 2023

Cited by 3 | Viewed by 2542

Abstract

Waterborne diseases are known as a leading cause of illness and death in both developing and developed countries. Several pathogens can be present in contaminated water, particularly waters containing faecal material; however, routine monitoring of all pathogens is not currently possible. Enterococcus faecalis [...] Read more.

Waterborne diseases are known as a leading cause of illness and death in both developing and developed countries. Several pathogens can be present in contaminated water, particularly waters containing faecal material; however, routine monitoring of all pathogens is not currently possible. Enterococcus faecalis, which is present in the microflora of human and animals has been used as a faecal indicator in water due to its abundance in surface water and soil. Accurate and fast detection methods are critical for the effective monitoring of E. faecalis in the environment. Although conventional and current molecular detection techniques provide sufficient sensitivity, specificity and throughput, their use is hampered by the long waiting period (1–6 days) to obtain results, the need for expensive laboratory equipment, skilled personnel, and cold-chain storage. Therefore, this study aimed to develop a detection system for E. faecalis that would be simple, rapid, and low-cost, using an isothermal DNA amplification assay called recombinase polymerase amplification (RPA), integrated with a lateral flow assay (LFA). The assay was found to be 100% selective for E. faecalis and capable of detecting rates as low as 2.8 × 10³ cells per 100 mL from water and wastewater, and 2.8 × 10⁴ cells per 100 mL from saline water. The assay was completed in approximately 30 min using one constant temperature (38 °C). In addition, this study demonstrated the quantitation of E. faecalis using a lateral flow strip reader for the first time, enhancing the potential use of RPA assay for the enumeration of E. faecalis in wastewater and heavily contaminated environmental waters, surface water, and wastewater. However, the sensitivity of the RPA-LFA assay for the detection of E. faecalis in tap water, saline water and in wastewater was 10–1000 times lower than that of the Enterolert-E test, depending on the water quality. Nevertheless, with further improvements, this low-cost RPA-LFA may be suitable to be used at the point-of-need (PON) if conjugated with a rapid field-deployable DNA extraction method. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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14 pages, 3703 KiB

Open AccessArticle

Luteibacter flocculans sp. nov., Isolated from a Eutrophic Pond and Isolation and Characterization of Luteibacter Phage vB_LflM-Pluto

by Ines Friedrich, Alisa Kuritsyn, Robert Hertel and Rolf Daniel

Microorganisms 2023, 11(2), 307; https://doi.org/10.3390/microorganisms11020307 - 24 Jan 2023

Cited by 3 | Viewed by 2380

Abstract

Luteibacter is a genus of the Rhodanobacteraceae family. The present study describes a novel species within the genus Luteibacter (EIF3^T). The strain was analyzed genomically, morphologically and physiologically. Average nucleotide identity analysis revealed that it is a new species of Luteibacter [...] Read more.

Luteibacter is a genus of the Rhodanobacteraceae family. The present study describes a novel species within the genus Luteibacter (EIF3^T). The strain was analyzed genomically, morphologically and physiologically. Average nucleotide identity analysis revealed that it is a new species of Luteibacter. In silico analysis indicated two putative prophages (one incomplete, one intact). EIF3^T cells form an elliptical morphotype with an average length of 2.0 µm and width of 0.7 µm and multiple flagella at one end. The bacterial strain is an aerobic Gram-negative with optimal growth at 30 °C. EIF3^T is resistant towards erythromycin, tetracycline and vancomycin. We propose the name Luteibacter flocculans sp. nov. with EIF3^T (=DSM 112537^T = LMG 32416^T) as type strain. Further, we describe the first known Luteibacter-associated bacteriophage called vB_LflM-Pluto. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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18 pages, 1228 KiB

Open AccessArticle

The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum

by Amirhossein Gheitanchi Mashini, Clinton A. Oakley, Sandeep S. Beepat, Lifeng Peng, Arthur R. Grossman, Virginia M. Weis and Simon K. Davy

Microorganisms 2023, 11(2), 292; https://doi.org/10.3390/microorganisms11020292 - 22 Jan 2023

Cited by 6 | Viewed by 2918

Abstract

The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian–dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography–mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont [...] Read more.

The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian–dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography–mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana (‘Aiptasia’). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host–endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian–dinoflagellate symbiosis. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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18 pages, 1206 KiB

Open AccessArticle

Responses of Free-Living Planktonic Bacterial Communities to Experimental Acidification and Warming

by Anastasia Tsiola, Evangelia Krasakopoulou, Daniele Daffonchio, Constantin Frangoulis, Tatiana M. Tsagaraki, Stilianos Fodelianakis and Paraskevi Pitta

Microorganisms 2023, 11(2), 273; https://doi.org/10.3390/microorganisms11020273 - 20 Jan 2023

Cited by 3 | Viewed by 2467

Abstract

Climate change driven by human activities encompasses the increase in atmospheric CO₂ concentration and sea-surface temperature. Little is known regarding the synergistic effects of these phenomena on bacterial communities in oligotrophic marine ecosystems that are expected to be particularly vulnerable. Here, we [...] Read more.

Climate change driven by human activities encompasses the increase in atmospheric CO₂ concentration and sea-surface temperature. Little is known regarding the synergistic effects of these phenomena on bacterial communities in oligotrophic marine ecosystems that are expected to be particularly vulnerable. Here, we studied bacterial community composition changes based on 16S rRNA sequencing at two fractions (0.1–0.2 and >0.2 μm) during a 10- day fully factorial mesocosm experiment in the eastern Mediterranean where the pH decreased by ~0.3 units and temperature increased by ~3 °C to project possible future changes in surface waters. The bacterial community experienced significant taxonomic differences driven by the combined effect of time and treatment; a community shift one day after the manipulations was noticed, followed by a similar state between all mesocosms at the third day, and mild shifts later on, which were remarkable mainly under sole acidification. The abundance of Synechococcus increased in response to warming, while the SAR11 clade immediately benefited from the combined acidification and warming. The effect of the acidification itself had a more persistent impact on community composition. This study highlights the importance of studying climate change consequences on ecosystem functioning both separately and simultaneously, considering the ambient environmental parameters. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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15 pages, 2386 KiB

Open AccessArticle

Isolation of Novel Bacterial Strains Pseudomonas extremaustralis CSW01 and Stutzerimonas stutzeri CSW02 from Sewage Sludge for Paracetamol Biodegradation

by Antonio Vargas-Ordóñez, Inés Aguilar-Romero, Jaime Villaverde, Fernando Madrid and Esmeralda Morillo

Microorganisms 2023, 11(1), 196; https://doi.org/10.3390/microorganisms11010196 - 12 Jan 2023

Cited by 13 | Viewed by 3455

Abstract

Paracetamol is one of the most used pharmaceuticals worldwide, but due to its widespread use it is detected in various environmental matrices, such as surface and ground waters, sediments, soils or even plants, where it is introduced mainly from the discharge of wastewater [...] Read more.

Paracetamol is one of the most used pharmaceuticals worldwide, but due to its widespread use it is detected in various environmental matrices, such as surface and ground waters, sediments, soils or even plants, where it is introduced mainly from the discharge of wastewater and the use of sewage sludge as fertilizer in agriculture. Its accumulation in certain organisms can induce reproductive, neurotoxic or endocrine disorders, being therefore considered an emerging pollutant. This study reports on the isolation, from sewage sludge produced in wastewater treatment plants (WWTPs), of bacterial strains capable of degrading paracetamol. Up to 17 bacterial strains were isolated, but only two of them, identified as Pseudomonas stutzeri CSW02 and Pseudomonas extremaustralis CSW01, were able to degrade very high concentrations of paracetamol in solution as a sole carbon and energy source, and none of them had been previously described as paracetamol degraders. These bacteria showed the ability to degrade up to 500 mg L⁻¹ of paracetamol in only 6 and 4 h, respectively, much quicker than any other paracetamol-degrader strain described in the literature. The two main paracetamol metabolites, 4-aminophenol and hydroquinone, which present high toxicity, were detected during the degradation process, although they disappeared very quickly for paracetamol concentrations up to 500 mg L⁻¹. The IC₅₀ of paracetamol for the growth of these two isolates was also calculated, indicating that P. extremaustralis CSW01 was more tolerant than S. stutzeri CSW02 to high concentrations of paracetamol and/or its metabolites in solution, and this is the reason for the much lower paracetamol degradation by S. stutzeri CSW02 at 2000–3000 mg L⁻¹. These findings indicate that both bacteria are very promising candidates for their use in paracetamol bioremediation in water and sewage sludge. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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13 pages, 2688 KiB

Open AccessArticle

pH and Nitrate Drive Bacterial Diversity in Oil Reservoirs at a Localized Geographic Scale

by Ying Xu, Jianwei Wang, Qingjie Liu, Qun Zhang, Jiazhong Wu, Minghui Zhou, Yong Nie and Xiao-Lei Wu

Microorganisms 2023, 11(1), 151; https://doi.org/10.3390/microorganisms11010151 - 6 Jan 2023

Cited by 5 | Viewed by 2166

Abstract

Oil reservoirs are one of the most important deep subsurface biospheres. They are inhabited by diverse microorganisms including bacteria and archaea with diverse metabolic activities. Although recent studies have investigated the microbial communities in oil reservoirs at large geographic scales, it is still [...] Read more.

Oil reservoirs are one of the most important deep subsurface biospheres. They are inhabited by diverse microorganisms including bacteria and archaea with diverse metabolic activities. Although recent studies have investigated the microbial communities in oil reservoirs at large geographic scales, it is still not clear how the microbial communities assemble, as the variation in the environment may be confounded with geographic distance. In this work, the microbial communities in oil reservoirs from the same oil field were identified at a localized geographic scale. We found that although the injected water contained diverse exogenous microorganisms, this had little effect on the microbial composition of the produced water. The Neutral Community Model analysis showed that both bacterial and archaeal communities are dispersal limited even at a localized scale. Further analysis showed that both pH and nitrate concentrations drive the assembly of bacterial communities, of which nitrate negatively correlated with bacterial alpha diversity and pH differences positively correlated with the dissimilarity of bacterial communities. In contrast, the physiochemical parameters had little effect on archaeal communities at the localized scale. Our results suggest that the assembly of microbial communities in oil reservoirs is scale- and taxonomy-dependent. Our work provides a comprehensive analysis of microbial communities in oil reservoirs at a localized geographic scale, which improves the understanding of the assembly of the microbial communities in oil reservoirs. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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16 pages, 2948 KiB

Open AccessArticle

Weapons against Themselves: Identification and Use of Quorum Sensing Volatile Molecules to Control Plant Pathogenic Fungi Growth

by Caroline De Clerck, Laurie Josselin, Valentine Vangoethem, Ludivine Lassois, Marie-Laure Fauconnier and Haïssam Jijakli

Microorganisms 2022, 10(12), 2459; https://doi.org/10.3390/microorganisms10122459 - 13 Dec 2022

Cited by 7 | Viewed by 1884

Abstract

Quorum sensing (QS) is often defined as a mechanism of microbial communication that can regulate microbial behaviors in accordance with population density. Much is known about QS mechanisms in bacteria, but fungal QS research is still in its infancy. In this study, the [...] Read more.

Quorum sensing (QS) is often defined as a mechanism of microbial communication that can regulate microbial behaviors in accordance with population density. Much is known about QS mechanisms in bacteria, but fungal QS research is still in its infancy. In this study, the molecules constituting the volatolomes of the plant pathogenic fungi Fusarium culmorum and Cochliobolus sativus have been identified during culture conditions involving low and high spore concentrations, with the high concentration imitating overpopulation conditions (for QS stimulation). We determined that volatolomes emitted by these species in conditions of overpopulation have a negative impact on their mycelial growth, with some of the emitted molecules possibly acting as QSM. Candidate VOCs related to QS have then been identified by testing the effect of individual volatile organic compounds (VOCs) on mycelial growth of their emitting species. The antifungal effect observed for the volatolome of F. culmorum in the overpopulation condition could be attributed to ethyl acetate, 2-methylpropan-1-ol, 3-methylbutyl ethanoate, 3-methylbutan-1-ol, and pentan-1-ol, while it could be attributed to longifolene, 3-methylbutan-1-ol, 2-methylpropan-1-ol, and ethyl acetate for C. sativus in the overpopulation condition. This work could pave the way to a sustainable alternative to chemical fungicides. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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24 pages, 4050 KiB

Open AccessArticle

Near-Infrared Metabolomic Fingerprinting Study of Lichen Thalli and Phycobionts in Culture: Aquaphotomics of Trebouxia lynnae Dehydration

by Irene Bruñas Gómez, Monica Casale, Eva Barreno and Myriam Catalá

Microorganisms 2022, 10(12), 2444; https://doi.org/10.3390/microorganisms10122444 - 10 Dec 2022

Cited by 4 | Viewed by 2501

Abstract

Near-infrared spectroscopy (NIRS) is an accurate, fast and safe technique whose full potential remains to be exploited. Lichens are a paradigm of symbiotic association, with extraordinary properties, such as abiotic stress tolerance and adaptation to anhydrobiosis, but subjacent mechanisms await elucidation. Our aim [...] Read more.

Near-infrared spectroscopy (NIRS) is an accurate, fast and safe technique whose full potential remains to be exploited. Lichens are a paradigm of symbiotic association, with extraordinary properties, such as abiotic stress tolerance and adaptation to anhydrobiosis, but subjacent mechanisms await elucidation. Our aim is characterizing the metabolomic NIRS fingerprints of Ramalina farinacea and Lobarina scrobiculata thalli, and of the cultured phycobionts Trebouxia lynnae and Trebouxia jamesii. Thalli collected in an air-dry state and fresh cultivated phycobionts were directly used for spectra acquisition in reflectance mode. Thalli water peaks were associated to the solvation shell (1354 nm) and sugar–water interactions (1438 nm). While northern–southern orientation related with two hydrogen bonded (S₂) water, the site was related to one hydrogen bonded (S₁). Water, lipids (saturated and unsaturated), and polyols/glucides contributed to the profiles of lichen thalli and microalgae. R. farinacea, with higher desiccation tolerance, shows higher S₂ water than L. scrobiculata. In contrast, fresh phycobionts are dominated by free water. Whereas T. jamesii shows higher solvation water content, T. lynnae possesses more unsaturated lipids. Aquaphotomics demonstrates the involvement of strongly hydrogen bonded water conformations, polyols/glucides, and unsaturated/saturated fatty acids in the dehydration process, and supports a “rubbery” state allowing enzymatic activity during anhydrobiosis. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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19 pages, 2421 KiB

Open AccessArticle

A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source

by Pauline Chaignaud, Christelle Gruffaz, Adrien Borreca, Stéphanie Fouteau, Lauriane Kuhn, Jérémy Masbou, Zoé Rouy, Philippe Hammann, Gwenaël Imfeld, David Roche and Stéphane Vuilleumier

Microorganisms 2022, 10(11), 2302; https://doi.org/10.3390/microorganisms10112302 - 21 Nov 2022

Cited by 11 | Viewed by 3188

Abstract

Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects [...] Read more.

Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects on aquatic life and potentially also on humans. We report on the isolation and characterisation of strain MD1, an aerobic methylotrophic bacterium growing with metformin as its sole carbon, nitrogen and energy source. Strain MD1 degrades metformin into dimethylamine used for growth, and guanylurea as a side-product. Sequence analysis of its fully assembled genome showed its affiliation to Aminobacter niigataensis. Differential proteomics and transcriptomics, as well as mini-transposon mutagenesis of the strain, point to genes and proteins essential for growth with metformin and potentially associated with hydrolytic C-N cleavage of metformin or with cellular transport of metformin and guanylurea. The obtained results suggest the recent evolution of the growth-supporting capacity of strain MD1 to degrade metformin. Our results identify candidate proteins of the enzymatic system for metformin transformation in strain MD1 and will inform future research on the fate of metformin and its degradation products in the environment and in humans. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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16 pages, 5341 KiB

Open AccessArticle

Building a Cell House from Cellulose: The Case of the Soil Acidobacterium Acidisarcina polymorpha SBC82^T

by Svetlana E. Belova, Daniil G. Naumoff, Natalia E. Suzina, Vladislav V. Kovalenko, Nataliya G. Loiko, Vladimir V. Sorokin and Svetlana N. Dedysh

Microorganisms 2022, 10(11), 2253; https://doi.org/10.3390/microorganisms10112253 - 14 Nov 2022

Cited by 1 | Viewed by 2360

Abstract

Acidisarcina polymorpha SBC82^T is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old [...] Read more.

Acidisarcina polymorpha SBC82^T is a recently described representative of the phylum Acidobacteriota from lichen-covered tundra soil. Cells of this bacterium occur within unusual saccular chambers, with the chamber envelope formed by tightly packed fibrils. These extracellular structures were most pronounced in old cultures of strain SBC82^T and were organized in cluster-like aggregates. The latter were efficiently destroyed by incubating cell suspensions with cellulase, thus suggesting that they were composed of cellulose. The diffraction pattern obtained for 45-day-old cultures of strain SBC82^T by using small angle X-ray scattering was similar to those reported earlier for mature wood samples. The genome analysis revealed the presence of a cellulose biosynthesis locus bcs. Cellulose synthase key subunits A and B were encoded by the bcsAB gene whose close homologs are found in genomes of many members of the order Acidobacteriales. More distant homologs of the acidobacterial bcsAB occurred in representatives of the Proteobacteria. A unique feature of bcs locus in strain SBC82^T was the non-orthologous displacement of the bcsZ gene, which encodes the GH8 family glycosidase with a GH5 family gene. Presumably, these cellulose-made extracellular structures produced by A. polymorpha have a protective function and ensure the survival of this acidobacterium in habitats with harsh environmental conditions. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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20 pages, 1893 KiB

Open AccessArticle

Accelerated Bioconversion of Chemically Solubilized Lignite Solution to Methane by Methanogenic Consortium: Experimental Results and Their Application to the Subsurface Cultivation and Gasification Method

by Akio Ueno, Satoshi Tamazawa, Shuji Tamamura, Takuma Murakami, Tamotsu Kiyama, Hidenori Inomata, Noritaka Aramaki, Kunihiko Yoshida, Shinji Yamaguchi, Hideo Aoyama, Takeshi Naganuma and Toshifumi Igarashi

Microorganisms 2022, 10(10), 1984; https://doi.org/10.3390/microorganisms10101984 - 7 Oct 2022

Cited by 2 | Viewed by 1883

Abstract

Lignite is an obsolete and less commercially circulated natural resource due to its low calorific value worldwide. The effective conversion of lignite into methane is important considering the global energy crunch. This study reported the effective bioconversion of organic matter released from chemically [...] Read more.

Lignite is an obsolete and less commercially circulated natural resource due to its low calorific value worldwide. The effective conversion of lignite into methane is important considering the global energy crunch. This study reported the effective bioconversion of organic matter released from chemically solubilized lignite to methane using two methanogenic consortia types: mixed methanogenic enrichment culture (mMEC) and SAL25-2. We demonstrated in a microcosm study that the start of methane generation was observed within seven days. Furthermore, the methane yield increased as the total organic carbon concentration of the chemically solubilized lignite solution increased. Surprisingly, methane production using mMEC was drastically enhanced by approximately 50–fold when pulverized lignite was added as conductive material (CM) to the microcosms. To the best of our knowledge, this is the highest number of times methane production increased relative to the control. Our results demonstrated that bioaugmentation using a methanogenic consortium and adding pulverized lignite as CM could facilitate the bioconversion of chemically solubilized lignite solution to methane and lead to effective utilization of subterranean lignite, regarded as a neglected natural resource, without any further excavation processes. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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14 pages, 1844 KiB

Open AccessArticle

Year-Long Microbial Succession on Microplastics in Wastewater: Chaotic Dynamics Outweigh Preferential Growth

by Alexander S. Tagg, Theodor Sperlea, Matthias Labrenz, Jesse P. Harrison, Jesús J. Ojeda and Melanie Sapp

Microorganisms 2022, 10(9), 1775; https://doi.org/10.3390/microorganisms10091775 - 2 Sep 2022

Cited by 5 | Viewed by 3439

Abstract

Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm [...] Read more.

Microplastics are a globally-ubiquitous aquatic pollutant and have been heavily studied over the last decade. Of particular interest are the interactions between microplastics and microorganisms, especially the pursuit to discover a plastic-specific biome, the so-called plastisphere. To follow this up, a year-long microcosm experimental setup was deployed to expose five different microplastic types (and silica beads control) to activated aerobic wastewater in controlled conditions, with microbial communities being measured four times over the course of the year using 16S rDNA (bacterial) and ITS (fungal) amplicon sequencing. The biofilm community shows no evidence of a specific plastisphere, even after a year of incubation. Indeed, the microbial communities (particularly bacterial) show a clear trend of increasing dissimilarity between plastic types as time increases. Despite little evidence for a plastic-specific community, there was a slight grouping observed for polyolefins (PE and PP) in 6–12-month biofilms. Additionally, an OTU assigned to the genus Devosia was identified on many plastics, increasing over time while showing no growth on silicate (natural particle) controls, suggesting this could be either a slow-growing plastic-specific taxon or a symbiont to such. Both substrate-associated findings were only possible to observe in samples incubated for 6–12 months, which highlights the importance of studying long-term microbial community dynamics on plastic surfaces. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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16 pages, 1613 KiB

Open AccessArticle

Adaptation and Resistance: How Bacteroides thetaiotaomicron Copes with the Bisphenol A Substitute Bisphenol F

by Sarah Riesbeck, Hannes Petruschke, Ulrike Rolle-Kampczyk, Christian Schori, Christian H. Ahrens, Christian Eberlein, Hermann J. Heipieper, Martin von Bergen and Nico Jehmlich

Microorganisms 2022, 10(8), 1610; https://doi.org/10.3390/microorganisms10081610 - 9 Aug 2022

Cited by 3 | Viewed by 3239

Abstract

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial [...] Read more.

Bisphenols are used in the process of polymerization of polycarbonate plastics and epoxy resins. Bisphenols can easily migrate out of plastic products and enter the gastrointestinal system. By increasing colonic inflammation in mice, disrupting the intestinal bacterial community structure and altering the microbial membrane transport system in zebrafish, bisphenols seem to interfere with the gut microbiome. The highly abundant human commensal bacterium Bacteroides thetaiotaomicron was exposed to bisphenols (Bisphenol A (BPA), Bisphenol F (BPF), Bisphenol S (BPS)), to examine the mode of action, in particular of BPF. All chemicals caused a concentration-dependent growth inhibition and the half-maximal effective concentration (EC50) corresponded to their individual logP values, a measure of their hydrophobicity. B. thetaiotaomicron exposed to BPF decreased membrane fluidity with increasing BPF concentrations. Physiological changes including an increase of acetate concentrations were observed. On the proteome level, a higher abundance of several ATP synthase subunits and multidrug efflux pumps suggested an increased energy demand for adaptive mechanisms after BPF exposure. Defense mechanisms were also implicated by a pathway analysis that identified a higher abundance of members of resistance pathways/strategies to cope with xenobiotics (i.e., antibiotics). Here, we present further insights into the mode of action of bisphenols in a human commensal gut bacterium regarding growth inhibition, and the physiological and functional state of the cell. These results, combined with microbiota-directed effects, could lead to a better understanding of host health disturbances and disease development based on xenobiotic uptake. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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19 pages, 4673 KiB

Open AccessArticle

Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui

by Qi Liu, Zichen He, Takeshi Naganuma, Ryosuke Nakai, Luz María Rodríguez, Rafael Carreño and Franco Urbani

Microorganisms 2022, 10(7), 1395; https://doi.org/10.3390/microorganisms10071395 - 11 Jul 2022

Cited by 5 | Viewed by 3229

Abstract

The diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were [...] Read more.

The diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were extracted from three speleothems of two types, i.e., one soft whitish mushroom-like speleothem and two hard blackish coral-like speleothems. The extracted DNAs were amplified for sequencing the V3–V4 region of the bacterial 16S rRNA gene by MiSeq. A total of 210,309 valid reads were obtained and clustered into 3184 phylotypes or operational taxonomic units (OTUs). The OTUs from the soft whitish speleothem were mostly affiliated with Acidobacteriota, Pseudomonadota (formerly, Proteobacteria), and Chloroflexota, with the OTUs ascribed to Nitrospirota being found specifically in this speleothem. The OTUs from the hard blackish speleothems were similar to each other and were mostly affiliated with Pseudomonadota, Acidobacteriota, and Actinomycetota (formerly, Actinobacteria). These OTU compositions were generally consistent with those reported for limestone and silicate caves. The OTUs were further used to infer metabolic features by using the PICRUSt bioinformatic tool, and membrane transport and amino acid metabolism were noticeably featured. These and other featured metabolisms may influence the pH microenvironment and, consequently, the formation, weathering, and re-deposition of silicate speleothems. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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7 pages, 1749 KiB

Open AccessCommunication

PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

by Ohana Y. A. Costa, Mattias de Hollander, Eiko E. Kuramae and Paul L. E. Bodelier

Microorganisms 2022, 10(6), 1093; https://doi.org/10.3390/microorganisms10061093 - 25 May 2022

Cited by 2 | Viewed by 2113

Abstract

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and [...] Read more.

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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19 pages, 4161 KiB

Open AccessArticle

A Novel Isolate of Spherical Multicellular Magnetotactic Prokaryotes Has Two Magnetosome Gene Clusters and Synthesizes Both Magnetite and Greigite Crystals

by Kaixuan Cui, Hongmiao Pan, Jianwei Chen, Jia Liu, Yicong Zhao, Si Chen, Wenyan Zhang, Tian Xiao and Long-Fei Wu

Microorganisms 2022, 10(5), 925; https://doi.org/10.3390/microorganisms10050925 - 28 Apr 2022

Cited by 3 | Viewed by 2634

Abstract

Multicellular magnetotactic prokaryotes (MMPs) are a unique group of magnetotactic bacteria that are composed of 10–100 individual cells and show coordinated swimming along magnetic field lines. MMPs produce nanometer-sized magnetite (Fe₃O₄) and/or greigite (Fe₃S₄) crystals—termed [...] Read more.

Multicellular magnetotactic prokaryotes (MMPs) are a unique group of magnetotactic bacteria that are composed of 10–100 individual cells and show coordinated swimming along magnetic field lines. MMPs produce nanometer-sized magnetite (Fe₃O₄) and/or greigite (Fe₃S₄) crystals—termed magnetosomes. Two types of magnetosome gene cluster (MGC) that regulate biomineralization of magnetite and greigite have been found. Here, we describe a dominant spherical MMP (sMMP) species collected from the intertidal sediments of Jinsha Bay, in the South China Sea. The sMMPs were 4.78 ± 0.67 μm in diameter, comprised 14–40 cells helical symmetrically, and contained bullet-shaped magnetite and irregularly shaped greigite magnetosomes. Two sets of MGCs, one putatively related to magnetite biomineralization and the other to greigite biomineralization, were identified in the genome of the sMMP, and two sets of paralogous proteins (Mam and Mad) that may function separately and independently in magnetosome biomineralization were found. Phylogenetic analysis indicated that the sMMPs were affiliated with Deltaproteobacteria. This is the first direct report of two types of magnetosomes and two sets of MGCs being detected in the same sMMP. The study provides new insights into the mechanism of biomineralization of magnetosomes in MMPs, and the evolutionary origin of MGCs. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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21 pages, 3058 KiB

Open AccessArticle

Proteome and Physiological Characterization of Halotolerant Nodule Endophytes: The Case of Rahnella aquatilis and Serratia plymuthica

by Giorgia Novello, Elisa Gamalero, Nadia Massa, Patrizia Cesaro, Guido Lingua, Valeria Todeschini, Alice Caramaschi, Francesco Favero, Davide Corà, Marcello Manfredi, Emilio Marengo, Micaela Pelagi, Loredana Pangaro, Giuseppina Caffiero, Fulvia Milano and Elisa Bona

Microorganisms 2022, 10(5), 890; https://doi.org/10.3390/microorganisms10050890 - 24 Apr 2022

Cited by 4 | Viewed by 2202

Abstract

Bacterial endophytes were isolated from nodules of pea and fava bean. The strains were identified and characterized for plant beneficial activities (phosphate solubilization, synthesis of indole acetic acid and siderophores) and salt tolerance. Based on these data, four strains of Rahnella aquatilis and [...] Read more.

Bacterial endophytes were isolated from nodules of pea and fava bean. The strains were identified and characterized for plant beneficial activities (phosphate solubilization, synthesis of indole acetic acid and siderophores) and salt tolerance. Based on these data, four strains of Rahnella aquatilis and three strains of Serratia plymuthica were selected. To shed light on the mechanisms underlying salt tolerance, the proteome of the two most performant strains (Ra4 and Sp2) grown in the presence or not of salt was characterized. The number of proteins expressed by the endophytes was higher in the presence of salt. The modulated proteome consisted of 302 (100 up-regulated, 202 down-regulated) and 323 (206 up-regulated, 117 down-regulated) proteins in Ra4 and Sp2, respectively. Overall, proteins involved in abiotic stress responses were up-regulated, while those involved in metabolism and flagellum structure were down-regulated. The main up-regulated proteins in Sp2 were thiol: disulfide interchange protein DsbA, required for the sulfur binding formation in periplasmic proteins, while in Ra4 corresponded to the soluble fraction of ABC transporters, having a role in compatible solute uptake. Our results demonstrated a conserved response to salt stress in the two taxonomically related species. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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14 pages, 4396 KiB

Open AccessArticle

Could Pontimonas Harbour Halophilic Members Able to Withstand Very Broad Salinity Variations?

by Susanna Gorrasi, Marcella Pasqualetti, Martina Braconcini, Barbara Muñoz-Palazon and Massimiliano Fenice

Microorganisms 2022, 10(4), 790; https://doi.org/10.3390/microorganisms10040790 - 8 Apr 2022

Cited by 3 | Viewed by 1994

Abstract

Pontimonas is currently described as a genus including only one species of slightly halophilic marine bacteria. Although some works revealed its presence in some hypersaline environments, the information on its habitat preference is still scant. This work investigated Pontimonas presence in selected ponds [...] Read more.

Pontimonas is currently described as a genus including only one species of slightly halophilic marine bacteria. Although some works revealed its presence in some hypersaline environments, the information on its habitat preference is still scant. This work investigated Pontimonas presence in selected ponds of the Saline di Tarquinia marine saltern and in the seawater intake area. The two-year metabarcoding survey documented its constant presence along the ponds establishing the salinity gradient and in a distinct basin with permanent hypersaline conditions (BSB). Pontimonas was higher in the ponds than in the sea, whereas it had similar abundances in the sea and in the BSB. Its representative OTUs showed significant trends according to different parameters. Along the salinity gradient, OTU1 abundance increased with decreasing water temperatures and increasing rainfalls, and it showed a maximum in January; OTU2 increased with increasing BOD₅ and it showed the highest abundances in the period August–October, and OTU 3194 increased at decreasing salinities. In BSB, a significant seasonal variation was shown by OTU 3194, which started increasing in spring to reach a maximum in summer. The results suggest that Pontimonas could easily settle in hypersaline habitats, having also broad euryhaline members and some possible extreme halophilic representatives. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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14 pages, 2551 KiB

Open AccessArticle

On the Efficacy of H₂O₂ or S₂O₈²⁻ at Promoting the Inactivation of a Consortium of Cyanobacteria and Bacteria in Algae-Laden Water

by Javier Moreno-Andrés, Ignacio Rivas-Zaballos, Asunción Acevedo-Merino and Enrique Nebot

Microorganisms 2022, 10(4), 735; https://doi.org/10.3390/microorganisms10040735 - 29 Mar 2022

Cited by 6 | Viewed by 2514

Abstract

Harmful algal blooms in coastal areas can significantly impact a water source. Microorganisms such as cyanobacteria and associated pathogenic bacteria may endanger an ecosystem and human health by causing significant eco-hazards. This study assesses the efficacy of two different reagents, H₂O [...] Read more.

Harmful algal blooms in coastal areas can significantly impact a water source. Microorganisms such as cyanobacteria and associated pathogenic bacteria may endanger an ecosystem and human health by causing significant eco-hazards. This study assesses the efficacy of two different reagents, H₂O₂ and S₂O₈²⁻, as (pre-)treatment options for algae-laden waters. Anabaena sp. and Vibrio alginolyticus have been selected as target microorganisms. With the objective of activating H₂O₂ or S₂O₈²⁻, additional experiments have been performed with the presence of small amounts of iron (18 µmol/L). For the cyanobacterial case, H₂O₂-based processes demonstrate greater efficiency over that of S₂O₈²⁻, as Anabaena sp. is particularly affected by H₂O₂, for which >90% of growth inhibition has been achieved with 0.088 mmol/L of H₂O₂ (at 72 h of exposure). The response of Anabaena sp. as a co-culture with V. alginolyticus implies the use of major H₂O₂ amounts for its inactivation (0.29 mmol/L of H₂O₂), while the effects of H₂O₂/Fe(II) suggests an improvement of ~60% compared to single H₂O₂. These H₂O₂ doses are not sufficient for preventing the regrowth of V. alginolyticus after 24 h. The effects of S₂O₈²⁻ (+ Fe(II)) are moderate, reaching maximum inhibition growth of ~50% for Anabaena sp. at seven days of exposure. Nevertheless, doses of 3 mmol/L of S₂O₈²⁻ can prevent the regrowth of V. alginolyticus. These findings have implications for the mitigation of HABs but also for the associated bacteria that threaten many coastal ecosystems. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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12 pages, 2441 KiB

Open AccessArticle

Responses of Phyllosphere Microbiome to Ozone Stress: Abundance, Community Compositions and Functions

by Jiayu Liu, Manjiao Song, Xinyuan Wei, Huanzhen Zhang, Zhihui Bai and Xuliang Zhuang

Microorganisms 2022, 10(4), 680; https://doi.org/10.3390/microorganisms10040680 - 22 Mar 2022

Cited by 14 | Viewed by 2868

Abstract

Ozone is a typical hazardous pollutant in Earth’s lower atmosphere, but the phyllosphere and its microbiome are promising for air pollution remediation. Despite research to explore the efficiency and mechanism of ozone phylloremediation, the response and role of the phyllosphere microbiome remains untouched. [...] Read more.

Ozone is a typical hazardous pollutant in Earth’s lower atmosphere, but the phyllosphere and its microbiome are promising for air pollution remediation. Despite research to explore the efficiency and mechanism of ozone phylloremediation, the response and role of the phyllosphere microbiome remains untouched. In this study, we exposed Euonymus japonicus to different ozone levels and revealed microbial successions and roles of the phyllosphere microbiome during the exposure. The low-level exposure (156 ± 20 ppb) induced limited response compared to other environmental factors. Fungi failed to sustain the community richness and diversity, despite the stable ITS concentration, while bacteria witnessed an abundance loss. We subsequently elevated the exposure level to 5000~10,000 ppb, which considerably deteriorated the bacterial and fungal diversity. Our results identified extremely tolerant species, including bacterial genera (Curtobacterium, Marmoricola, and Microbacterium) and fungal genera (Cladosporium and Alternaria). Compositional differences suggested that most core fungal taxa were related to plant diseases and biocontrol, and ozone exposure might intensify such antagonism, thus possibly influencing plant health and ozone remediation. This assumption was further evidenced in the functional predictions via a pathogen predominance. This study shed light on microbial responses to ozone exposure in the phyllosphere and enlightened the augmentation of ozone phylloremediation through the microbial role. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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19 pages, 4028 KiB

Open AccessArticle

Bermudagrass Cultivars with Different Tolerance to Nematode Damage Are Characterized by Distinct Fungal but Similar Bacterial and Archaeal Microbiomes

by Chang Jae Choi, Jacqueline Valiente, Marco Schiavon, Braham Dhillon, William T. Crow and Ulrich Stingl

Microorganisms 2022, 10(2), 457; https://doi.org/10.3390/microorganisms10020457 - 16 Feb 2022

Cited by 4 | Viewed by 3493

Abstract

Turfgrass landscapes have expanded rapidly in recent decades and are a major vegetation type in urbanizing ecosystems. While turfgrass areas provide numerous ecosystem services in urban environments, ecological side effects from intensive management are raising concerns regarding their sustainability. One potentially promising approach [...] Read more.

Turfgrass landscapes have expanded rapidly in recent decades and are a major vegetation type in urbanizing ecosystems. While turfgrass areas provide numerous ecosystem services in urban environments, ecological side effects from intensive management are raising concerns regarding their sustainability. One potentially promising approach to ameliorate the ecological impact and decrease the use of agricultural chemicals is to take advantage of naturally evolved turfgrass-associated microbes by harnessing beneficial services provided by microbiomes. Unfortunately, especially compared to agricultural crops, the microbiomes of turfgrasses are not well understood. Here, we analyzed microbial communities inhabiting the leaf and root endospheres as well as soil in two bermudagrass cultivars, ‘Latitude 36’ and ‘TifTuf’, which exhibit distinct tolerance to nematode damage, with the goal of identifying potential differences in the microbiomes that might explain their distinct phenotype. We used 16S rRNA gene V4 and ITS2 amplicon sequencing to characterize the microbiomes in combination with microbial cultivation efforts to identify potentially beneficial endophytic fungi and bacteria. Our results show that Latitude 36 and TifTuf showed markedly different fungal microbiomes, each harboring unique taxa from Ascomycota and Glomeromycota, respectively. In contrast, less difference was observed from bacterial and archaeal microbiomes, which were dominated by Bacteroidetes and Thaumarchaeota, respectively. The TifTuf microbiomes exhibited lower microbial diversity compared to Latitude 36. Many sequences could not be classified to a higher taxonomic resolution, indicating a relatively high abundance of hitherto undescribed microorganisms. Our results provide new insights into the structure and composition of turfgrass microbiomes but also raise important questions regarding the functional attributes of key taxa. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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13 pages, 2226 KiB

Open AccessArticle

Rokubacteria in Northern Peatlands: Habitat Preferences and Diversity Patterns

by Anastasia A. Ivanova, Igor Y. Oshkin, Olga V. Danilova, Dmitriy A. Philippov, Nikolai V. Ravin and Svetlana N. Dedysh

Microorganisms 2022, 10(1), 11; https://doi.org/10.3390/microorganisms10010011 - 22 Dec 2021

Cited by 19 | Viewed by 3922

Abstract

Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, [...] Read more.

Rokubacteria is a phylogenetic clade of as-yet-uncultivated prokaryotes, which are detected in diverse terrestrial habitats and are commonly addressed as members of the rare biosphere. This clade was originally described as a candidate phylum; however, based on the results of comparative genome analysis, was later defined as the order-level lineage, Rokubacteriales, within the phylum Methylomirabilota. The physiology and lifestyles of these bacteria are poorly understood. A dataset of 16S rRNA gene reads retrieved from four boreal raised bogs and six eutrophic fens was examined for the presence of the Rokubacteriales; the latter were detected exclusively in fens. Their relative abundance varied between 0.2 and 4% of all bacteria and was positively correlated with pH, total nitrogen content, and availability of Ca and Mg. To test an earlier published hypothesis regarding the presence of methanotrophic capabilities in Rokubacteria, peat samples were incubated with 10% methane for four weeks. No response to methane availability was detected for the Rokubacteriales, while clear a increase in relative abundance was observed for the conventional Methylococcales methanotrophs. The search for methane monooxygenase encoding genes in 60 currently available Rokubacteriales metagenomes yielded negative results, although copper-containing monooxygenases were encoded by some members of this order. This study suggests that peat-inhabiting Rokubacteriales are neutrophilic non-methanotrophic bacteria that colonize nitrogen-rich wetlands. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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Review

Jump to: Research

37 pages, 7287 KiB

Open AccessReview

“Ectomosphere”: Insects and Microorganism Interactions

by Ugo Picciotti, Viviane Araujo Dalbon, Aurelio Ciancio, Mariantonietta Colagiero, Giuseppe Cozzi, Luigi De Bellis, Mariella Matilde Finetti-Sialer, Davide Greco, Antonio Ippolito, Nada Lahbib, Antonio Francesco Logrieco, Luis Vicente López-Llorca, Federico Lopez-Moya, Andrea Luvisi, Annamaria Mincuzzi, Juan Pablo Molina-Acevedo, Carlo Pazzani, Marco Scortichini, Maria Scrascia, Domenico Valenzano, Francesca Garganese and Francesco Porcelli Show full author list Hide full author list

Microorganisms 2023, 11(2), 440; https://doi.org/10.3390/microorganisms11020440 - 9 Feb 2023

Cited by 21 | Viewed by 6254

Abstract

This study focuses on interacting with insects and their ectosymbiont (lato sensu) microorganisms for environmentally safe plant production and protection. Some cases help compare ectosymbiont microorganisms that are insect-borne, -driven, or -spread relevant to endosymbionts’ behaviour. Ectosymbiotic bacteria can interact with [...] Read more.

This study focuses on interacting with insects and their ectosymbiont (lato sensu) microorganisms for environmentally safe plant production and protection. Some cases help compare ectosymbiont microorganisms that are insect-borne, -driven, or -spread relevant to endosymbionts’ behaviour. Ectosymbiotic bacteria can interact with insects by allowing them to improve the value of their pabula. In addition, some bacteria are essential for creating ecological niches that can host the development of pests. Insect-borne plant pathogens include bacteria, viruses, and fungi. These pathogens interact with their vectors to enhance reciprocal fitness. Knowing vector-phoront interaction could considerably increase chances for outbreak management, notably when sustained by quarantine vector ectosymbiont pathogens, such as the actual Xylella fastidiosa Mediterranean invasion episode. Insect pathogenic viruses have a close evolutionary relationship with their hosts, also being highly specific and obligate parasites. Sixteen virus families have been reported to infect insects and may be involved in the biological control of specific pests, including some economic weevils. Insects and fungi are among the most widespread organisms in nature and interact with each other, establishing symbiotic relationships ranging from mutualism to antagonism. The associations can influence the extent to which interacting organisms can exert their effects on plants and the proper management practices. Sustainable pest management also relies on entomopathogenic fungi; research on these species starts from their isolation from insect carcasses, followed by identification using conventional light or electron microscopy techniques. Thanks to the development of omics sciences, it is possible to identify entomopathogenic fungi with evolutionary histories that are less-shared with the target insect and can be proposed as pest antagonists. Many interesting omics can help detect the presence of entomopathogens in different natural matrices, such as soil or plants. The same techniques will help localize ectosymbionts, localization of recesses, or specialized morphological adaptation, greatly supporting the robust interpretation of the symbiont role. The manipulation and modulation of ectosymbionts could be a more promising way to counteract pests and borne pathogens, mitigating the impact of formulates and reducing food insecurity due to the lesser impact of direct damage and diseases. The promise has a preventive intent for more manageable and broader implications for pests, comparing what we can obtain using simpler, less-specific techniques and a less comprehensive approach to Integrated Pest Management (IPM). Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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19 pages, 2454 KiB

Open AccessReview

Current Trends and Perspectives on Predictive Models for Mildew Diseases in Vineyards

by Luisa Velasquez-Camacho, Marta Otero, Boris Basile, Josep Pijuan and Giandomenico Corrado

Microorganisms 2023, 11(1), 73; https://doi.org/10.3390/microorganisms11010073 - 27 Dec 2022

Cited by 14 | Viewed by 6940

Abstract

Environmental and economic costs demand a rapid transition to more sustainable farming systems, which are still heavily dependent on chemicals for crop protection. Despite their widespread application, powdery mildew (PM) and downy mildew (DM) continue to generate serious economic penalties for grape and [...] Read more.

Environmental and economic costs demand a rapid transition to more sustainable farming systems, which are still heavily dependent on chemicals for crop protection. Despite their widespread application, powdery mildew (PM) and downy mildew (DM) continue to generate serious economic penalties for grape and wine production. To reduce these losses and minimize environmental impacts, it is important to predict infections with high confidence and accuracy, allowing timely and efficient intervention. This review provides an appraisal of the predictive tools for PM and DM in a vineyard, a specialized farming system characterized by high crop protection cost and increasing adoption of precision agriculture techniques. Different methodological approaches, from traditional mechanistic or statistic models to machine and deep learning, are outlined with their main features, potential, and constraints. Our analysis indicated that strategies are being continuously developed to achieve the required goals of ease of monitoring and timely prediction of diseases. We also discuss that scientific and technological advances (e.g., in weather data, omics, digital solutions, sensing devices, data science) still need to be fully harnessed, not only for modelling plant–pathogen interaction but also to develop novel, integrated, and robust predictive systems and related applied technologies. We conclude by identifying key challenges and perspectives for predictive modelling of phytopathogenic disease in vineyards. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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37 pages, 1139 KiB

Open AccessReview

Environmental Neurotoxin β-N-Methylamino-L-alanine (BMAA) as a Widely Occurring Putative Pathogenic Factor in Neurodegenerative Diseases

by Srdjan Lopicic, Zorica Svirčev, Tamara Palanački Malešević, Aleksandar Kopitović, Aleksandra Ivanovska and Jussi Meriluoto

Microorganisms 2022, 10(12), 2418; https://doi.org/10.3390/microorganisms10122418 - 6 Dec 2022

Cited by 13 | Viewed by 3674

Abstract

In the present review we have discussed the occurrence of β-N-methylamino-L-alanine (BMAA) and its natural isomers, and the organisms and sample types in which the toxin(s) have been detected. Further, the review discusses general pathogenic mechanisms of neurodegenerative diseases, and how [...] Read more.

In the present review we have discussed the occurrence of β-N-methylamino-L-alanine (BMAA) and its natural isomers, and the organisms and sample types in which the toxin(s) have been detected. Further, the review discusses general pathogenic mechanisms of neurodegenerative diseases, and how modes of action of BMAA fit in those mechanisms. The biogeography of BMAA occurrence presented here contributes to the planning of epidemiological research based on the geographical distribution of BMAA and human exposure. Analysis of BMAA mechanisms in relation to pathogenic processes of neurodegeneration is used to critically assess the potential significance of the amino acid as well as to identify gaps in our understanding. Taken together, these two approaches provide the basis for the discussion on the potential role of BMAA as a secondary factor in neurodegenerative diseases, the rationale for further research and possible directions the research can take, which are outlined in the conclusions. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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16 pages, 1529 KiB

Open AccessReview

Myo-D-inositol Trisphosphate Signalling in Oomycetes

by Indu Muraleedharan Nair, Emma Condon, Barbara Doyle Prestwich and John James Mackrill

Microorganisms 2022, 10(11), 2157; https://doi.org/10.3390/microorganisms10112157 - 31 Oct 2022

Cited by 2 | Viewed by 2378

Abstract

Oomycetes are pathogens of plants and animals, which cause billions of dollars of global losses to the agriculture, aquaculture and forestry sectors each year. These organisms superficially resemble fungi, with an archetype being Phytophthora infestans, the cause of late blight of tomatoes [...] Read more.

Oomycetes are pathogens of plants and animals, which cause billions of dollars of global losses to the agriculture, aquaculture and forestry sectors each year. These organisms superficially resemble fungi, with an archetype being Phytophthora infestans, the cause of late blight of tomatoes and potatoes. Comparison of the physiology of oomycetes with that of other organisms, such as plants and animals, may provide new routes to selectively combat these pathogens. In most eukaryotes, myo-inositol 1,4,5 trisphosphate is a key second messenger that links extracellular stimuli to increases in cytoplasmic Ca²⁺, to regulate cellular activities. In the work presented in this study, investigation of the molecular components of myo-inositol 1,4,5 trisphosphate signaling in oomycetes has unveiled similarities and differences with that in other eukaryotes. Most striking is that several oomycete species lack detectable phosphoinositide-selective phospholipase C homologues, the enzyme family that generates this second messenger, but still possess relatives of myo-inositol 1,4,5 trisphosphate-gated Ca²⁺-channels. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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13 pages, 12177 KiB

Open AccessReview

Chronicle of Research into Lichen-Associated Bacteria

by Zichen He and Takeshi Naganuma

Microorganisms 2022, 10(11), 2111; https://doi.org/10.3390/microorganisms10112111 - 26 Oct 2022

Cited by 6 | Viewed by 3589

Abstract

Lichens are mutually symbiotic systems consisting of fungal and algal symbionts. While diverse lichen-forming fungal species are known, limited species of algae form lichens. Plasticity in the combination of fungal and algal species with different eco-physiological properties may contribute to the worldwide distribution [...] Read more.

Lichens are mutually symbiotic systems consisting of fungal and algal symbionts. While diverse lichen-forming fungal species are known, limited species of algae form lichens. Plasticity in the combination of fungal and algal species with different eco-physiological properties may contribute to the worldwide distribution of lichens, even in extreme habitats. Lichens have been studied systematically for more than 200 years; however, plasticity in fungal–algal/cyanobacterial symbiotic combinations is still unclear. In addition, the association between non-cyanobacterial bacteria and lichens has attracted attention in recent years. The types, diversity, and functions of lichen-associated bacteria have been studied using both culture-based and culture-independent methods. This review summarizes the history of systematic research on lichens and lichen-associated bacteria and provides insights into the current status of research in this field. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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17 pages, 1014 KiB

Open AccessReview

Obtaining Bioproducts from the Studies of Signals and Interactions between Microalgae and Bacteria

by Évellin do Espirito Santo, Marina Ishii, Uelinton Manoel Pinto, Marcelo Chuei Matsudo and João Carlos Monteiro de Carvalho

Microorganisms 2022, 10(10), 2029; https://doi.org/10.3390/microorganisms10102029 - 14 Oct 2022

Cited by 11 | Viewed by 3633

Abstract

The applications of microalgae biomass have been widely studied worldwide. The classical processes used in outdoor cultivations of microalgae, in closed or open photobioreactors, occur in the presence of bacteria. Understanding how communication between cells occurs through quorum sensing and evaluating co-cultures allows [...] Read more.

The applications of microalgae biomass have been widely studied worldwide. The classical processes used in outdoor cultivations of microalgae, in closed or open photobioreactors, occur in the presence of bacteria. Understanding how communication between cells occurs through quorum sensing and evaluating co-cultures allows the production of microalgae and cyanobacteria to be positively impacted by bacteria, in order to guarantee safety and profitability in the production process. In addition, the definition of the effects that occur during an interaction, promotes insights to improve the production of biomolecules, and to develop innovative products. This review presents the interactions between microalgae and bacteria, including compounds exchanges and communication, and addresses the development of new pharmaceutical, cosmetic and food bioproducts from microalgae based on these evaluations, such as prebiotics, vegan skincare products, antimicrobial compounds, and culture media with animal free protein for producing vaccines and other biopharmaceutical products. The use of microalgae as raw biomass or in biotechnological platforms is in line with the fulfillment of the 2030 Agenda related to the Sustainable Development Goals (SDGs). Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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40 pages, 4891 KiB

Open AccessReview

Current Techniques to Study Beneficial Plant-Microbe Interactions

by Elisa Gamalero, Elisa Bona and Bernard R. Glick

Microorganisms 2022, 10(7), 1380; https://doi.org/10.3390/microorganisms10071380 - 8 Jul 2022

Cited by 35 | Viewed by 6944

Abstract

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant [...] Read more.

Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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21 pages, 1092 KiB

Open AccessReview

A Review on Biotechnological Approaches Applied for Marine Hydrocarbon Spills Remediation

by Farzad Rahmati, Behnam Asgari Lajayer, Najmeh Shadfar, Peter M. van Bodegom and Eric D. van Hullebusch

Microorganisms 2022, 10(7), 1289; https://doi.org/10.3390/microorganisms10071289 - 25 Jun 2022

Cited by 14 | Viewed by 4772

Abstract

The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological [...] Read more.

The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological and physico-chemical remediation technologies can be efficient in terms of spill cleanup and microorganisms—mainly bacteria—are the main ones responsible for petroleum hydrocarbons (PHCs) degradation such as crude oil. Currently, biodegradation is considered as one of the most sustainable and efficient techniques for the removal of PHCs. However, environmental factors associated with the functioning and performance of microorganisms involved in hydrocarbon-degradation have remained relatively unclear. This has limited our understanding on how to select and inoculate microorganisms within technologies of cleaning and to optimize physico-chemical remediation and degradation methods. This review article presents the latest discoveries in bioremediation techniques such as biostimulation, bioaugmentation, and biosurfactants as well as immobilization strategies for increasing the efficiency. Besides, environmental affecting factors and microbial strains engaged in bioremediation and biodegradation of PHCs in marines are discussed. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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