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A special issue of International Journal of Environmental Research and Public Health (ISSN 1660-4601). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 May 2022) | Viewed by 31063

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Special Issue Editors

Dr. Giovanni Bacci

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Chief Guest Editor

Department of Biology, Florence University, Via Madonna del Piano, 6, 50019 Sesto Fiorentino, Italy
Interests: metagenomics; genomics; computational biology; molecular evolution
Special Issues, Collections and Topics in MDPI journals

Prof. Matteo Ramazzotti

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Guest Editor

Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Viale Morgagni, 50, 50134 Firenze FI, Italy
Interests: bioinformatics; molecular biology; -omics data analysis

Dr. Niccolò Meriggi

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Guest Editor

Department of Biology, Florence University, Via Madonna del Piano, 6, 50019 Sesto Fiorentino, Italy
Interests: microbiology; host-microbe interaction

Special Issue Information

Dear Colleagues,

Microorganisms are everywhere, and thanks to their great functional and taxonomic variability, they play central roles in almost all environments. In soil, they are responsible for biogeochemical cycles (i.e., carbon and nitrogen) and for the cycling of organic compounds. They reside both on the surface and in the deep layers of human skin, in the saliva and oral mucosa, in the conjunctiva, and in the gastrointestinal tracts performing tasks that can be useful for human hosts. They colonize extreme environments like volcanoes and acidic ponds, and thanks to their ability to break down hazardous substances into less toxic or non-toxic ones, they act as bioremediation agents for removing pollutant from contaminated sites. Nevertheless, the study of microbial diversity patterns is still hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. A range of novel methods, mostly based on molecular analyses, have uncovered part of the microbial diversity, but the percentage of characterized organisms remains low (approximately 1%–5% of the whole bacterial biodiversity). We invite for this Special Issue papers approaching these topics which will provide novel insights into different aspects of microbiology from hard science to a more applied view of emerging concepts.

Dr. Giovanni Bacci
Prof. Matteo Ramazzotti
Dr. Niccolò Meriggi
Guest Editors

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Keywords

metagenomics
environmental microbiology
host-microbiome interactions
host–pathogen interactions
computational biology

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Published Papers (10 papers)

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Research

15 pages, 2675 KiB

Open AccessArticle

Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes

by Irene Stefanini, Monica Di Paola, Gianni Liti, Andrea Marranci, Federico Sebastiani, Enrico Casalone and Duccio Cavalieri

Int. J. Environ. Res. Public Health 2022, 19(13), 8119; https://doi.org/10.3390/ijerph19138119 - 1 Jul 2022

Cited by 6 | Viewed by 1893

Abstract

Arsenic is one of the most prevalent toxic elements in the environment, and its toxicity affects every organism. Arsenic resistance has mainly been observed in microorganisms, and, in bacteria, it has been associated with the presence of the Ars operon. In Saccharomyces cerevisiae, three genes confer arsenic resistance: ARR1, ARR2, and ARR3. Unlike bacteria, in which the presence of the Ars genes confers per se resistance to arsenic, most of the S. cerevisiae isolates present the three ARR genes, regardless of whether the strain is resistant or sensitive to arsenic. To assess the genetic features that make natural S. cerevisiae strains resistant to arsenic, we used a combination of comparative genomic hybridization, whole-genome sequencing, and transcriptomics profiling with microarray analyses. We observed that both the presence and the genomic location of multiple copies of the whole cluster of ARR genes were central to the escape from subtelomeric silencing and the acquisition of resistance to arsenic. As a result of the repositioning, the ARR genes were expressed even in the absence of arsenic. In addition to their relevance in improving our understanding of the mechanism of arsenic resistance in yeast, these results provide evidence for a new cluster of functionally related genes that are independently duplicated and translocated. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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9 pages, 857 KiB

Open AccessArticle

Fast, Ungapped Reads Mapping Using Squid

by Christopher Riccardi, Gabriel Innocenti, Marco Fondi and Giovanni Bacci

Int. J. Environ. Res. Public Health 2022, 19(9), 5442; https://doi.org/10.3390/ijerph19095442 - 29 Apr 2022

Viewed by 1680

Abstract

Advances in Next Generation Sequencing technologies allow us to inspect and unlock the genome to a level of detail that was unimaginable only a few decades ago. Omics-based studies are casting a light on the patterns and determinants of disease conditions in populations, as well as on the influence of microbial communities on human health, just to name a few. Through increasing volumes of sequencing information, for example, it is possible to compare genomic features and analyze the modulation of the transcriptome under different environmental stimuli. Although protocols for NGS preparation are intended to leave little to no space for contamination of any kind, a noticeable fraction of sequencing reads still may not uniquely represent what was intended to be sequenced in the first place. If a natural consequence of a sequencing sample is to assess the presence of features of interest by mapping the obtained reads to a genome of reference, sometimes it is useful to determine the fraction of those that do not map, or that map discordantly, and store this information to a new file for subsequent analyses. Here we propose a new mapper, which we called Squid, that among other accessory functionalities finds and returns sequencing reads that match or do not match to a reference sequence database in any orientation. We encourage the use of Squid prior to any quantification pipeline to assess, for instance, the presence of contaminants, especially in RNA-Seq experiments. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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16 pages, 1256 KiB

Open AccessArticle

Comparative Nanopore Sequencing-Based Evaluation of the Midgut Microbiota of the Summer Chafer (Amphimallon solstitiale L.) Associated with Possible Resistance to Entomopathogenic Nematodes

by Ewa Sajnaga, Marcin Skowronek, Agnieszka Kalwasińska, Waldemar Kazimierczak, Magdalena Lis, Monika Elżbieta Jach and Adrian Wiater

Int. J. Environ. Res. Public Health 2022, 19(6), 3480; https://doi.org/10.3390/ijerph19063480 - 15 Mar 2022

Cited by 1 | Viewed by 2243

Abstract

Root-feeding Amphimallon solstitiale larvae and certain other scarab beetles are the main soil-dwelling pests found in Europe, while entomopathogenic nematodes (EPN) have been used as a biocontrol agent against these species. Our study provides the first detailed characterization of the bacterial community of the midgut in wild A. solstitiale larvae, based on the nanopore sequencing of the 16S rRNA gene. In the whole dataset, we detected 2586 different genera and 11,641 species, with only 83 diverse bacterial genera shared by all studied individuals, which may represent members of the core midgut microbiota of A. solstitiale larvae. Subsequently, we compared the midgut microbiota of EPN-resistant and T0 (prior to EPN exposure) individuals, hypothesizing that resistance to this parasitic infection may be linked to the altered gut community. Compared to the control, the resistant insect microbiota demonstrated lower Shannon and Evenness indices and significant differences in the community structure. Our studies confirmed that the gut microbiota alternation is associated with resistant insects; however, there are many processes involved that can affect the bacterial community. Further research on the role of gut microbiota in insect-parasitic nematode interaction may ultimately lead to the improvement of biological control strategies in insect pest management. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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14 pages, 1387 KiB

Open AccessArticle

Insights into Asparaginase from Endophytic Fungus Lasiodiplodia theobromae: Purification, Characterization and Antileukemic Activity

by Hani A. Moubasher, Bassem A. Balbool, Yosra A. Helmy, Amnah Mohammed Alsuhaibani, Ahmed A. Atta, Donia H. Sheir and Ahmed M. Abdel-Azeem

Int. J. Environ. Res. Public Health 2022, 19(2), 680; https://doi.org/10.3390/ijerph19020680 - 7 Jan 2022

Cited by 22 | Viewed by 2548

Abstract

Endobiotic fungi are considered as a reservoir of numerous active metabolites. Asparaginase is used as an antileukemic drug specially to treat acute lymphoblastic leukaemia. The presented study aims to optimize the media conditions, purify, characterize, and test the antileukemic activity of the asparaginase induced from Lasiodiplodia theobromae. The culture medium was optimized using an experiment designed by The Taguchi model with an activity ranging from 10 to 175 IU/mL. Asparaginase was induced with an activity of 315 IU/mL. Asparaginase was purified with a specific activity of 468.03 U/mg and total activity of 84.4 IU/mL. The purified asparaginase showed an approximate size of 70 kDa. The purified asparaginase showed an optimum temperature of 37 °C and an optimum pH of 6. SDS reduced the activity of asparaginase to 0.65 U/mL while the used ionic surfactants enhanced the enzyme activity up to 151.92 IU/mL. The purified asparaginase showed a K_m of 9.37 µM and V_max of 127.00 µM/mL/min. The purified asparaginase showed an IC₅₀ of 35.2 ± 0.7 IU/mL with leukemic M-NFS-60 cell lines and CC₅₀ of 79.4 ± 1.9 IU/mL with the normal WI-38 cell line. The presented study suggests the use of endophytic fungi as a sustainable source for metabolites such as asparaginase, provides an opportunity to develop a facile, eco-friendly, cost-effective, and rapid synthesis of antileukemic drugs, which have the potential to be used as alternative and reliable sources for potent anticancer agents. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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12 pages, 5186 KiB

Open AccessArticle

Development of Colorimetric Whole-Cell Biosensor for Detection of Heavy Metals in Environment for Public Health

by Yihyang Kim, Hyeunseok Choi, Weon Ho Shin, Jong-Min Oh, Sang-Mo Koo, Younghun Kim, Taek Lee, Byung Jo Yu and Chulhwan Park

Int. J. Environ. Res. Public Health 2021, 18(23), 12721; https://doi.org/10.3390/ijerph182312721 - 2 Dec 2021

Cited by 7 | Viewed by 3184

Abstract

Heavy metals cause various fetal diseases in humans. Heavy metals from factory wastewater can contaminate drinking water, fish, and crops. Inductively coupled plasma-mass spectrometry (ICP-MS) and atomic absorption spectrometry (AAS) are commonly used to analyze heavy metal contents; however, these methods require pre-treatment processes and are expensive and complex. To overcome these limitations, three metal-sensing materials using a whole-cell biosensor in Escherichia coli (E. coli) were developed. Strains were engineered to harbor three kinds of plasmids containing the copA, zntA, and mer promoters for sensing copper, cadmium, and mercury, respectively. The luciferase (lux) gene was inserted as a reporter into the plasmid, which was later replaced with a fused protein sequence containing OmpA (1–159) and mCherry for optical detection. The constructed strains could detect mercury, cadmium, and copper at 0.1–0.75 ppm, 0.2–0.75 ppm, and 2–7.5 ppm, respectively, with linearity values of 0.99030, 0.99676, and 0.95933, respectively. The immobilization linearity value was 0.99765. Notably, these three heavy metals could be detected by visual analysis of the strains. Overall, these findings establish this novel sensor as a potential approach for heavy metal detection in biological samples and foods. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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19 pages, 2375 KiB

Open AccessArticle

Urbanization Affects Soil Microbiome Profile Distribution in the Russian Arctic Region

by Maria V. Korneykova, Viacheslav I. Vasenev, Dmitry A. Nikitin, Anastasia S. Soshina, Andrey V. Dolgikh and Yulia L. Sotnikova

Int. J. Environ. Res. Public Health 2021, 18(21), 11665; https://doi.org/10.3390/ijerph182111665 - 6 Nov 2021

Cited by 12 | Viewed by 3172

Abstract

Urbanization in the Arctic results in considerable and still poorly known environmental consequences. The effect of urbanization on soil microbiome—an ecosystem component highly sensitive to anthropogenic disturbance—remains overlooked for the Arctic region. The research compared chemical and microbial properties of the natural Podzol soils and urban soils of Murmansk—the largest Arctic city. Particular attention was given to the profile distribution, which is almost completely ignored by most microbial studies. Soil microbiome was investigated by the quantitative indicators based on fluorescence microscopy (microbial biomass) and PCR real-time methods (amount of rRNA genes copies of archaea, bacteria, and fungi). The principal changes in urban soils’ properties compared to the natural references included a shift in pH and an increase in C and nutrients’ contents, especially remarkable for the subsoil. The numbers of rRNA genes copies of archaea, bacteria, and fungi in urban topsoils (10⁶–10¹⁰, 10⁹–10¹⁰, and 10⁷–10⁹, respectively) were lower than in Podzol; however, the opposite pattern was shown for the subsoil. Similarly, the total microbial biomass in urban topsoils (0.55–0.75 mg g⁻¹) was lower compared to the 1.02 mg g⁻¹ in Podzols, while urban subsoil microbial biomass was 2–2.5 times higher than in the natural conditions. Both for urban and natural soils and throughout the profiles, fungi were dominated by mycelium forms; however, the ratios of mycelium–spores were lower, and the amount of thin mycelium was higher in urban soils than in natural Podzols. Urbanization in the Arctic altered soil morphological and chemical properties and created a new niche for microbial development in urban subsoils; its contribution to biodiversity and nutrient cycling promises to become increasingly important under projected climate change. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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13 pages, 2465 KiB

Open AccessArticle

A Rapid Culture Method for the Detection of Campylobacter from Water Environments

by Nicol Strakova, Kristyna Korena, Tereza Gelbicova, Pavel Kulich and Renata Karpiskova

Int. J. Environ. Res. Public Health 2021, 18(11), 6098; https://doi.org/10.3390/ijerph18116098 - 5 Jun 2021

Cited by 4 | Viewed by 4161

Abstract

The natural environment and water are among the sources of Campylobacter jejuni and Campylobacter coli. A limited number of protocols exist for the isolation of campylobacters in poorly filterable water. Therefore, the goal of our work was to find a more efficient method of Campylobacter isolation and detection from wastewater and surface water than the ISO standard. In the novel rapid culture method presented here, samples are centrifuged at high speed, and the resuspended pellet is inoculated on a filter, which is placed on Campylobacter selective mCCDA agar. The motile bacteria pass through the filter pores, and mCCDA agar suppresses the growth of background microbiota on behalf of campylobacters. This culture-based method is more efficient for the detection and isolation of Campylobacter jejuni and Campylobacter coli from poorly filterable water than the ISO 17995 standard. It also is less time-consuming, taking only 72 h and comprising three steps, while the ISO standard method requires five or six steps and 144–192 h. This novel culture method, based on high-speed centrifugation, bacterial motility, and selective cultivation conditions, can be used for the detection and isolation of various bacteria from water samples. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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15 pages, 1610 KiB

Open AccessArticle

The First Polish Isolate of a Novel Species Pectobacterium aquaticum Originates from a Pomeranian Lake

by Weronika Babinska, Agata Motyka-Pomagruk, Wojciech Sledz, Agnieszka Kowalczyk, Zbigniew Kaczynski and Ewa Lojkowska

Int. J. Environ. Res. Public Health 2021, 18(9), 5041; https://doi.org/10.3390/ijerph18095041 - 10 May 2021

Cited by 7 | Viewed by 3379

Abstract

Pectinolytic bacteria from the genus Pectobacterium cause high economic losses in various crops, vegetables, and ornamentals including potato. Thus far, these strains have been isolated from distinct environments such as rotten or asymptomatic plants, soil, and waterways. The prevalence of soft rot Pectobacteriaceae in different depths of Pomeranian lakes was performed by a qualified scuba diver over 2 years of monitoring. It allowed for the isolation and broad characterization of a strain from the newly established species Pectobacterium aquaticum. Phylogenetic analysis on the sequences of dnaX and recA genes revealed the highest similarity of this strain to P. aquaticum CFBP 8637^T. In addition to the determination of analytical profile index (API 20E), we discovered that this strain possesses a smooth form of a lipopolysaccharide with O-polysaccharide consisting of mannose, glucose, and abequose. Moreover, the characterized strain, described as P. aquaticum IFB5637, produced plant-cell–wall-degrading enzymes, such as pectinases, cellulases, proteases, and was capable of macerating potato and chicory tissues under laboratory conditions. In view of more frequent irrigation of seed potato fields resulting from the ongoing climate warming, it is important to monitor the occurrence of potential disease-causing agents in natural waterways. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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12 pages, 790 KiB

Open AccessArticle

Genomic and Physiological Investigation of Heavy Metal Resistance from Plant Endophytic Methylobacterium radiotolerans MAMP 4754, Isolated from Combretum erythrophyllum

by Mampolelo M. Photolo, Lungile Sitole, Vuyo Mavumengwana and Matsobane G. Tlou

Int. J. Environ. Res. Public Health 2021, 18(3), 997; https://doi.org/10.3390/ijerph18030997 - 23 Jan 2021

Cited by 18 | Viewed by 3445

Abstract

Combretum erythrophyllum is an indigenous southern African tree species, a metal hyperaccumulator that has been used as a phytoextraction option for tailing dams in Johannesburg, South Africa. In hyperaccumulators, metal detoxification has also been linked or attributed to the activities of endophytes, and, in this regard, metal detoxification can be considered a form of endophytic behavior. Therefore, we report herein on the identification of proteins that confer heavy metal resistance, the in vitro characterization of heavy metal resistance, and the production of plant growth-promoting (PGP) volatiles by Methylobacterium radiotolerans MAMP 4754. Multigenome comparative analyses of M. radiotolerans MAMP 4754 against eight other endophytic strains led to the identification of zinc, copper, and nickel resistance proteins in the genome of this endophyte. The maximum tolerance concentration (MTC) of this strain towards these metals was also investigated. The metal-exposed cells were analyzed by transmission electron microscopy (TEM). The ethyl acetate and chloroform extracts (1:1 v/v) of heavy metal untreated M. radiotolerans MAMP 4754 were also screened for the production of PGP compounds by Gas Chromatography–Mass Spectroscopy (GC/MS). The MTC was recorded at 15 mM, 4 mM, and 12 mM for zinc, copper, and nickel, respectively. The TEM analysis showed the accumulation of metals in the intracellular environment of M. radiotolerans MAMP 4754, while the GC/MS analysis revealed several plant growth-promoting compounds, including alcohols, phthalate esters, alkenes, ketones, sulfide derivatives, phenols, and thiazoles. Our findings suggest that the genetic makeup of M. radiotolerans MAMP 4754 encodes heavy metal resistant proteins that indicate hyperaccumulator-specific endophytic behavior and the potential for application in bioremediation. The production of plant growth-promoting volatiles in pure culture by M. raditotolerans MAMP 4754 is a characteristic feature for plant growth-promoting bacteria. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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12 pages, 1400 KiB

Open AccessArticle

ARDEP, a Rapid Degenerate Primer Design Pipeline Based on k-mers for Amplicon Microbiome Studies

by Yueni Wu, Kai Feng, Ziyan Wei, Zhujun Wang and Ye Deng

Int. J. Environ. Res. Public Health 2020, 17(16), 5958; https://doi.org/10.3390/ijerph17165958 - 17 Aug 2020

Cited by 4 | Viewed by 3406

Abstract

The survey of microbial diversity in various environments has relied upon the widespread use of well-evaluated amplification primers for taxonomic marker genes (e.g., prokaryotic 16S and fungal ITS). However, it is urgent to develop a fast and accurate bioinformatic program to design primers for microbial functional genes to explore more mechanisms in the microbial community. Here, we provide a rapid degenerate primer design pipeline (ARDEP) based on the k-mer algorithm, which can bypass the time-consuming step of sequence alignment to greatly reduce run times while ensuring accuracy. In addition, we developed an open-access platform for the implementation of primer design projects that could also calculate the amplification product length, GC content, Annealing Temperature (Tm), and ΔG of primer self-folding, and identify covered species and functional groups. Using this new platform, we designed primers for several functional genes in the nitrogen cycle, including napA and amoA. Our newly designed primers achieved higher coverage than the commonly used primers for all tested genes. The program and the associated platform that applied the k-mer algorithm could greatly enhance the design and evaluation of primers for environmental microbiome studies. Full article

(This article belongs to the Special Issue New Advances in Environmental Microbiology)

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