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Applied Sciences
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Advances in Industrial and Environmental Microbiology
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Advances in Industrial and Environmental Microbiology

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Applied Biosciences and Bioengineering".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 18045

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Dr. Slawomir Ciesielski

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Guest Editor
Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, 10-907 Olsztyn, Poland
Interests: biotechnology; microbial biopolymers; metagenomics and metatranscriptomics; diversity of microbial communities; prokaryotic gene regulation
Special Issues, Collections and Topics in MDPI journals
Dr. Ivone Vaz-Moreira

E-Mail Website
Guest Editor
Centre for Biotechnology and Fine Chemistry (CBQF), Universidade Catolica Portuguesa, 4200-374 Porto, Portugal
Interests: drinking water; antimicrobial resistance; bacterial diversity; metagenomics; wastewater; taxonomy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The development of civilization entails the need to find new technological solutions leading to products with new properties. Allies in these efforts are microorganisms that have developed skills to synthesize products with properties of interest to the industry. Recently, in the omics era, information about the genetic machinery of microorganisms can be applied in synthetic biology towards new products and services development.

Naturally occurring microorganisms are a potential source of promising bioproducts. Therefore we should take a closer look at the microorganisms inhabiting different environments. However, we know that most microorganisms occupying natural and semi-natural environments are uncultured, and new methodologies leading to new knowledge about these microbes should be promoted. The study of microbial communities and their interactions with an environment is extremely exciting, as is the application of new approaches to try to cultivate new microorganisms.

This Special Issue covers all aspects of the industrial applications of microorganisms including fermentation, biodegradation, biodeterioration, and treatment of waste streams. Articles focused on novel techniques in the bioprocess engineering of peptides, enzymes, and biopolymers as well as their production and purification will be published. In this Special Issue, research papers as well as review articles addressing recent advances on environmental microbiology will be welcomed. Potential topics include microbial diversity, culturomics, microbiomics, microbial community genetics, evolutionary processes, and antibiotic resistance. We also look forward to receiving your manuscripts in which metagenomics, metatranscriptomics, and metaproteomics are used as the main methodology.

Dr. Slawomir Ciesielski
Dr. Ivone Vaz-Moreira
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Applied Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Antibiotic resistance
  • Applied microbiology
  • Bioproducts
  • Biotechnology
  • Culturomics
  • Metagenomics
  • Metaproteomics
  • Metatranscriptomics
  • Microbial communities
  • Microbiomics
  • Microorganisms in food processing
  • Next generation sequencing
  • Wastewater treatment

Published Papers (6 papers)

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Editorial

Jump to: Research, Review

3 pages, 181 KiB  
Editorial
Advances in Industrial and Environmental Microbiology
by Slawomir Ciesielski and Ivone Vaz-Moreira
Appl. Sci. 2021, 11(20), 9774; https://0-doi-org.brum.beds.ac.uk/10.3390/app11209774 - 19 Oct 2021
Viewed by 1461
Abstract
Understanding microorganisms in terms of their functionality, diversity, and interactions with other organisms is crucial for better understanding of our Biosphere [...] Full article
(This article belongs to the Special Issue Advances in Industrial and Environmental Microbiology)

Research

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18 pages, 2221 KiB  
Article
Effect of Aeration Mode on Microbial Structure and Efficiency of Treatment of TSS-Rich Wastewater from Meat Processing
by Piotr Jachimowicz, Agnieszka Cydzik-Kwiatkowska and Patrycja Szklarz
Appl. Sci. 2020, 10(21), 7414; https://0-doi-org.brum.beds.ac.uk/10.3390/app10217414 - 22 Oct 2020
Cited by 9 | Viewed by 2980
Abstract
The present study investigated the effect of aeration mode on microbial structure and efficiency of treatment of wastewater with a high concentration of suspended solids (TSS) from meat processing in sequencing batch reactors (R). R1 was constantly aerated, while in R2 [...] Read more.
The present study investigated the effect of aeration mode on microbial structure and efficiency of treatment of wastewater with a high concentration of suspended solids (TSS) from meat processing in sequencing batch reactors (R). R1 was constantly aerated, while in R2 intermittent aeration was applied. DNA was isolated from biomass and analyzed using next-generation sequencing (NGS) and real-time PCR. As a result, in R1 aerobic granular sludge was cultivated (SVI30 = 44 mL g−1 MLSS), while in R2 a very well-settling mixture of aerobic granules and activated sludge was obtained (SVI30 = 65 mL g−1 MLSS). Intermittent aeration significantly increased denitrification and phosphorus removal efficiencies (68% vs. 43%, 73% vs. 65%, respectively) but resulted in decomposition of extracellular polymeric substances and worse-settling properties of biomass. In both reactors, microbial structure significantly changed in time; an increase in relative abundances of Arenimonas sp., Rhodobacterace, Thauera sp., and Dokdonella sp. characterized the biomass of stable treatment of meat-processing wastewater. Constant aeration in R1 cycle favored growth of glycogen-accumulating Amaricoccus tamworthensis (10.9%) and resulted in 2.4 times and 1.4 times greater number of ammonia-oxidizing bacteria and full-denitrifiers genes in biomass, respectively, compared to the R2. Full article
(This article belongs to the Special Issue Advances in Industrial and Environmental Microbiology)
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13 pages, 266 KiB  
Article
Occurrence of Fluoroquinolones and Sulfonamides Resistance Genes in Wastewater and Sludge at Different Stages of Wastewater Treatment: A Preliminary Case Study
by Damian Rolbiecki, Monika Harnisz, Ewa Korzeniewska, Łukasz Jałowiecki and Grażyna Płaza
Appl. Sci. 2020, 10(17), 5816; https://0-doi-org.brum.beds.ac.uk/10.3390/app10175816 - 22 Aug 2020
Cited by 15 | Viewed by 2670
Abstract
This study identified differences in the prevalence of antibiotic resistance genes (ARGs) between wastewater treatment plants (WWTPs) processing different proportions of hospital and municipal wastewater as well as various types of industrial wastewater. The influence of treated effluents discharged from WWTPs on the [...] Read more.
This study identified differences in the prevalence of antibiotic resistance genes (ARGs) between wastewater treatment plants (WWTPs) processing different proportions of hospital and municipal wastewater as well as various types of industrial wastewater. The influence of treated effluents discharged from WWTPs on the receiving water bodies (rivers) was examined. Genomic DNA was isolated from environmental samples (river water, wastewater and sewage sludge). The presence of genes encoding resistance to sulfonamides (sul1, sul2) and fluoroquinolones (qepA, aac(6′)-Ib-cr) was determined by standard polymerase chain reaction (PCR). The effect of the sampling season (summer – June, fall – November) was analyzed. Treated wastewater and sewage sludge were significant reservoirs of antibiotic resistance and contained all of the examined ARGs. All wastewater samples contained sul1 and aac(6′)-lb-cr genes, while the qepA and sul2 genes occurred less frequently. These observations suggest that the prevalence of ARGs is determined by the type of processed wastewater. The Warmia and Mazury WWTP was characterized by higher levels of the sul2 gene, which could be attributed to the fact that this WWTP processes agricultural sewage containing animal waste. However, hospital wastewater appears to be the main source of the sul1 gene. The results of this study indicate that WWTPs are significant sources of ARGs, contributing to the spread of antibiotic resistance in rivers receiving processed wastewater. Full article
(This article belongs to the Special Issue Advances in Industrial and Environmental Microbiology)
13 pages, 1716 KiB  
Article
Composition Characteristics of Organic Matter and Bacterial Communities under the Alternanthera philoxeroide Invasion in Wetlands
by Qingqing Cao, Haijie Zhang, Wen Ma, Renqing Wang and Jian Liu
Appl. Sci. 2020, 10(16), 5571; https://0-doi-org.brum.beds.ac.uk/10.3390/app10165571 - 12 Aug 2020
Cited by 2 | Viewed by 1662
Abstract
The influence of Alternanthera philoxeroide (alligator weed) invasion on wetland organic matter (OM) accumulation and bacterial changes is rarely studied, but is possibly an important step for revealing the invasion mechanism. Thus, the distribution characteristics of light fraction organic carbon and nitrogen (LFOC [...] Read more.
The influence of Alternanthera philoxeroide (alligator weed) invasion on wetland organic matter (OM) accumulation and bacterial changes is rarely studied, but is possibly an important step for revealing the invasion mechanism. Thus, the distribution characteristics of light fraction organic carbon and nitrogen (LFOC and LFON), and heavy fractions organic carbon and nitrogen (HFOC and HFON) were analyzed. Sampling was done on two sediment depths (0–15 cm and 15–25 cm) of invaded and normal habitats of two natural wetlands and two constructed wetlands, and bacterial taxa and composition in surface sediments were also analyzed by high-throughput sequencing. In the surface sediments, the LFOC and LFON contents were significantly higher in the constructed wetlands (0.791 and 0.043 g·kg−1) than in the natural wetlands (0.500 and 0.022 g·kg−1), and the contents of the C and N fractions were also prominently higher in the invaded areas than in normal wetland habitats. The OM storage was relatively stable. Proteobacteria (55.94%), Bacteroidetes (5.74%), Acidobacteria (6.66%), and Chloroflexi (4.67%) were the dominant bacterial phyla in the wetlands. The abundance of Acidobacteria, Actinobacteria, and Gemmatimonadetes were significantly higher in the invaded areas than in the normal habitats. The relative high abundance-based coverage estimator (ACE) index in the constructed wetlands and invaded areas suggested the corresponding high bacterial diversity. The significant and positive relationship between Acidobacteria and organic nitrogen concentrations suggested their potential and positive interrelationships. This study demonstrated that the alligator weed invasion could significantly change the compositions of sediment organic matterand bacteria, thus further changing the nutrition cycle and wetland microhabitat. Full article
(This article belongs to the Special Issue Advances in Industrial and Environmental Microbiology)
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Review

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14 pages, 761 KiB  
Review
A Review on the Importance of Microbial Biopolymers Such as Xanthan Gum to Improve Soil Properties
by Amanda Mendonça, Paula V. Morais, Ana Cecília Pires, Ana Paula Chung and Paulo Venda Oliveira
Appl. Sci. 2021, 11(1), 170; https://0-doi-org.brum.beds.ac.uk/10.3390/app11010170 - 27 Dec 2020
Cited by 30 | Viewed by 4972
Abstract
Chemical stabilization of soils is one of the most used techniques to improve the properties of weak soils in order to allow their use in geotechnical works. Although several binders can be used for this purpose, Portland cement is still the most used [...] Read more.
Chemical stabilization of soils is one of the most used techniques to improve the properties of weak soils in order to allow their use in geotechnical works. Although several binders can be used for this purpose, Portland cement is still the most used binder (alone or combined with others) to stabilize soils. However, the use of Portland cement is associated with many environmental problems, so microbiological-based approaches have been explored to replace conventional methods of soil stabilization as sustainable alternatives. Thus, the use of biopolymers, produced by microorganisms, has emerged as a technical alternative for soil improvement, mainly due to soil pore-filling, which is called the bioclogging method. Many studies have been carried out in the last few years to investigate the suitability and efficiency of the soil–biopolymer interaction and consequent properties relevant to geotechnical engineering. This paper reviews some of the recent applications of the xanthan gum biopolymer to evaluate its viability and potential to improve soil properties. In fact, recent results have shown that the use of xanthan gum in soil treatment induces the partial filling of the soil voids and the generation of additional links between the soil particles, which decreases the permeability coefficient and increases the mechanical properties of the soil. Moreover, the biopolymer’s economic viability was also analyzed in comparison to cement, and studies have demonstrated that xanthan gum has a strong potential, both from a technical and economical point of view, to be applied as a soil treatment. Full article
(This article belongs to the Special Issue Advances in Industrial and Environmental Microbiology)
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18 pages, 1529 KiB  
Review
Microbial Activity in Subterranean Ecosystems: Recent Advances
by Tamara Martin-Pozas, Jose Luis Gonzalez-Pimentel, Valme Jurado, Soledad Cuezva, Irene Dominguez-Moñino, Angel Fernandez-Cortes, Juan Carlos Cañaveras, Sergio Sanchez-Moral and Cesareo Saiz-Jimenez
Appl. Sci. 2020, 10(22), 8130; https://0-doi-org.brum.beds.ac.uk/10.3390/app10228130 - 17 Nov 2020
Cited by 10 | Viewed by 3036
Abstract
Of the several critical challenges present in environmental microbiology today, one is the assessment of the contribution of microorganisms in the carbon cycle in the Earth-climate system. Karstic subterranean ecosystems have been overlooked until recently. Covering up to 25% of the land surface [...] Read more.
Of the several critical challenges present in environmental microbiology today, one is the assessment of the contribution of microorganisms in the carbon cycle in the Earth-climate system. Karstic subterranean ecosystems have been overlooked until recently. Covering up to 25% of the land surface and acting as a rapid CH4 sink and alternately as a CO2 source or sink, karstic subterranean ecosystems play a decisive role in the carbon cycle in terms of their contribution to the global balance of greenhouse gases. Recent data indicate that microbiota must play a significant ecological role in the biogeochemical processes that control the composition of the subterranean atmosphere, as well as in the availability of nutrients for the ecosystem. Nevertheless, there are still essential gaps in our knowledge concerning the budgets of greenhouse gases at the ecosystem scale and the possible feedback mechanisms between environmental-microclimatic conditions and the rates and type of activity of microbial communities in subterranean ecosystems. Another challenge is searching for bioactive compounds (antibiotics) used for treating human diseases. At present, there is a global health emergency and a strong need for novel biomolecules. In recent decades, great research efforts have been made to extract antibiotics from marine organisms. More recently, caves have been receiving considerable attention in search of novel antibiotics. Cave methanotrophic and heterotrophic bacteria are producers of bioactive compounds and may be potential sources of metabolites with antibacterial, antifungal or anticancer activities of interest in pharmacological and medical research, as well as enzymes with a further biotechnological use. Here we also show that bacteria isolated from mines, a still unexplored niche for scientists in search of novel compounds, can be a source of novel secondary metabolites. Full article
(This article belongs to the Special Issue Advances in Industrial and Environmental Microbiology)
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