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Microorganisms
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Marine Microorganisms in Biodegradation and Bioremediation
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Marine Microorganisms in Biodegradation and Bioremediation

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

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 10604

Special Issue Editor

Prof. Dr. Yangguo Zhao

E-Mail Website
Guest Editor
College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
Interests: structure and dynamics of microbial community; bioremediation of mariculture habitat; occurrence and biodegradation of antibiotics and resistance genes; nitrate removal in mariculture wastewater

Special Issue Information

Dear Colleagues,

The ocean contains abundant mineral and biological resources, on which human beings depend for survival. However, the ocean is also a sink where all types of matters finally come together. For this reason, a variety of pollutants, such as crude oil, pesticides, antibiotics, polycyclic aromatic hydrocarbons, heavy metals and other emerging contaminants due to anthropogenic factors, are eventually transported to the ocean through runoff or atmospheric deposition. These pollutants will definitely impact the marine ecosystem and the microorganisms (microalgae, fungi, bacteria, viruses, etc.) in the ocean. Marine microorganisms are diverse and metabolically active, and they play significant roles in pollutant degradation, ecological restoration and maintenance of marine ecosystem health. Microbial degradation of pollutants and the application of ecological restoration have become hot topics in current research.

This Special Issue focuses on all aspects of marine microorganisms in biodegradation and bioremediation. We seek contributions from authors that include, but are not limited to, the following areas:

  • Exploitation of marine microbial resources, such as enrichment and characteristics of pollutants degradation isolates or microbiota and immobilization of marine functional microorganisms;
  • Ecology of marine microbial communities subjected to anthropogenic events, such as diversity, dynamics, the abundance of the microbial community in marine biodegradation and bioremediation and the roles of marine microorganisms in nitrogen, sulfur and phosphorus biogeochemical cycles;
  • The roles of microorganisms in nitrogen and phosphorus pollutant removal in mariculture wastewater;
  • Interesting and typical cases of marine microorganisms in the degradation of petroleum hydrocarbons, antibiotics, pesticides, microplastics and other emerging pollutants;
  • The roles of marine microorganisms in the bioremediation of damaged marine habitats and polluted coastal waters.

Prof. Dr. Yangguo Zhao
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All 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. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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

  • marine microorganisms
  • microbial resources
  • microbial ecology
  • microbial community
  • biogeochemical cycles
  • biological nitrogen and phosphorus removal
  • petroleum hydrocarbons
  • antibiotics
  • pesticides
  • microplastics
  • emerging pollutants
  • biodegradation
  • bioremediation

Published Papers (5 papers)

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Research

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12 pages, 5011 KiB  
Article
Isolation and Identification of Efficient Malathion-Degrading Bacteria from Deep-Sea Hydrothermal Sediment
by Ling Ma, Xin Dai, Guomin Ai, Xiaofang Zheng, Yanfeng Zhang, Chaozhi Pan, Meng Hu, Chengying Jiang, Li Wang and Zhiyang Dong
Microorganisms 2022, 10(9), 1797; https://doi.org/10.3390/microorganisms10091797 - 6 Sep 2022
Cited by 3 | Viewed by 1761
Abstract
The genetic and metabolic diversity of deep-sea microorganisms play important roles in phosphorus and sulfur cycles in the ocean, distinguishing them from terrestrial counterparts. Malathion is a representative organophosphorus component in herbicides, pesticides, and insecticides and is analogues of neurotoxic agent. Malathion has [...] Read more.
The genetic and metabolic diversity of deep-sea microorganisms play important roles in phosphorus and sulfur cycles in the ocean, distinguishing them from terrestrial counterparts. Malathion is a representative organophosphorus component in herbicides, pesticides, and insecticides and is analogues of neurotoxic agent. Malathion has been one of the best-selling generic organophosphate insecticides from 1980 to 2012. Most of the sprayed malathion has migrated by surface runoff to ocean sinks, and it is highly toxic to aquatic organisms. Hitherto, there is no report on bacterial cultures capable of degrading malathion isolated from deep-sea sediment. In this study, eight bacterial strains, isolated from sediments from deep-sea hydrothermal regions, were identified as malathion degradators. Two of the tested strains, Pseudidiomarina homiensis strain FG2 and Pseudidiomarina sp. strain CB1, can completely degrade an initial concentration of 500 mg/L malathion within 36 h. Since the two strains have abundant carboxylesterases (CEs) genes, malathion monocarboxylic acid (MMC α and MMC β) and dibasic carboxylic acid were detected as key intermediate metabolites of malathion degradation, and the pathway of malathion degradation between the two strains was identified as a passage from malathion monocarboxylic acid to malathion dicarboxylic acid. Full article
(This article belongs to the Special Issue Marine Microorganisms in Biodegradation and Bioremediation)
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13 pages, 3745 KiB  
Article
Potential Use of Deep-Sea Sediment Bacteria for Oil Spill Biodegradation: A Laboratory Simulation
by Tri Prartono, Angga Dwinovantyo, Syafrizal Syafrizal and Agung Dhamar Syakti
Microorganisms 2022, 10(8), 1616; https://doi.org/10.3390/microorganisms10081616 - 10 Aug 2022
Cited by 5 | Viewed by 2136
Abstract
Deep-sea sedimentary hydrocarbonoclastic bacteria are still not widely used in the bioremediation field, especially for crude oil spill biodegradation. This study utilized a mixed culture of Raoultella sp., Enterobacter sp., and Pseudomonas sp. isolated from deep-sea sediment to determine the abilities of bacteria [...] Read more.
Deep-sea sedimentary hydrocarbonoclastic bacteria are still not widely used in the bioremediation field, especially for crude oil spill biodegradation. This study utilized a mixed culture of Raoultella sp., Enterobacter sp., and Pseudomonas sp. isolated from deep-sea sediment to determine the abilities of bacteria to degrade petroleum hydrocarbons while incorporating environmental variations in a microcosm study. The oil biodegradation extent was determined by measuring the remaining oil and grease in the sample vials. The highest percentage of biodegradation was 88.6%, with a constant degradation rate of 0.399 day–1. GC-MS analysis showed that the most degradable compound in the oil samples was paraffin. This study also observed that microbial degradation was optimized within three days of exposure and that degradation ability decreased at 35 °C. The salinity variation effects were insignificant. Based on all analyses, deep-sea sediment bacteria have great potential in oil spill biodegradation in a microcosm scale. Full article
(This article belongs to the Special Issue Marine Microorganisms in Biodegradation and Bioremediation)
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16 pages, 3290 KiB  
Article
Aerobic Degradation Characteristics of Decabromodiphenyl ether through Rhodococcus ruber TAW-CT127 and Its Preliminary Genome Analysis
by Hao Xu, Qingtao Cai, Qiuying An, Chen Tang, Wanpeng Wang, Guangshun Wang, Wanting You, Dongbei Guo and Ran Zhao
Microorganisms 2022, 10(7), 1441; https://doi.org/10.3390/microorganisms10071441 - 17 Jul 2022
Cited by 1 | Viewed by 1931
Abstract
Decabromodiphenyl ether (BDE-209), a polybrominated diphenyl ether (PBDE) homolog, seriously threatens human health. In this study, a Rhodococcus ruber strain with high BDE-209 degradation activity, named TAW-CT127, was isolated from Tong’an Bay, Xiamen. Under laboratory conditions, the strain’s optimal growth temperature, pH, and [...] Read more.
Decabromodiphenyl ether (BDE-209), a polybrominated diphenyl ether (PBDE) homolog, seriously threatens human health. In this study, a Rhodococcus ruber strain with high BDE-209 degradation activity, named TAW-CT127, was isolated from Tong’an Bay, Xiamen. Under laboratory conditions, the strain’s optimal growth temperature, pH, and salinity are 45 °C, 7.0, and 0–2.5%, respectively. Scanning electron microscopy (SEM) analysis shows that TAW-CT127 is damaged when grown in manual marine culture (MMC) medium with BDE-209 as the sole carbon source instead of eutrophic conditions. In the dark, under the conditions of 28 °C, 160 rpm, and 3 g/L (wet weight) TAW-CT127, the degradation rate of 50 mg/L BDE-209 is 81.07%. The intermediate metabolites are hexabromo-, octabromo-, and nonabromo-diphenyl ethers. Through whole-genome sequencing, multiple dehalogenases were found in the genome of TAW-CT127; these may be involved in the production of lower-brominated diphenyl ethers. Additionally, biphenyl-2,3-dioxygenase (BDO) in TAW-CT127 may catalyze the debromination reaction of BDE-209. Our research provides a new high-efficiency strain for bioremediation of BDE-209 pollution, and lays the foundation for the preliminary exploration of genes associated with BDE-209 degradation. Full article
(This article belongs to the Special Issue Marine Microorganisms in Biodegradation and Bioremediation)
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15 pages, 2650 KiB  
Article
Effects of Chlorella vulgaris Enhancement on Endogenous Microbial Degradation of Marine Oil Spills and Community Diversity
by Zhao Song, Mei Liu, Bo Bao, Jian Guo, Hengcong Tao, Baikang Zhu and Qingguo Chen
Microorganisms 2022, 10(5), 905; https://doi.org/10.3390/microorganisms10050905 - 26 Apr 2022
Cited by 3 | Viewed by 1945
Abstract
Biofortification could improve the bioremediation efficiency of microbes in the reparation of marine environmental damage caused by oil spills. In this paper, Chlorella vulgaris LH-1 was used as a fortifier to enhance the degradation of a marine oil spill by endogenous microorganisms. The [...] Read more.
Biofortification could improve the bioremediation efficiency of microbes in the reparation of marine environmental damage caused by oil spills. In this paper, Chlorella vulgaris LH-1 was used as a fortifier to enhance the degradation of a marine oil spill by endogenous microorganisms. The addition of C. vulgaris LH-1 increased the degradation efficiency of crude oil by 11.09–42.41% and considerably accelerated oil degradation efficiency. Adding C. vulgaris LH-1 to a crude oil environment can improve the activity of endogenous seawater microorganisms. The results of high-throughput sequencing showed that the main bacterial genera were Oceanicola, Roseibacillus, and Rhodovulum when exotrophic C. vulgaris LH-1 and seawater endogenous microorganisms degraded low-concentration crude oil together. However, the addition of high-concentration nutrient salts changed the main bacterial genera in seawater to unclassified Microbacterium, Erythrobacter, and Phaeodactylibacter. The addition of C. vulgaris LH-1 increased the abundance of marine bacteria, Rhodococcus, and Methylophaga and decreased the abundance of Pseudomonas, Cladosporium, and Aspergillus. The functional prediction results of phylogenetic investigation of communities by reconstruction of unobserved states indicated that C. vulgaris LH-1 could improve the metabolic ability of seawater endogenous microorganisms to degrade endogenous bacteria and fungi in crude oil. Full article
(This article belongs to the Special Issue Marine Microorganisms in Biodegradation and Bioremediation)
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Review

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20 pages, 6913 KiB  
Review
Linking Copper-Associated Signal Transduction Systems with Their Environment in Marine Bacteria
by Pratima Gautam, Ivan Erill and Kathleen D. Cusick
Microorganisms 2023, 11(4), 1012; https://doi.org/10.3390/microorganisms11041012 - 13 Apr 2023
Viewed by 1742
Abstract
Copper is an essential trace element for living cells. However, copper can be potentially toxic for bacterial cells when it is present in excess amounts due to its redox potential. Due to its biocidal properties, copper is prevalent in marine systems due to [...] Read more.
Copper is an essential trace element for living cells. However, copper can be potentially toxic for bacterial cells when it is present in excess amounts due to its redox potential. Due to its biocidal properties, copper is prevalent in marine systems due to its use in antifouling paints and as an algaecide. Thus, marine bacteria must possess means of sensing and responding to both high copper levels and those in which it is present at only typical trace metal levels. Bacteria harbor diverse regulatory mechanisms that respond to intracellular and extracellular copper and maintain copper homeostasis in cells. This review presents an overview of the copper-associated signal transduction systems in marine bacteria, including the copper efflux systems, detoxification, and chaperone mechanisms. We performed a comparative genomics study of the copper-regulatory signal transduction system on marine bacteria to examine the influence of the environment on the presence, abundance, and diversity of copper-associated signal transduction systems across representative phyla. Comparative analyses were performed among species isolated from sources, including seawater, sediment, biofilm, and marine pathogens. Overall, we observed many putative homologs of copper-associated signal transduction systems from various copper systems across marine bacteria. While the distribution of the regulatory components is mainly influenced by phylogeny, our analyses identified several intriguing trends: (1) Bacteria isolated from sediment and biofilm displayed an increased number of homolog hits to copper-associated signal transduction systems than those from seawater. (2) A large variability exists for hits to the putative alternate σ factor CorE hits across marine bacteria. (3) Species isolated from seawater and marine pathogens harbored fewer CorE homologs than those isolated from the sediment and biofilm. Full article
(This article belongs to the Special Issue Marine Microorganisms in Biodegradation and Bioremediation)
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