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de Souza Rodrigues R, de Souza AQL, Feitoza MDO, Alves TCL, Barbosa AN, da Silva Santiago SRS, de Souza ADL. Biotechnological potential of actinomycetes in the 21st century: a brief review. Antonie Van Leeuwenhoek 2024; 117:82. [PMID: 38789815 DOI: 10.1007/s10482-024-01964-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 04/07/2024] [Indexed: 05/26/2024]
Abstract
This brief review aims to draw attention to the biotechnological potential of actinomycetes. Their main uses as sources of antibiotics and in agriculture would be enough not to neglect them; however, as we will see, their biotechnological application is much broader. Far from intending to exhaust this issue, we present a short survey of the research involving actinomycetes and their applications published in the last 23 years. We highlight a perspective for the discovery of new active ingredients or new applications for the known metabolites of these microorganisms that, for approximately 80 years, since the discovery of streptomycin, have been the main source of antibiotics. Based on the collected data, we organize the text to show how the cosmopolitanism of actinomycetes and the evolutionary biotic and abiotic ecological relationships of actinomycetes translate into the expression of metabolites in the environment and the richness of biosynthetic gene clusters, many of which remain silenced in traditional laboratory cultures. We also present the main strategies used in the twenty-first century to promote the expression of these silenced genes and obtain new secondary metabolites from known or new strains. Many of these metabolites have biological activities relevant to medicine, agriculture, and biotechnology industries, including candidates for new drugs or drug models against infectious and non-infectious diseases. Below, we present significant examples of the antimicrobial spectrum of actinomycetes, which is the most commonly investigated and best known, as well as their non-antimicrobial spectrum, which is becoming better known and increasingly explored.
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Affiliation(s)
- Rafael de Souza Rodrigues
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil.
| | - Antonia Queiroz Lima de Souza
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
| | | | | | - Anderson Nogueira Barbosa
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
| | - Sarah Raquel Silveira da Silva Santiago
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
| | - Afonso Duarte Leão de Souza
- Programa de Pós-Graduação em Biodiversidade e Biotecnologia, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
- Central Analítica, Centro de Apoio Multidisciplinar, Universidade Federal do Amazonas, Av. General Rodrigo Octavio Jordão Ramos, 6200, Coroado I, Manaus, Amazonas, CEP 69.077-000, Brazil
- Departamento de Química, Instituto de Ciências Exatas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil
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Hu YQ, Zhang YH, Han W, Hu T, Du Y, Zeng YX. Complete genome sequence of the novel Antarctic Oceanisphaera sp. IT1-181 that carried five plasmids. Mar Genomics 2024; 74:101083. [PMID: 38485293 DOI: 10.1016/j.margen.2024.101083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/01/2024] [Indexed: 03/19/2024]
Abstract
Bacteria of the genus Oceanisphaera in the class Gammaproteobacteria are widely distributed in marine environments. Oceanisphaera sp. IT1-181 was isolated from intertidal sediment in the coastal region of the Chinese Great Wall Station on the Fildes Peninsula, King George Island, Antarctica. Here, we sequenced the complete genome of strain IT1-181, which contained a single chromosome of 3,572,184 bp (G + C content of 49.89 mol%) with five plasmids. A total of 3229 protein-coding genes, 88 tRNA genes, and 25 rRNA genes were obtained. Genome sequence analysis revealed that strain IT1-181 was not only a potentially novel species of the genus Oceanisphaera, but also harbored genes involved in biosynthesizing ectoine as well as poly-β-hydroxybutyric acid (PHB). In addition, genes of a complete type I-E CRISPR-Cas system were found in the bacterium. The results indicate the potential of strain Oceanisphaera sp. IT1-181 in biotechnology and are helpful for us understanding its ecological roles in the changing Antarctic intertidal zone environment.
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Affiliation(s)
- Yong-Qiang Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Yi-He Zhang
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Wei Han
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Ting Hu
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Yu Du
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China
| | - Yin-Xin Zeng
- Key Laboratory for Polar Science, Polar Research Institute of China, Ministry of Natural Resources, Shanghai 200136, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai 200030, China.
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Kim H, Yoo K. Marine plastisphere selectively enriches microbial assemblages and antibiotic resistance genes during long-term cultivation periods. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123450. [PMID: 38280464 DOI: 10.1016/j.envpol.2024.123450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 01/29/2024]
Abstract
Several studies have focused on identifying and quantifying suspended plastics in surface and subsurface seawater. Microplastics (MPs) have attracted attention as carriers of antibiotic resistance genes (ARGs) in the marine environment. Plastispheres, specific biofilms on MP, can provide an ideal niche to spread more widely through horizontal gene transfer (HGT), thereby increasing risks to ecosystems and human health. However, the microbial communities formed on different plastic types and ARG abundances during exposure time in natural marine environments remain unclear. Four types of commonly used MPs (polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyvinyl chloride (PVC)) were periodically cultured (46, 63, and 102 d) in a field-based marine environment to study the co-selection of ARGs and microbial communities in marine plastispheres. After the first 63 d of incubation (p < 0.05), the initial 16S rRNA gene abundance of microorganisms in the plastisphere increased significantly, and the biomass subsequently decreased. These results suggest that MPs can serve as vehicles for various microorganisms to travel to different environments and eventually provide a niche for a variety of microorganisms. Additionally, the qPCR results showed that MPs selectively enriched ARGs. In particular, tetA, tetQ, sul1, and qnrS were selectively enriched in the PVC-MPs. The abundances of intl1, a mobile genetic element, was measured in all MP types for 46 d (5.22 × 10-5 ± 8.21 × 10-6 copies/16s rRNA gene copies), 63 d (5.90 × 10-5 ± 2.49 × 10-6 copies/16s rRNA gene copies), and 102 d (4.00 × 10-5 ± 5.11 × 10-6 copies/16s rRNA gene copies). Network analysis indicated that ARG profiles co-occurred with key biofilm-forming bacteria. This study suggests that the selection of ARGs and their co-occurring bacteria in MPs could potentially accelerate their transmission through HGT in natural marine plastics.
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Affiliation(s)
- Hyunsu Kim
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea
| | - Keunje Yoo
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, Busan, 49112, South Korea.
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Lin M, Pan C, Qian C, Tang F, Zhao S, Guo J, Zhang Y, Song J, Rittmann BE. Core taxa, co-occurrence pattern, diversity, and metabolic pathways contributing to robust anaerobic biodegradation of chlorophenol. ENVIRONMENTAL RESEARCH 2024; 241:117591. [PMID: 37926226 DOI: 10.1016/j.envres.2023.117591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/07/2023]
Abstract
It is hard to achieve robustness in anaerobic biodegradation of trichlorophenol (TCP). We hypothesized that specific combinations of environmental factors determine phylogenetic diversity and play important roles in the decomposition and stability of TCP-biodegrading bacteria. The anaerobic bioreactor was operated at 35 °C (H condition) or 30 °C (L condition) and mainly fed with TCP (from 28 μM to 180 μM) and organic material. Metagenome sequencing was combined with 16S rRNA gene amplicon sequencing for the microbial community analysis. The results exhibited that the property of robustness occurred in specific conditions. The corresponding co-occurrence and diversity patterns suggest high collectivization, degree and evenness for robust communities. Two types of core functional taxa were recognized: dechlorinators (unclassified Anaerolineae, Thermanaerothrix and Desulfovibrio) and ring-opening members (unclassified Proteobacteria, Methanosarcina, Methanoperedens, and Rubrobacter). The deterministic process of the expansion of niche of syntrophic bacteria at higher temperatures was confirmed. The reductive and hydrolytic dechlorination mechanisms jointly lead to C-Cl bond cleavage. H ultimately adapted to the stress of high TCP loading, with more abundant ring-opening enzyme (EC 3.1.1.45, ∼55%) and hydrolytic dechlorinase (EC 3.8.1.5, 26.5%) genes than L (∼47%, 10.5%). The functional structure (based on KEGG) in H was highly stable despite the high loading of TCP (up to 60 μM), but not in L. Furthermore, an unknown taxon with multiple functions (dechlorinating and ring-opening) was found based on genetic sequencing; its functional contribution of EC 3.8.1.5 in H (26.5%) was higher than that in L (10.5%), and it possessed a new metabolic pathway for biodegradation of halogenated aromatic compounds. This new finding is supplementary to the robust mechanisms underlying organic chlorine biodegradation, which can be used to support the engineering, regulation, and design of synthetic microbiomes.
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Affiliation(s)
- Ming Lin
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Chenhui Pan
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Chenyi Qian
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Fei Tang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Siwen Zhao
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Jun Guo
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Department of Environmental Science and Engineering, Fudan University, Shanghai, 200238, PR China
| | - Yongming Zhang
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China
| | - Jiaxiu Song
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai, 200234, PR China; Yangtze River Delta Urban Wetland Ecosystem National Field Scientific Observation and Research Station, Shanghai, 200234, PR China.
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, 85287-5701, USA
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Brzeszcz J, Steliga T, Ryszka P, Kaszycki P, Kapusta P. Bacteria degrading both n-alkanes and aromatic hydrocarbons are prevalent in soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:5668-5683. [PMID: 38127231 PMCID: PMC10799122 DOI: 10.1007/s11356-023-31405-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
This study was undertaken to determine the distribution of soil bacteria capable of utilizing both n-alkanes and aromatic hydrocarbons. These microorganisms have not been comprehensively investigated so far. Ten contaminated (4046-43,861 mg of total petroleum hydrocarbons (TPH) kg-1 of dry weight of soil) and five unpolluted (320-2754 mg TPH kg-1 of dry weight of soil) soil samples from temperate, arid, and Alpine soils were subjected to isolation of degraders with extended preferences and shotgun metagenomic sequencing (selected samples). The applied approach allowed to reveal that (a) these bacteria can be isolated from pristine and polluted soils, and (b) the distribution of alkane monooxygenase (alkB) and aromatic ring hydroxylating dioxygenases (ARHDs) encoding genes is not associated with the contamination presence. Some alkB and ARHD genes shared the same taxonomic affiliation; they were most often linked with the Rhodococcus, Pseudomonas, and Mycolicibacterium genera. Moreover, these taxa together with the Paeniglutamicibacter genus constituted the most numerous groups among 132 culturable strains growing in the presence of both n-alkanes and aromatic hydrocarbons. All those results indicate (a) the prevalence of the hydrocarbon degraders with extended preferences and (b) the potential of uncontaminated soil as a source of hydrocarbon degraders applied for bioremediation purposes.
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Affiliation(s)
- Joanna Brzeszcz
- Department of Microbiology, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland.
| | - Teresa Steliga
- Department of Production Technology of Reservoir Fluids, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland
| | - Przemysław Ryszka
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University in Kraków, ul. Gronostajowa 7, 30-387, Kraków, Poland
| | - Paweł Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Kraków, Al. Mickiewicza 21, 31-425, Kraków, Poland
| | - Piotr Kapusta
- Department of Microbiology, Oil and Gas Institute - National Research Institute, ul. Lubicz 25A, 31-503, Kraków, Poland
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Semenova EM, Tourova TP, Babich TL, Logvinova EY, Sokolova DS, Loiko NG, Myazin VA, Korneykova MV, Mardanov AV, Nazina TN. Crude Oil Degradation in Temperatures Below the Freezing Point by Bacteria from Hydrocarbon-Contaminated Arctic Soils and the Genome Analysis of Sphingomonas sp. AR_OL41. Microorganisms 2023; 12:79. [PMID: 38257905 PMCID: PMC10818417 DOI: 10.3390/microorganisms12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 12/24/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Intensive human activity in the Arctic region leads to hydrocarbon pollution of reservoirs and soils. Isolation of bacteria capable of growing at low temperatures and degrading oil and petroleum products is of scientific and practical value. The aim of this work was to study the physiology and growth in oil at temperatures below 0 °C of four strains of bacteria of the genera Pseudomonas, Rhodococcus, Arthrobacter, and Sphingomonas-previously isolated from diesel-contaminated soils of the Franz Josef Land archipelago-as well as genomic analysis of the Sphingomonas sp. AR_OL41 strain. The studied strains grew on hydrocarbons at temperatures from -1.5 °C to 35 °C in the presence of 0-8% NaCl (w/v). Growth at a negative temperature was accompanied by visual changes in the size of cells as well as a narrowing of the spectrum of utilized n-alkanes. The studied strains were psychrotolerant, degraded natural biopolymers (xylan, chitin) and n-alkanes of petroleum, and converted phosphates into a soluble form. The ability to degrade n-alkanes is rare in members of the genus Sphingomonas. To understand how the Sphingomonas sp. AR_OL41 strain has adapted to a cold, diesel-contaminated environment, its genome was sequenced and analyzed. The Illumina HiSeq 2500 platform was used for AR_OL41 genome strain sequencing. The genome analysis of the AR_OL41 strain showed the presence of genes encoding enzymes of n-alkane oxidation, pyruvate metabolism, desaturation of membrane lipids, and the formation of exopolysaccharides, confirming the adaptation of the strain to hydrocarbon pollution and low habitat temperature. Average nucleotide identity and digital DNA-DNA hybridization values for genomes of the AR_OL41 strain with that of the phylogenetically relative Sphingomonas alpine DSM 22537T strain were 81.9% and 20.9%, respectively, which allows the AR_OL41 strain to be assigned to a new species of the genus Sphingomonas. Phenomenological observations and genomic analysis indicate the possible participation of the studied strains in the self-purification of Arctic soils from hydrocarbons and their potential for biotechnological application in bioremediation of low-temperature environments.
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Affiliation(s)
- Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Ekaterina Y. Logvinova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Nataliya G. Loiko
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
| | - Vladimir A. Myazin
- Institute of North Industrial Ecology Problems–Subdivision of the Federal Research Centre “Kola Science Centre of Russian Academy of Science”, 184209 Apatity, Russia;
- Agrarian and Technological Institute, People’s Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Maria V. Korneykova
- Institute of North Industrial Ecology Problems–Subdivision of the Federal Research Centre “Kola Science Centre of Russian Academy of Science”, 184209 Apatity, Russia;
- Agrarian and Technological Institute, People’s Friendship University of Russia (RUDN University), 117198 Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia;
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (E.M.S.); (T.P.T.); (T.L.B.); (E.Y.L.); (D.S.S.); (N.G.L.)
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Ciric M, Šaraba V, Budin C, de Boer T, Nikodinovic-Runic J. Polyurethane-Degrading Potential of Alkaline Groundwater Bacteria. MICROBIAL ECOLOGY 2023; 87:21. [PMID: 38153543 DOI: 10.1007/s00248-023-02338-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/24/2023] [Indexed: 12/29/2023]
Abstract
Plastic waste is a global environmental burden and long-lasting plastic polymers, including ubiquitous and toxic polyurethanes (PUs), rapidly accumulate in the water environments. In this study, samples were collected from the three alkaline groundwater occurrences in the geotectonic regions of the Pannonian basin of northern Serbia (Torda and Slankamen Banja) and Inner Dinarides of western Serbia (Mokra Gora) with aim to isolate and identify bacteria with plastic- and lignocellulose-degrading potential, that could be applied to reduce the burden of environmental plastic pollution. The investigated occurrences belong to cold, mildly alkaline (pH: 7.6-7.9) brackish and hyperalkaline (pH: 11.5) fresh groundwaters of the SO4 - Na + K, Cl - Na + K and OH, Cl - Ca, Na + K genetic type. Full-length 16S rDNA sequencing, using Oxford Nanopore sequencing device, was performed with DNA extracted from colonies obtained by cultivation of all groundwater samples, as well as with DNA extracted directly from one groundwater sample. The most abundant genera belong to Pseudomonas, Acidovorax, Kocuria and Methylotenera. All screened isolates (100%) had the ability to grow on at least 3 of the tested plastic and lignocellulosic substrates, with 53.9% isolates degrading plastic substrate Impranil® DLN-SD (SD), a model compound for PUs degradation. Isolates degrading SD that were identified by partial 16S rDNA sequencing belong to the Stenotrophomonas, Pseudomonas, Paraburkholderia, Aeromonas, Vibrio and Acidovorax genera. Taking into account that plastics, including commonly produced PUs, are widespread in groundwater, identification of PUs-degrading bacteria may have potential applications in bioremediation of groundwater polluted with this polymer.
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Affiliation(s)
- Milica Ciric
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.
| | - Vladimir Šaraba
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Clémence Budin
- Microlife Solutions, Science Park 406, 1098XH, Amsterdam, The Netherlands
| | - Tjalf de Boer
- Microlife Solutions, Science Park 406, 1098XH, Amsterdam, The Netherlands
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Antonioli R, de Faria Poloni J, Riveros Escalona MA, Dorn M. Functional response of microbial communities in lab-controlled oil-contaminated marine sediment. Mol Omics 2023; 19:756-768. [PMID: 37477619 DOI: 10.1039/d3mo00007a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.
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Affiliation(s)
- Regis Antonioli
- Center for Biotechnology, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil
| | - Joice de Faria Poloni
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, 90619-900, Porto Alegre, Brazil
| | | | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil
- National Institute of Science and Technology - Forensic Science, Porto Alegre, Brazil
- Institute of Informatics, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, Brazil.
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Singleton SL, Davis EW, Arnold HK, Daniels AMY, Brander SM, Parsons RJ, Sharpton TJ, Giovannoni SJ. Identification of rare microbial colonizers of plastic materials incubated in a coral reef environment. Front Microbiol 2023; 14:1259014. [PMID: 37869676 PMCID: PMC10585116 DOI: 10.3389/fmicb.2023.1259014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023] Open
Abstract
Plastic waste accumulation in marine environments has complex, unintended impacts on ecology that cross levels of community organization. To measure succession in polyolefin-colonizing marine bacterial communities, an in situ time-series experiment was conducted in the oligotrophic coastal waters of the Bermuda Platform. Our goals were to identify polyolefin colonizing taxa and isolate bacterial cultures for future studies of the biochemistry of microbe-plastic interactions. HDPE, LDPE, PP, and glass coupons were incubated in surface seawater for 11 weeks and sampled at two-week intervals. 16S rDNA sequencing and ATR-FTIR/HIM were used to assess biofilm community structure and chemical changes in polymer surfaces. The dominant colonizing taxa were previously reported cosmopolitan colonizers of surfaces in marine environments, which were highly similar among the different plastic types. However, significant differences in rare community composition were observed between plastic types, potentially indicating specific interactions based on surface chemistry. Unexpectedly, a major transition in community composition occurred in all material treatments between days 42 and 56 (p < 0.01). Before the transition, Alteromonadaceae, Marinomonadaceae, Saccharospirillaceae, Vibrionaceae, Thalassospiraceae, and Flavobacteriaceae were the dominant colonizers. Following the transition, the relative abundance of these taxa declined, while Hyphomonadaceae, Rhodobacteraceae and Saprospiraceae increased. Over the course of the incubation, 8,641 colonizing taxa were observed, of which 25 were significantly enriched on specific polyolefins. Seven enriched taxa from families known to include hydrocarbon degraders (Hyphomonadaceae, Parvularculaceae and Rhodobacteraceae) and one n-alkane degrader (Ketobacter sp.). The ASVs that exhibited associations with specific polyolefins are targets of ongoing investigations aimed at retrieving plastic-degrading microbes in culture.
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Affiliation(s)
| | - Edward W. Davis
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K. Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | | | - Susanne M. Brander
- Department of Fisheries, Wildlife, and Conservation Sciences, Coastal Oregon Marine Experiment Station, Oregon State University, Newport, OR, United States
| | | | - Thomas J. Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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Zhang M, Xiong J, Zhou L, Li J, Fan J, Li X, Zhang T, Yin Z, Yin H, Liu X, Meng D. Community ecological study on the reduction of soil antimony bioavailability by SRB-based remediation technologies. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132256. [PMID: 37567138 DOI: 10.1016/j.jhazmat.2023.132256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023]
Abstract
Sulfate-reducing bacteria (SRB) were effective in stabilizing Sb. However, the influence of electron donors and acceptors during SRB remediation, as well as the ecological principles involved, remained unclear. In this study, Desulfovibrio desulfuricans ATCC 7757 was utilized to stabilize soil Sb within microcosm. Humic acid (HA) or sodium sulfate (Na2SO4) were employed to enhance SRB capacity. The SRB+HA treatment exhibited the highest Sb stabilization rate, achieving 58.40%. Bacterial community analysis revealed that SRB altered soil bacterial diversity, community composition, and assembly processes, with homogeneous selection as the predominant assembly processes. When HA and Na2SO4 significantly modified the stimulated microbial community succession trajectories, shaped the taxonomic composition and interactions of the bacterial community, they showed converse effect in shaping bacterial community which were both helpful for promoting dissimilatory sulfate reduction. Na2SO4 facilitated SRB-mediated anaerobic reduction and promoted interactions between SRB and bacteria involved in nitrogen and sulfur cycling. The HA stimulated electron generation and storage, and enhanced the interactions between SRB and bacteria possessing heavy metal tolerance or carbohydrate degradation capabilities.
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Affiliation(s)
- Min Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Jing Xiong
- Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing 101148, China
| | - Jingjing Li
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Jianqiang Fan
- Technology Center, China Tobacco Fujian Industrial Co., Ltd., Xiamen, Fujian 361000, China
| | - Xing Li
- Hunan HIKEE Environmental Technology CO., LTD, Changsha 410221, China
| | - Teng Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Hunan urban and Rural Environmental Construction Co., Ltd, Changsha 410118, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Zhuzhong Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China; Key laboratory of Biometallurgy, Ministry of Education, Changsha 410083, China.
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Ershov AP, Babich TL, Grouzdev DS, Sokolova DS, Semenova EM, Avtukh AN, Poltaraus AB, Ianutsevich EA, Nazina TN. Genome Analysis and Potential Ecological Functions of Members of the Genus Ensifer from Subsurface Environments and Description of Ensifer oleiphilus sp. nov. Microorganisms 2023; 11:2314. [PMID: 37764159 PMCID: PMC10538136 DOI: 10.3390/microorganisms11092314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/06/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15-33 °C and 0-1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0-100.0%). Nevertheless, genomic characteristics of strain HO-A22T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7-92.4% (<95%), and digital DNA-DNA hybridization (dDDH) values were within the range of 25.4-45.9% (<70%), which supported our conclusion that HO-A22T (=VKM B-3646T = KCTC 92427T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species 'Ensifer canadensis', which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment.
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Affiliation(s)
- Alexey P. Ershov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Tamara L. Babich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | | | - Diyana S. Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Ekaterina M. Semenova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Alexander N. Avtukh
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Elena A. Ianutsevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
| | - Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.P.E.); (T.L.B.); (D.S.S.); (E.M.S.); (E.A.I.)
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12
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Abdullah K, Wilkins D, Ferrari BC. Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach. Front Microbiol 2023; 14:1113102. [PMID: 37396353 PMCID: PMC10313077 DOI: 10.3389/fmicb.2023.1113102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/02/2023] [Indexed: 07/04/2023] Open
Abstract
Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.
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Affiliation(s)
- Kristopher Abdullah
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Wilkins
- Environmental Stewardship Program, Australian Antarctic Division, Department of Climate Change, Energy, Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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