1
|
Bharali P, Gogoi B, Sorhie V, Acharjee SA, Walling B, Alemtoshi, Vishwakarma V, Shah MP. Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments. Biodegradation 2024; 35:1-46. [PMID: 37436665 DOI: 10.1007/s10532-023-10042-5] [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: 03/16/2023] [Accepted: 05/30/2023] [Indexed: 07/13/2023]
Abstract
Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.
Collapse
Affiliation(s)
- Pranjal Bharali
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India.
| | - Bhagyudoy Gogoi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Viphrezolie Sorhie
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Shiva Aley Acharjee
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Bendangtula Walling
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Alemtoshi
- Applied Environmental Microbial Biotechnology Laboratory, Department of Environmental Science, Nagaland University, Lumami, Nagaland, 798627, India
| | - Vinita Vishwakarma
- Centre for Nanoscience and Nanotechnology, Galgotias University, Greater Noida, NCR Delhi, India
| | - Maulin Pramod Shah
- Industrial Waste Water Research Lab, Division of Applied and Environmental Microbiology Lab at Enviro Technology Ltd., Ankleshwar, Gujarat, India
| |
Collapse
|
2
|
Tonteri O, Reunamo A, Nousiainen A, Koskinen L, Nuutinen J, Truu J, Jørgensen KS. Effects of Dispersant on the Petroleum Hydrocarbon Biodegradation and Microbial Communities in Seawater from the Baltic Sea and Norwegian Sea. Microorganisms 2023; 11:microorganisms11040882. [PMID: 37110305 PMCID: PMC10142239 DOI: 10.3390/microorganisms11040882] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Dispersants have been used in several oil spill accidents, but little information is available on their effectiveness in Baltic Sea conditions with low salinity and cold seawater. This study investigated the effects of dispersant use on petroleum hydrocarbon biodegradation rates and bacterial community structures. Microcosm experiments were conducted at 5 °C for 12 days with North Sea crude oil and dispersant Finasol 51 with open sea Gulf of Bothnia and coastal Gulf of Finland and Norwegian Sea seawater. Petroleum hydrocarbon concentrations were analysed with GC-FID. Bacterial community structures were studied using 16S rDNA gene amplicon sequencing, and the abundance of genes involved in hydrocarbon degradation with quantitative PCR. The highest oil degradation gene abundances and oil removal were observed in microcosms with coastal seawater from the Gulf of Bothnia and Gulf of Finland, respectively, and the lowest in the seawater from the Norwegian Sea. Dispersant usage caused apparent effects on bacterial communities in all treatments; however, the dispersant’s effect on the biodegradation rate was unclear due to uncertainties with chemical analysis and variation in oil concentrations used in the experiments.
Collapse
Affiliation(s)
- Ossi Tonteri
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
- Correspondence:
| | - Anna Reunamo
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Aura Nousiainen
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Laura Koskinen
- Laboratory Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Jari Nuutinen
- Laboratory Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| | - Jaak Truu
- Institute of Molecular and Cell Biology, Faculty of Science and Technology, University of Tartu, Riia 23, 51010 Tartu, Estonia
| | - Kirsten S. Jørgensen
- Marine Research Centre, Finnish Environmental Institute, Latokartanonkaari 11, FI-00790 Helsinki, Finland
| |
Collapse
|
3
|
Current research on simultaneous oxidation of aliphatic and aromatic hydrocarbons by bacteria of genus Pseudomonas. Folia Microbiol (Praha) 2022; 67:591-604. [PMID: 35318574 DOI: 10.1007/s12223-022-00966-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/15/2022] [Indexed: 11/04/2022]
Abstract
One of the most frequently used methods for elimination of oil pollution is the use of biological preparations based on oil-degrading microorganisms. Such microorganisms often relate to bacteria of the genus Pseudomonas. Pseudomonads are ubiquitous microorganisms that often have the ability to oxidize various pollutants, including oil hydrocarbons. To date, individual biochemical pathways of hydrocarbon degradation and the organization of the corresponding genes have been studied in detail. Almost all studies of this kind have been performed on degraders of individual hydrocarbons belonging to a single particular class. Microorganisms capable of simultaneous degradation of aliphatic and aromatic hydrocarbons are very poorly studied. Most of the works on such objects have been devoted only to phenotype characteristic and some to genetic studies. To identify the patterns of interaction of several metabolic systems depending on the growth conditions, the most promising are such approaches as transcriptomics and proteomics, which make it possible to obtain a comprehensive assessment of changes in the expression of hundreds of genes and proteins at the same time. This review summarizes the existing data on bacteria of the genus Pseudomonas capable of the simultaneous oxidation of hydrocarbons of different classes (alkanes, monoaromatics, and polyaromatics) and presents the most important results obtained in the studies on the biodegradation of hydrocarbons by representatives of this genus using methods of transcriptomic and proteomic analyses.
Collapse
|
4
|
Bagi A, Knapik K, Baussant T. Abundance and diversity of n-alkane and PAH-degrading bacteria and their functional genes - Potential for use in detection of marine oil pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152238. [PMID: 34896501 DOI: 10.1016/j.scitotenv.2021.152238] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/26/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection.
Collapse
Affiliation(s)
- Andrea Bagi
- NORCE Norwegian Research Centre, Bergen, Norway.
| | | | | |
Collapse
|
5
|
Miettinen H, Bomberg M, Nyyssönen M, Reunamo A, Jørgensen KS, Vikman M. Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area. PLoS One 2019; 14:e0218834. [PMID: 31265451 PMCID: PMC6605675 DOI: 10.1371/journal.pone.0218834] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/10/2019] [Indexed: 11/19/2022] Open
Abstract
Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.
Collapse
Affiliation(s)
- Hanna Miettinen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
- * E-mail:
| | - Malin Bomberg
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
| | - Mari Nyyssönen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
| | - Anna Reunamo
- Marine Research Centre, Finnish Environment Institute SYKE, Helsinki, Finland
| | | | - Minna Vikman
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
| |
Collapse
|
6
|
Iqbal A, Mukherjee M, Rashid J, Khan SA, Ali MA, Arshad M. Development of plant-microbe phytoremediation system for petroleum hydrocarbon degradation: An insight from alkb gene expression and phytotoxicity analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 671:696-704. [PMID: 30939322 DOI: 10.1016/j.scitotenv.2019.03.331] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/09/2019] [Accepted: 03/21/2019] [Indexed: 05/18/2023]
Abstract
Aim of present work was to assess in-planta association potential of isolated endophytic bacterial strain Pseudomonas sp. (J10) (KY608252) with two cultivars of Lolium perenne L. (small & jumbo) and Arabidopsis thaliana L. for total petroleum hydrocarbon (TPH) degradation, alkane monooxygenase (alkb) gene expression and phytotoxicity analysis. A plant-microbe phytoremediation system was established to investigate the bacteria's ability to colonize the plant body and quantification of alkb gene to help withstand TPH stress in soil as well as in hydroponics. A real-time PCR method was developed to analyze bacterial colonization and survival within the plant body. Analysis revealed that J10 efficiently colonized all the tested plant species and expressed alkb gene under hydrocarbon stress ranging between 3.7 × 102-3.9 × 106 in A. thaliana and L. perenne (small), respectively. The colonization was more pronounced in soil as compared to hydroponic system. J10 inoculation reduced phytotoxicity and suggested that inoculation had a positive effect on plant growth under stress conditions as compared to control. L. perenne (small) showed significant TPH removal efficiency (45.6%) followed by L. perenne jumbo (24.5%) and A. thaliana (6.2%). In hydroponics, L. perenne (small) degraded about 28.2% TPH followed by L. perenne (jumbo) as 24.4%. Potential of the indigenously isolated plant endophytes may be exploited further for phytoremediation efficiency and industrial applications.
Collapse
Affiliation(s)
- Aneela Iqbal
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Sector H-12, Islamabad 44000, Pakistan; Soil and Crop Sciences, Texas A&M University, College Station 77843, TX, USA
| | - Maitreyee Mukherjee
- Soil and Crop Sciences, Texas A&M University, College Station 77843, TX, USA
| | - Jamshaid Rashid
- Department of Environmental Science, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Saud Ahmed Khan
- Department of Econometrics, Pakistan Institute of Development Economics (PIDE), Quaid-i-Azam University Campus, P.O. Box. 1091, Islamabad 44000, Pakistan
| | - Muhammad Arif Ali
- Department of Soil Sciences, Faculty of Agriculture Sciences and Technology, Bahauddin Zakariya University Multan, Pakistan
| | - Muhammad Arshad
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Sector H-12, Islamabad 44000, Pakistan.
| |
Collapse
|
7
|
Ogonowski M, Motiei A, Ininbergs K, Hell E, Gerdes Z, Udekwu KI, Bacsik Z, Gorokhova E. Evidence for selective bacterial community structuring on microplastics. Environ Microbiol 2018; 20:2796-2808. [DOI: 10.1111/1462-2920.14120] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Martin Ogonowski
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
- Aquabiota Water Research AB; Stockholm SE-115 50 Sweden
| | - Asa Motiei
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
| | - Karolina Ininbergs
- Department of Molecular Biosciences; The Wenner-Gren Institute, Stockholm University; Stockholm SE-106 91 Sweden
| | - Eva Hell
- Department of Molecular Biosciences; The Wenner-Gren Institute, Stockholm University; Stockholm SE-106 91 Sweden
| | - Zandra Gerdes
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
| | - Klas I. Udekwu
- Department of Molecular Biosciences; The Wenner-Gren Institute, Stockholm University; Stockholm SE-106 91 Sweden
| | - Zoltan Bacsik
- Department of Materials and Environmental Chemistry; Stockholm University; Stockholm SE-106 91 Sweden
| | - Elena Gorokhova
- Department of Environmental Science & Analytical Chemistry (ACES); Stockholm University; Stockholm SE-106 91 Sweden
| |
Collapse
|
8
|
Izmalkova TY, Gafarov AB, Sazonova OI, Sokolov SL, Kosheleva IA, Boronin AM. Diversity of Oil-Degrading Microorganisms in the Gulf of Finland (Baltic Sea) in Spring and in Summer. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718020054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
9
|
Viggor S, Jõesaar M, Vedler E, Kiiker R, Pärnpuu L, Heinaru A. Occurrence of diverse alkane hydroxylase alkB genes in indigenous oil-degrading bacteria of Baltic Sea surface water. MARINE POLLUTION BULLETIN 2015; 101:507-516. [PMID: 26541986 DOI: 10.1016/j.marpolbul.2015.10.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/21/2015] [Accepted: 10/23/2015] [Indexed: 06/05/2023]
Abstract
Formation of specific oil degrading bacterial communities in diesel fuel, crude oil, heptane and hexadecane supplemented microcosms of the Baltic Sea surface water samples was revealed. The 475 sequences from constructed alkane hydroxylase alkB gene clone libraries were grouped into 30 OPFs. The two largest groups were most similar to Pedobacter sp. (245 from 475) and Limnobacter sp. (112 from 475) alkB gene sequences. From 56 alkane-degrading bacterial strains 41 belonged to the Pseudomonas spp. and 8 to the Rhodococcus spp. having redundant alkB genes. Together 68 alkB gene sequences were identified. These genes grouped into 20 OPFs, half of them being specific only to the isolated strains. Altogether 543 diverse alkB genes were characterized in the brackish Baltic Sea water; some of them representing novel lineages having very low sequence identities with corresponding genes of the reference strains.
Collapse
Affiliation(s)
- Signe Viggor
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia.
| | - Merike Jõesaar
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Eve Vedler
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Riinu Kiiker
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Liis Pärnpuu
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| | - Ain Heinaru
- Institute of Molecular and Cell Biology, Department of Genetics, University of Tartu, 23 Riia Street, Tartu 51010, Estonia
| |
Collapse
|
10
|
Lujanienė G, Mažeika J, Li HC, Petrošius R, Barisevičiūtė R, Jokšas K, Remeikaitė-Nikienė N, Malejevas V, Garnaga G, Stankevičius A, Povinec PP. Δ14C and δ 13C as tracers of organic carbon in Baltic Sea sediments collected in coastal waters off Lithuania and in the Gotland Deep. J Radioanal Nucl Chem 2015. [DOI: 10.1007/s10967-015-4547-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
11
|
Otto S, Streibel T, Erdmann S, Klingbeil S, Schulz-Bull D, Zimmermann R. Pyrolysis-gas chromatography-mass spectrometry with electron-ionization or resonance-enhanced-multi-photon-ionization for characterization of polycyclic aromatic hydrocarbons in the Baltic Sea. MARINE POLLUTION BULLETIN 2015; 99:35-42. [PMID: 26277803 DOI: 10.1016/j.marpolbul.2015.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 07/31/2015] [Accepted: 08/02/2015] [Indexed: 06/04/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAH), as a part of dissolved organic matter (DOM), are environmental pollutants of the marine compartment. This study investigates the origin of PAH, which is supposed to derive mainly from anthropogenic activities, and their alteration along the salinity gradient of the Baltic Sea. Pyrolysis in combination with gas chromatography and two mass selective detectors in one measurement cycle are utilized as a tool for an efficient trace analysis of such complex samples, by which it is possible to detect degradation products of high molecular structures. Along the north-south transect of the Baltic Sea a slightly rising trend for PAH is visible. Their concentration profiles correspond to the ship traffic as a known anthropogenic source, underlined by the value of special isomer ratios such as phenanthrene and anthracene (0.31-0.45) or pyrene and fluoranthene (0.44-0.53). The detection of naphthalene and the distribution of its alkylated representatives support this statement.
Collapse
Affiliation(s)
- Stefan Otto
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, Institute of Chemistry, University of Rostock, 18059 Rostock, Germany
| | - Thorsten Streibel
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, Institute of Chemistry, University of Rostock, 18059 Rostock, Germany; Joint Mass Spectrometry Centre, Cooperation Group Comprehensive Molecular Analytics, Institute of Ecological Chemistry, Helmholtz Zentrum München-German Research Center of Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
| | - Sabrina Erdmann
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, Institute of Chemistry, University of Rostock, 18059 Rostock, Germany
| | - Sophie Klingbeil
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, Institute of Chemistry, University of Rostock, 18059 Rostock, Germany
| | - Detlef Schulz-Bull
- Marine Chemistry, Leibniz Institute for Baltic Sea Research, Seestrasse 15, 18119 Warnemünde, Rostock, Germany
| | - Ralf Zimmermann
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, Institute of Chemistry, University of Rostock, 18059 Rostock, Germany; Joint Mass Spectrometry Centre, Cooperation Group Comprehensive Molecular Analytics, Institute of Ecological Chemistry, Helmholtz Zentrum München-German Research Center of Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| |
Collapse
|
12
|
Genomics and Ecophysiology of Heterotrophic Nitrogen-Fixing Bacteria Isolated from Estuarine Surface Water. mBio 2015; 6:e00929. [PMID: 26152586 PMCID: PMC4495170 DOI: 10.1128/mbio.00929-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ability to reduce atmospheric nitrogen (N2) to ammonia, known as N2 fixation, is a widely distributed trait among prokaryotes that accounts for an essential input of new N to a multitude of environments. Nitrogenase reductase gene (nifH) composition suggests that putative N2-fixing heterotrophic organisms are widespread in marine bacterioplankton, but their autecology and ecological significance are unknown. Here, we report genomic and ecophysiology data in relation to N2 fixation by three environmentally relevant heterotrophic bacteria isolated from Baltic Sea surface water: Pseudomonas stutzeri strain BAL361 and Raoultella ornithinolytica strain BAL286, which are gammaproteobacteria, and Rhodopseudomonas palustris strain BAL398, an alphaproteobacterium. Genome sequencing revealed that all were metabolically versatile and that the gene clusters encoding the N2 fixation complex varied in length and complexity between isolates. All three isolates could sustain growth by N2 fixation in the absence of reactive N, and this fixation was stimulated by low concentrations of oxygen in all three organisms (≈4 to 40 µmol O2 liter−1). P. stutzeri BAL361 did, however, fix N at up to 165 µmol O2 liter−1, presumably accommodated through aggregate formation. Glucose stimulated N2 fixation in general, and reactive N repressed N2 fixation, except that ammonium (NH4+) stimulated N2 fixation in R. palustris BAL398, indicating the use of nitrogenase as an electron sink. The lack of correlations between nitrogenase reductase gene expression and ethylene (C2H4) production indicated tight posttranscriptional-level control. The N2 fixation rates obtained suggested that, given the right conditions, these heterotrophic diazotrophs could contribute significantly to in situ rates. The biological process of importing atmospheric N2 is of paramount importance in terrestrial and aquatic ecosystems. In the oceans, a diverse array of prokaryotes seemingly carry the genetic capacity to perform this process, but lack of knowledge about their autecology and the factors that constrain their N2 fixation hamper an understanding of their ecological importance in marine waters. The present study documents a high variability of genomic and ecophysiological properties related to N2 fixation in three heterotrophic isolates obtained from estuarine surface waters and shows that these organisms fix N2 under a surprisingly broad range of conditions and at significant rates. The observed intricate regulation of N2 fixation for the isolates indicates that indigenous populations of heterotrophic diazotrophs have discrete strategies to cope with environmental controls of N2 fixation. Hence, community-level generalizations about the regulation of N2 fixation in marine heterotrophic bacterioplankton may be problematic.
Collapse
|