1
|
Espenberg M, Pille K, Yang B, Maddison M, Abdalla M, Smith P, Li X, Chan PL, Mander Ü. Towards an integrated view on microbial CH 4, N 2O and N 2 cycles in brackish coastal marsh soils: A comparative analysis of two sites. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170641. [PMID: 38325442 PMCID: PMC10884468 DOI: 10.1016/j.scitotenv.2024.170641] [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: 09/17/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Coastal ecosystems, facing threats from global change and human activities like excessive nutrients, undergo alterations impacting their function and appearance. This study explores the intertwined microbial cycles of carbon (C) and nitrogen (N), encompassing methane (CH4), nitrous oxide (N2O), and nitrogen gas (N2) fluxes, to determine nutrient transformation processes between the soil-plant-atmosphere continuum in the coastal ecosystems with brackish water. Water salinity negatively impacted denitrification, bacterial nitrification, N fixation, and n-DAMO processes, but did not significantly affect archaeal nitrification, COMAMMOX, DNRA, and ANAMMOX processes in the N cycle. Plant species age and biomass influenced CH4 and N2O emissions. The highest CH4 emissions were from old Spartina and mixed Spartina and Scirpus sites, while Phragmites sites emitted the most N2O. Nitrification and incomplete denitrification mainly governed N2O emissions depending on the environmental conditions and plants. The higher genetic potential of ANAMMOX reduced excessive N by converting it to N2 in the sites with higher average temperatures. The presence of plants led to a decrease in the N fixers' abundance. Plant biomass negatively affected methanogenetic mcrA genes. Microbes involved in n-DAMO processes helped mitigate CH4 emissions. Over 93 % of the total climate forcing came from CH4 emissions, except for the Chinese bare site where the climate forcing was negative, and for Phragmites sites, where almost 60 % of the climate forcing came from N2O emissions. Our findings indicate that nutrient cycles, CH4, and N2O fluxes in soils are context-dependent and influenced by environmental factors and vegetation. This underscores the need for empirical analysis of both C and N cycles at various levels (soil-plant-atmosphere) to understand how habitats or plants affect nutrient cycles and greenhouse gas emissions.
Collapse
Affiliation(s)
- Mikk Espenberg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia; Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
| | - Kristin Pille
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Bin Yang
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Martin Maddison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mohamed Abdalla
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Xiuzhen Li
- State Key Laboratory of Estuarine and Coastal Research, Institute of Eco-Chongming, East China Normal University, Shanghai, China
| | - Ping-Lung Chan
- School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, China
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| |
Collapse
|
2
|
Liu Q, He W, Zhang W, Wang L, Tang J. Metagenomic analysis reveals the microbial response to petroleum contamination in oilfield soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168972. [PMID: 38043822 DOI: 10.1016/j.scitotenv.2023.168972] [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: 09/21/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
The response of the microbes to total petroleum hydrocarbons (TPHs) in three types of oilfield soils was researched using metagenomic analysis. The ranges of TPH concentrations in the grassland, abandoned well, working well soils were 1.16 × 102-3.50 × 102 mg/kg, 1.14 × 103-1.62 × 104 mg/kg, and 5.57 × 103-3.33 × 104 mg/kg, respectively. The highest concentration of n-alkanes and 16 PAHs were found in the working well soil of Shengli (SL) oilfield compared with those in Nanyang (NY) and Yanchang (YC) oilfields. The abandoned well soils showed a greater extent of petroleum biodegradation than the grassland and working well soils. Α-diversity indexes based on metagenomic taxonomy showed higher microbial diversity in grassland soils, whereas petroleum-degrading microbes Actinobacteria and Proteobacteria were more abundant in working and abandoned well soils. RDA demonstrated that low moisture content (MOI) in YC oilfield inhibited the accumulation of the petroleum-degrading microbes. Synergistic networks of functional genes and Spearman's correlation analysis showed that heavy petroleum contamination (over 2.10 × 104 mg/kg) negatively correlated with the abundance of the nitrogen fixation genes nifHK, however, in grassland soils, low petroleum content facilitated the accumulation of nitrogen fixation genes. A positive correlation was observed between the abundance of petroleum-degrading genes and denitrification genes (bphAa vs. nirD, todC vs. nirS, and nahB vs. nosZ), whereas a negative correlation was observed between alkB (alkane- degrading genes) and amo (ammonia oxidation), hao (nitrification). The ecotoxicity of petroleum contamination, coupled with petroleum hydrocarbons (PH) degradation competing with nitrifiers for ammonia inhibited ammonia oxidation and nitrification, whereas PH metabolism promoted the denitrification process. Moreover, positive correlations were observed between the abundance of amo gene and MOI, as well as between the abundance of the dissimilatory nitrate reduction gene nirA and clay content. Thus, improving the soil physicochemical properties is a promising approach for decreasing nitrogen loss and alleviating petroleum contamination in oilfield soils.
Collapse
Affiliation(s)
- Qinglong Liu
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Wenxiang He
- College of Natural Resources and Environment, Northwest A&F University, Key Laboratory of Plant Nutrition and Agro-environment in Northwest China, Ministry of Agriculture, Shaanxi, Yangling 712100, China
| | - Wenzhu Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Lan Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China
| | - Jingchun Tang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria/Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, China.
| |
Collapse
|
3
|
Galván V, Pascutti F, Sandoval NE, Lanfranconi MP, Lozada M, Arabolaza AL, Mac Cormack WP, Alvarez HM, Gramajo HC, Dionisi HM. High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments. PLoS One 2023; 18:e0288509. [PMID: 37459319 PMCID: PMC10351704 DOI: 10.1371/journal.pone.0288509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/28/2023] [Indexed: 07/20/2023] Open
Abstract
The wax ester (WE) and triacylglycerol (TAG) biosynthetic potential of marine microorganisms is poorly understood at the microbial community level. The goal of this work was to uncover the prevalence and diversity of bacteria with the potential to synthesize these neutral lipids in coastal sediments of two high latitude environments, and to characterize the gene clusters related to this process. Homolog sequences of the key enzyme, the wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) were retrieved from 13 metagenomes, including subtidal and intertidal sediments of a Subantarctic environment (Ushuaia Bay, Argentina), and subtidal sediments of an Antarctic environment (Potter Cove, Antarctica). The abundance of WS/DGAT homolog sequences in the sediment metagenomes was 1.23 ± 0.42 times the abundance of 12 single-copy genes encoding ribosomal proteins, higher than in seawater (0.13 ± 0.31 times in 338 metagenomes). Homolog sequences were highly diverse, and were assigned to the Pseudomonadota, Actinomycetota, Bacteroidota and Acidobacteriota phyla. The genomic context of WS/DGAT homologs included sequences related to WE and TAG biosynthesis pathways, as well as to other related pathways such as fatty-acid metabolism, suggesting carbon recycling might drive the flux to neutral lipid synthesis. These results indicate the presence of abundant and taxonomically diverse bacterial populations with the potential to synthesize lipid storage compounds in marine sediments, relating this metabolic process to bacterial survival.
Collapse
Affiliation(s)
- Virginia Galván
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Federico Pascutti
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Natalia E. Sandoval
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana P. Lanfranconi
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Mariana Lozada
- Instituto de Biología de Organismos Marinos (IBIOMAR-CONICET), Puerto Madryn, Chubut, Argentina
| | - Ana L. Arabolaza
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Walter P. Mac Cormack
- Instituto de Nanobiotecnología (NANOBIOTEC-UBA-CONICET), San Martín, Ciudad Autónoma de Buenos Aires, Argentina
- Instituto Antártico Argentino (IAA), San Martín, Buenos Aires, Argentina
| | - Héctor M. Alvarez
- Instituto de Biociencias de la Patagonia (INBIOP-UNPSJB-CONICET), Comodoro Rivadavia, Chubut, Argentina
| | - Hugo C. Gramajo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET, FBIOyF–UNR), Rosario, Santa Fe, Argentina
| | - Hebe M. Dionisi
- Centro para el Estudio de Sistemas Marinos (CESIMAR-CONICET), Puerto Madryn, Chubut, Argentina
| |
Collapse
|
4
|
Dionisi HM, Lozada M, Campos E. Diversity of GH51 α-L-arabinofuranosidase homolog sequences from subantarctic intertidal sediments. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
|
5
|
Silva JB, Centurion VB, Duarte AWF, Galazzi RM, Arruda MAZ, Sartoratto A, Rosa LH, Oliveira VM. Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands. FEMS Microbiol Ecol 2022; 99:6847214. [PMID: 36427064 DOI: 10.1093/femsec/fiac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/08/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.
Collapse
Affiliation(s)
- Jéssica B Silva
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil.,Institute of Biology, UNICAMP, Zip code 13083-862, Campinas, São Paulo, Brazil
| | - Victor B Centurion
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil.,Institute of Biology, UNICAMP, Zip code 13083-862, Campinas, São Paulo, Brazil
| | - Alysson W F Duarte
- Federal University of Alagoas, Campus Arapiraca (UFAL), Zip code 57309-005, Araparica, Alagoas, Brazil
| | - Rodrigo M Galazzi
- Spectrometry, Sample Preparation and Mechanization Group (GEPAM), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas São Paulo, Brazil.,National Institute of Science and Technology for Bioanalytics (INCTBio), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas, São Paulo, Brazil
| | - Marco A Z Arruda
- Spectrometry, Sample Preparation and Mechanization Group (GEPAM), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas São Paulo, Brazil.,National Institute of Science and Technology for Bioanalytics (INCTBio), Institute of Chemistry (UNICAMP), Zip code 13083-970, Campinas, São Paulo, Brazil
| | - Adilson Sartoratto
- Organic Chemistry and Pharmaceutical Division, Pluridisciplinary Research Center for Chemistry, Biology, and Agriculture (CPQBA), UNICAMP, Zip code 13081-970, Paulínia, São Paulo, Brazil
| | - Luiz H Rosa
- Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Zip code 31270-901, Belo Horizonte, Minas Gerais, Brazil
| | - Valéria M Oliveira
- Research Center for Chemistry, Biology and Agriculture (CPQBA), UNICAMP, Division of Microbial Resources, Zip code 13148-218, Paulínia, São Paulo, Brazil
| |
Collapse
|
6
|
Lyu L, Li J, Chen Y, Mai Z, Wang L, Li Q, Zhang S. Degradation potential of alkanes by diverse oil-degrading bacteria from deep-sea sediments of Haima cold seep areas, South China Sea. Front Microbiol 2022; 13:920067. [PMID: 36338091 PMCID: PMC9626528 DOI: 10.3389/fmicb.2022.920067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/28/2022] [Indexed: 11/17/2022] Open
Abstract
Marine oil spills are a significant concern worldwide, destroying the ecological environment and threatening the survival of marine life. Various oil-degrading bacteria have been widely reported in marine environments in response to marine oil pollution. However, little information is known about culturable oil-degrading bacteria in cold seep of the deep-sea environments, which are rich in hydrocarbons. This study enriched five oil-degrading consortia from sediments collected from the Haima cold seep areas of the South China Sea. Parvibaculum, Erythrobacter, Acinetobacter, Alcanivorax, Pseudomonas, Marinobacter, Halomonas, and Idiomarina were the dominant genera. Further results of bacterial growth and degradation ability tests indicated seven efficient alkane-degrading bacteria belonging to Acinetobacter, Alcanivorax, Kangiella, Limimaricola, Marinobacter, Flavobacterium, and Paracoccus, whose degradation rates were higher in crude oil (70.3–78.0%) than that in diesel oil (62.7–66.3%). From the view of carbon chain length, alkane degradation rates were medium chains > long chains > short chains. In addition, Kangiella aquimarina F7, Acinetobacter venetianus F1, Limimaricola variabilis F8, Marinobacter nauticus J5, Flavobacterium sediminis N3, and Paracoccus sediminilitoris N6 were first identified as oil-degrading bacteria from deep-sea environments. This study will provide insight into the bacterial community structures and oil-degrading bacterial diversity in the Haima cold seep areas, South China Sea, and offer bacterial resources to oil bioremediation applications.
Collapse
Affiliation(s)
- Lina Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Lina Lyu,
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yu Chen
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Zhimao Mai
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lin Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- *Correspondence: Si Zhang,
| |
Collapse
|
7
|
Bacterial diversity and competitors for degradation of hazardous oil refining waste under selective pressures of temperature and oxygen. JOURNAL OF HAZARDOUS MATERIALS 2022; 427:128201. [PMID: 34999399 DOI: 10.1016/j.jhazmat.2021.128201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 02/08/2023]
Abstract
Oil refining waste (ORW) contains complex, hazardous, and refractory components, causing more severe long-term environmental pollution than petroleum. Here, ORW was used to simulate the accelerated domestication of bacteria from oily sludges and polymer-flooding wastewater, and the effects of key factors, oxygen and temperature, on the ORW degradation were evaluated. Bacterial communities acclimated respectively in 30/60 °C, aerobic/anaerobic conditions showed differentiated degradation rates of ORW, ranging from 5% to 34%. High-throughput amplicon sequencing and ORW component analysis revealed significant correlation between bacterial diversity/biomass and degradation efficiency/substrate preference. Under mesophilic and oxygen-rich condition, the high biomass and abundant biodiversity with diverse genes and pathways for petroleum hydrocarbons degradation, effectively promoted the rapid and multi-component degradation of ORW. While under harsh conditions, a few dominant genera still contributed to ORW degradation, although the biodiversity was severely restricted. The typical dominant facultative anaerobes Bacillus (up to 99.8% abundance anaerobically) and Geobacillus (up to 99.9% abundance aerobically and anaerobically) showed oxygen-independent sustainable degradation ability and broad-spectrum of temperature adaptability, making them promising and competitive bioremediation candidates for future application. Our findings provide important strategies for practical bioremediation of varied environments polluted by hazardous ORW.
Collapse
|
8
|
Microbial Consortiums of Putative Degraders of Low-Density Polyethylene-Associated Compounds in the Ocean. mSystems 2022; 7:e0141521. [PMID: 35229650 PMCID: PMC8941889 DOI: 10.1128/msystems.01415-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polyethylene (PE) is one of the most abundant plastics in the ocean. The development of a biofilm on PE in the ocean has been reported, yet whether some of the biofilm-forming organisms can biodegrade this plastic in the environment remains unknown. Via metagenomics analysis, we taxonomically and functionally analyzed three biofilm communities using low-density polyethylene (LDPE) as their sole carbon source for 2 years. Several of the taxa that increased in relative abundance over time were closely related to known degraders of alkane and other hydrocarbons. Alkane degradation has been proposed to be involved in PE degradation, and most of the organisms increasing in relative abundance over time harbored genes encoding proteins essential in alkane degradation, such as the genes alkB and CYP153, encoding an alkane monooxygenase and a cytochrome P450 alkane hydroxylase, respectively. Weight loss of PE sheets when incubated with these communities and chemical and electron microscopic analyses provided evidence for alteration of the PE surface over time. Taken together, these results provide evidence for the utilization of LDPE-associated compounds by the prokaryotic communities. This report identifies a group of genes potentially involved in the degradation of the LDPE polymeric structure and/or associated plastic additives in the ocean and describes a phylogenetically diverse community of plastic biofilm-dwelling microbes with the potential for utilizing LDPE-associated compounds as carbon and energy source. IMPORTANCE Low-density polyethylene (LDPE) is one of the most used plastics worldwide, and a large portion of it ends up in the ocean. Very little is known about its fate in the ocean and whether it can be biodegraded by microorganisms. By combining 2-year incubations with metagenomics, respiration measurements, and LDPE surface analysis, we identified bacteria and associated genes and metabolic pathways potentially involved in LDPE biodegradation. After 2 years of incubation, two of the microbial communities exhibited very similar taxonomic compositions mediating changes to the LDPE pieces they were incubated with. We provide evidence that there are plastic-biofilm dwelling bacteria in the ocean that might have the potential to degrade LDPE-associated compounds and that alkane degradation pathways might be involved.
Collapse
|
9
|
Jurelevicius D, Pereira RDS, da Mota FF, Cury JC, de Oliveira IC, Rosado AS, Mason OU, Jansson JK, Seldin L. Metagenomic analysis of microbial communities across a transect from low to highly hydrocarbon-contaminated soils in King George Island, Maritime Antarctica. GEOBIOLOGY 2022; 20:98-111. [PMID: 34545693 DOI: 10.1111/gbi.12472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/28/2021] [Accepted: 08/27/2021] [Indexed: 06/13/2023]
Abstract
Soil samples from a transect from low to highly hydrocarbon-contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p-value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative-PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon-contaminated soils in polar environments.
Collapse
Affiliation(s)
- Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raphael da Silva Pereira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Juliano C Cury
- Universidade Federal de São João del-Rei, São João del-Rei, Brazil
| | - Ivan Cardoso de Oliveira
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre S Rosado
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Olivia U Mason
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lucy Seldin
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
10
|
Dinter T, Geihser S, Gube M, Daniel R, Kuzyakov Y. Impact of sea level change on coastal soil organic matter, priming effects and prokaryotic community assembly. FEMS Microbiol Ecol 2020; 95:5551479. [PMID: 31425573 DOI: 10.1093/femsec/fiz129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/18/2019] [Indexed: 01/09/2023] Open
Abstract
Salt marshes are coastal areas storing high amounts of soil organic matter (SOM) while simultaneously being prone to tidal changes. Here, SOM-decomposition and accompanied priming effects (PE), which describe interactions between labile and old SOM, were studied under controlled flooding conditions. Soil samples from two Wadden Sea salt marsh zones, pioneer (Pio), flooded two times/day, and lower salt marsh (Low), flooded ∼eight times/month, were measured for 56 days concerning CO2-efflux and prokaryotic community shifts during three different inundation-treatments: total-drained (Drained), all-time-flooded (Waterlogged) or temporal-flooding (Tidal). Priming was induced by 14C-glucose addition. CO2-efflux from soil followed Low>Pio and Tidal>Drained>Waterlogged, likely due to O2-depletion and moisture maintenance, two key factors governed by tidal inundation with regard to SOM mineralisation. PEs in both zones were positive (Drained) or absent (Waterlogged, Tidal), presumably as a result of prokaryotes switching from production of extracellular enzymes to direct incorporation of labile C. A doubled amount of prokaryotic biomass in Low compared to Pio probably induced higher chances of cometabolic effects and higher PE. 16S-rRNA-gene-amplicon-based analysis revealed differences in bacterial and archaeal community composition between both zones, revealing temporal niche adaptation with flooding treatment. Strongest alterations were found in Drained, likely due to inundation-mediated changes in C-binding capacities.
Collapse
Affiliation(s)
- Thomas Dinter
- Soil Science of Temperate Ecosystems, Büsgenweg 2, 37077 Göttingen, University of Göttingen, Germany
| | - Simone Geihser
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Grisebachstraße 8, 37077 Göttingen, University of Göttingen, Germany
| | - Matthias Gube
- Soil Science of Temperate Ecosystems, Büsgenweg 2, 37077 Göttingen, University of Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Grisebachstraße 8, 37077 Göttingen, University of Göttingen, Germany
| | - Yakov Kuzyakov
- Soil Science of Temperate Ecosystems, Büsgenweg 2, 37077 Göttingen, University of Göttingen, Germany
| |
Collapse
|
11
|
Delegan Y, Sargsyan A, Hovhannisyan N, Babayan B, Petrikov K, Vainstein M. Analysis of genome sequence and trehalose lipid production peculiarities of the thermotolerant Gordonia
strain. J Basic Microbiol 2019; 60:14-21. [DOI: 10.1002/jobm.201900439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Yanina Delegan
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”; Pushchino Russian Federation
- G K Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS; Pushchino Russian Federation
| | - Armen Sargsyan
- Armbiotechnology Scientific and Production Center; Yerevan Armenia
| | - Nelli Hovhannisyan
- Armbiotechnology Scientific and Production Center; Yerevan Armenia
- Institute of Pharmacy; Yerevan State University; Yerevan Armenia
| | - Bella Babayan
- Armbiotechnology Scientific and Production Center; Yerevan Armenia
| | - Kirill Petrikov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”; Pushchino Russian Federation
- G K Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS; Pushchino Russian Federation
| | - Mikhail Vainstein
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”; Pushchino Russian Federation
- G K Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS; Pushchino Russian Federation
| |
Collapse
|
12
|
Valencia-Agami SS, Cerqueda-García D, Putzeys S, Uribe-Flores MM, García-Cruz NU, Pech D, Herrera-Silveira J, Aguirre-Macedo ML, García-Maldonado JQ. Changes in the Bacterioplankton Community Structure from Southern Gulf of Mexico During a Simulated Crude Oil Spill at Mesocosm Scale. Microorganisms 2019; 7:microorganisms7100441. [PMID: 31614583 PMCID: PMC6843455 DOI: 10.3390/microorganisms7100441] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/28/2019] [Accepted: 10/10/2019] [Indexed: 12/24/2022] Open
Abstract
The southern Gulf of Mexico (sGoM) is highly susceptible to receiving environmental impacts due to the recent increase in oil-related activities. In this study, we assessed the changes in the bacterioplankton community structure caused by a simulated oil spill at mesocosms scale. The 16S rRNA gene sequencing analysis indicated that the initial bacterial community was mainly represented by Gamma-proteobacteria, Alpha-proteobacteria, Flavobacteriia, and Cyanobacteria. The hydrocarbon degradation activity, measured as the number of culturable hydrocarbonoclastic bacteria (CHB) and by the copy number of the alkB gene, was relatively low at the beginning of the experiment. However, after four days, the hydrocarbonoclastic activity reached its maximum values and was accompanied by increases in the relative abundance of the well-known hydrocarbonoclastic Alteromonas. At the end of the experiment, the diversity was restored to similar values as those observed in the initial time, although the community structure and composition were clearly different, where Marivita, Pseudohongiella, and Oleibacter were detected to have differential abundances on days eight–14. These changes were related with total nitrogen (p value = 0.030 and r2 = 0.22) and polycyclic aromatic hydrocarbons (p value = 0.048 and r2 = 0.25), according to PERMANOVA. The results of this study contribute to the understanding of the potential response of the bacterioplankton from sGoM to crude oil spills.
Collapse
Affiliation(s)
- Sonia S Valencia-Agami
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Sébastien Putzeys
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - María Magdalena Uribe-Flores
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Norberto Ulises García-Cruz
- Consorcio de Investigación del Golfo de México (CIGoM)-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Lerma Campeche, Campeche 24500, Mexico.
| | - Jorge Herrera-Silveira
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - M Leopoldina Aguirre-Macedo
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| | - José Q García-Maldonado
- CONACYT - Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán 97310, Mexico.
| |
Collapse
|
13
|
Bulseco AN, Giblin AE, Tucker J, Murphy AE, Sanderman J, Hiller-Bittrolff K, Bowen JL. Nitrate addition stimulates microbial decomposition of organic matter in salt marsh sediments. GLOBAL CHANGE BIOLOGY 2019; 25:3224-3241. [PMID: 31317634 DOI: 10.1111/gcb.14726] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 02/21/2019] [Accepted: 04/16/2019] [Indexed: 06/10/2023]
Abstract
Salt marshes sequester carbon at rates more than an order of magnitude greater than their terrestrial counterparts, helping to mitigate climate change. As nitrogen loading to coastal waters continues, primarily in the form of nitrate, it is unclear what effect it will have on carbon storage capacity of these highly productive systems. This uncertainty is largely driven by the dual role nitrate can play in biological processes, where it can serve as a nutrient-stimulating primary production or a thermodynamically favorable electron acceptor fueling heterotrophic metabolism. Here, we used a controlled flow-through reactor experiment to test the role of nitrate as an electron acceptor, and its effect on organic matter decomposition and the associated microbial community in salt marsh sediments. Organic matter decomposition significantly increased in response to nitrate, even at sediment depths typically considered resistant to decomposition. The use of isotope tracers suggests that this pattern was largely driven by stimulated denitrification. Nitrate addition also significantly altered the microbial community and decreased alpha diversity, selecting for taxa belonging to groups known to reduce nitrate and oxidize more complex forms of organic matter. Fourier Transform-Infrared Spectroscopy further supported these results, suggesting that nitrate facilitated decomposition of complex organic matter compounds into more bioavailable forms. Taken together, these results suggest the existence of organic matter pools that only become accessible with nitrate and would otherwise remain stabilized in the sediment. The existence of such pools could have important implications for carbon storage, since greater decomposition rates as N loading increases may result in less overall burial of organic-rich sediment. Given the extent of nitrogen loading along our coastlines, it is imperative that we better understand the resilience of salt marsh systems to nutrient enrichment, especially if we hope to rely on salt marshes, and other blue carbon systems, for long-term carbon storage.
Collapse
Affiliation(s)
- Ashley N Bulseco
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Anne E Giblin
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Jane Tucker
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts
| | - Anna E Murphy
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
| | | | | | - Jennifer L Bowen
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, Massachusetts
| |
Collapse
|
14
|
Khudur LS, Shahsavari E, Webster GT, Nugegoda D, Ball AS. The impact of lead co-contamination on ecotoxicity and the bacterial community during the bioremediation of total petroleum hydrocarbon-contaminated soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 253:939-948. [PMID: 31351302 DOI: 10.1016/j.envpol.2019.07.107] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/19/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
The continued increase in the global demand for oil, which reached 4,488 Mtoe in 2018, leads to large quantities of petroleum products entering the environment posing serious risks to natural ecosystems if left untreated. In this study, we evaluated the impact of co-contamination with lead on the efficacy of two bioremediation processes, natural attenuation and biostimulation of Total Petroleum Hydrocarbons (TPH) as well as the associated toxicity and the changes in the microbial community in contaminated soils. The biostimulated treatment resulted in 96% and 84% reduction in TPH concentration in a single and a co-contamination scenario, respectively, over 28 weeks of a mesocosm study. This reduction was significantly more in comparison to natural attenuation in a single and a co-contamination scenario, which was 56% and 59% respectively. In contrast, a significantly greater reduction in the associated toxicity of in soils undergoing natural attenuation was evident compared with soils undergoing biostimulation despite the lower TPH degradation when bioassays were applied. The earthworm toxicity test showed a decrease of 72% in the naturally attenuated toxicity versus only 62% in the biostimulated treatment of a single contamination scenario. In a co-contamination scenario, toxicity decreased only 30% and 8% after natural attenuation and biostimulation treatments, respectively. 16s rDNA sequence analysis was used to assess the impact of both the co-contamination and the bioremediation treatment. NGS data revealed major bacterial domination by Nocardioides spp., which reached 40% in week 20 of the natural attenuation treatment. In the biostimulated soil samples, more than 50% of the bacterial community was dominated by Alcanivorax spp. in week 12. The presence of Pb in the natural attenuation treatment resulted in an increased abundance of a few Pb-resistant genera such as Sphingopyxis spp. and Thermomonas spp in addition to Nocardioides spp. In contrast, Pb co-contamination completely shifted the bacterial pattern in the stimulated treatment with Pseudomonas spp. comprising approximately 45% of the bacterial profile in week 12. This study confirms the effectiveness of biostimulation over natural attenuation in remediating TPH and TPH-Pb contaminated soils. In addition, the presence of co-contaminants (e.g. Pb) results in serious impacts on the efficacy of bioremediation of TPH in contaminated soils, which must be considered prior to designing any bioremediation strategy.
Collapse
Affiliation(s)
- Leadin S Khudur
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia.
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Grant T Webster
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Dayanthi Nugegoda
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| |
Collapse
|
15
|
Khudur LS, Gleeson DB, Ryan MH, Shahsavari E, Haleyur N, Nugegoda D, Ball AS. Implications of co-contamination with aged heavy metals and total petroleum hydrocarbons on natural attenuation and ecotoxicity in Australian soils. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 243:94-102. [PMID: 30172128 DOI: 10.1016/j.envpol.2018.08.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/27/2018] [Accepted: 08/13/2018] [Indexed: 06/08/2023]
Abstract
The bioremediation of historic industrial contaminated sites is a complex process. Co-contamination, often with lead which was commonly added to gasoline until 16 years ago is one of the biggest challenges affecting the clean-up of these sites. In this study, the effect of heavy metals, as co-contaminant, together with total petroleum hydrocarbons (TPH) is reported, in terms of remaining soil toxicity and the structure of the microbial communities. Contaminated soil samples from a relatively hot and dry climate in Western Australia were collected (n = 27). Analysis of soils showed the presence of both contaminants, TPHs and heavy metals. The Microtox test confirmed that their co-presence elevated the remaining ecotoxicity. Toxicity was correlated with the presence of lead, zinc and TPH (0.893, 0.599 and 0.488), respectively, assessed using Pearson Correlation coefficient factor. Next Generation Sequencing of soil bacterial 16S rRNA, revealed a lack of dominate genera; however, despite the variation in soil type, a few genera including Azospirillum spp. and Conexibacter were present in most soil samples (85% and 82% of all soils, respectively). Likewise, many genera of hydrocarbon-degrading bacteria were identified in all soil samples. Streptomyces spp. was presented in 93% of the samples with abundance between 7% and 40%. In contrast, Acinetobacter spp. was found in only one sample but was a dominant member of (45%) of the microbial community. In addition, some bacterial genera were correlated to the presence of the heavy metals, such as Geodermatophilus spp., Rhodovibrio spp. and Rubrobacter spp. which were correlated with copper, lead and zinc, respectively. This study concludes that TPH and heavy metal co-contamination significantly elevated the associated toxicity. This is an important consideration when carrying out risk assessment associated with natural attenuation. This study also improves knowledge about the dynamics of microbial communities in mixed contamination scenarios.
Collapse
Affiliation(s)
- Leadin S Khudur
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia.
| | - Deirdre B Gleeson
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Megan H Ryan
- School of Agriculture and Environment, The University of Western Australia, Crawley, WA, 6009, Australia
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Nagalakshmi Haleyur
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Dayanthi Nugegoda
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Science, RMIT University, Bundoora, VIC, 3083, Australia
| |
Collapse
|
16
|
Calderoli PA, Espínola FJ, Dionisi HM, Gil MN, Jansson JK, Lozada M. Predominance and high diversity of genes associated to denitrification in metagenomes of subantarctic coastal sediments exposed to urban pollution. PLoS One 2018; 13:e0207606. [PMID: 30496195 PMCID: PMC6264515 DOI: 10.1371/journal.pone.0207606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/02/2018] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to characterize the microbial nitrogen cycling potential in sediments from Ushuaia Bay, a subantarctic environment that has suffered a recent explosive demographic growth. Subtidal sediment samples were retrieved in triplicate from two urban points in the Bay, and analyzed through metagenomic shotgun sequencing. Sequences assigned to genes related to nitrification, nitrate reduction and denitrification were predominant in this environment with respect to metagenomes from other environments, including other marine sediments. The nosZ gene, responsible for nitrous oxide transformation into di-nitrogen, presented a high diversity. The majority of NosZ sequences were classified as Clade II (atypical) variants affiliated to different bacterial lineages such as Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, Verrucomicrobia, as well as to Archaea. The analysis of a fosmid metagenomic library from the same site showed that the genomic context of atypical variants was variable, and was accompanied by distinct regulatory elements, suggesting the evolution of differential ecophysiological roles. This work increases our understanding of the microbial ecology of nitrogen transformations in cold coastal environments and provides evidence of an enhanced denitrification potential in impacted sediment microbial communities. In addition, it highlights the role of yet overlooked populations in the mitigation of environmentally harmful forms of nitrogen.
Collapse
Affiliation(s)
- Priscila A Calderoli
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Fernando J Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| | - Mónica N Gil
- Laboratorio de Oceanografía Química y Contaminación de Aguas, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina.,Laboratorio de Química General y Análisis de Elementos, CCT CONICET CENPAT, Puerto Madryn, Chubut Province, Argentina
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut Province, Argentina
| |
Collapse
|
17
|
Roy A, Sar P, Sarkar J, Dutta A, Sarkar P, Gupta A, Mohapatra B, Pal S, Kazy SK. Petroleum hydrocarbon rich oil refinery sludge of North-East India harbours anaerobic, fermentative, sulfate-reducing, syntrophic and methanogenic microbial populations. BMC Microbiol 2018; 18:151. [PMID: 30348104 PMCID: PMC6198496 DOI: 10.1186/s12866-018-1275-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/28/2018] [Indexed: 11/29/2022] Open
Abstract
Background Sustainable management of voluminous and hazardous oily sludge produced by petroleum refineries remains a challenging problem worldwide. Characterization of microbial communities of petroleum contaminated sites has been considered as the essential prerequisite for implementation of suitable bioremediation strategies. Three petroleum refinery sludge samples from North Eastern India were analyzed using next-generation sequencing technology to explore the diversity and functional potential of inhabitant microorganisms and scope for their on-site bioremediation. Results All sludge samples were hydrocarbon rich, anaerobic and reduced with sulfate as major anion and several heavy metals. High throughput sequencing of V3-16S rRNA genes from sludge metagenomes revealed dominance of strictly anaerobic, fermentative, thermophilic, sulfate-reducing bacteria affiliated to Coprothermobacter, Fervidobacterium, Treponema, Syntrophus, Thermodesulfovibrio, Anaerolinea, Syntrophobacter, Anaerostipes, Anaerobaculum, etc., which have been well known for hydrocarbon degradation. Relatively higher proportions of archaea were detected by qPCR. Archaeal 16S rRNA gene sequences showed presence of methanogenic Methanobacterium, Methanosaeta, Thermoplasmatales, etc. Detection of known hydrocarbon utilizing aerobic/facultative anaerobic (Mycobacterium, Pseudomonas, Longilinea, Geobacter, etc.), nitrate reducing (Gordonia, Novosphigobium, etc.) and nitrogen fixing (Azovibrio, Rhodobacter, etc.) bacteria suggested niche specific guilds with aerobic, facultative anaerobic and strict anaerobic populations. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) predicted putative genetic repertoire of sludge microbiomes and their potential for hydrocarbon degradation; lipid-, nitrogen-, sulfur- and methane- metabolism. Methyl coenzyme M reductase A (mcrA) and dissimilatory sulfite reductase beta-subunit (dsrB) genes phylogeny confirmed methanogenic and sulfate-reducing activities within sludge environment endowed by hydrogenotrophic methanogens and sulfate-reducing Deltaproteobacteria and Firmicutes members. Conclusion Refinery sludge microbiomes were comprised of hydrocarbon degrading, fermentative, sulfate-reducing, syntrophic, nitrogen fixing and methanogenic microorganisms, which were in accordance with the prevailing physicochemical nature of the samples. Analysis of functional biomarker genes ascertained the activities of methanogenic and sulfate-reducing organisms within sludge environment. Overall data provided better insights on microbial diversity and activity in oil contaminated environment, which could be exploited suitably for in situ bioremediation of refinery sludge. Electronic supplementary material The online version of this article (10.1186/s12866-018-1275-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ajoy Roy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713 209, India
| | - Pinaki Sar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721 302, India
| | - Jayeeta Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721 302, India
| | - Avishek Dutta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721 302, India.,School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721 302, India
| | - Poulomi Sarkar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721 302, India
| | - Abhishek Gupta
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721 302, India
| | - Balaram Mohapatra
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, WB, 721 302, India
| | - Siddhartha Pal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713 209, India
| | - Sufia K Kazy
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, WB, 713 209, India.
| |
Collapse
|
18
|
Ribicic D, Netzer R, Winkler A, Brakstad OG. Microbial communities in seawater from an Arctic and a temperate Norwegian fjord and their potentials for biodegradation of chemically dispersed oil at low seawater temperatures. MARINE POLLUTION BULLETIN 2018; 129:308-317. [PMID: 29680553 DOI: 10.1016/j.marpolbul.2018.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/09/2018] [Accepted: 02/12/2018] [Indexed: 05/20/2023]
Abstract
Biodegradation of chemically dispersed oil at low temperature (0-2 °C) was compared in natural seawater from Arctic (Svalbard) and a temperate (Norway) fjords. The oil was premixed with a dispersant (Corexit 9500) and small-droplet oil dispersions prepared. Faster biotransformation of n-alkanes in the Arctic than in the temperate seawater were associated with the initially higher abundance of the alkane-degrading genus Oleispira in the Arctic than the temperate seawater. Comparable transformation of aromatic hydrocarbons was further associated with the late emergences Cycloclasticus in both seawater sources. The results showed that chemically dispersed oil may be rapidly biodegraded by microbial communities in Arctic seawater. Compared to oil biodegradation studies at higher seawater temperatures, longer lag-periods were experienced here, and may be attributed to both microbial and oil properties at these low seawater temperatures.
Collapse
Affiliation(s)
- Deni Ribicic
- The Norwegian University of Science and Technology, Dept. Cancer Research and Molecular Medicine, 7491 Trondheim, Norway
| | - Roman Netzer
- SINTEF Ocean, Dept. Environmental Technology, Brattørkaia 17C, 7010 Trondheim, Norway
| | - Anika Winkler
- Bielefeld University, Centre for Biotechnology (CeBiTec), 33501 Bielefeld, Germany
| | - Odd Gunnar Brakstad
- SINTEF Ocean, Dept. Environmental Technology, Brattørkaia 17C, 7010 Trondheim, Norway.
| |
Collapse
|
19
|
Brakstad OG, Ribicic D, Winkler A, Netzer R. Biodegradation of dispersed oil in seawater is not inhibited by a commercial oil spill dispersant. MARINE POLLUTION BULLETIN 2018; 129:555-561. [PMID: 29079303 DOI: 10.1016/j.marpolbul.2017.10.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 05/20/2023]
Abstract
Chemical dispersants are well-established as oil spill response tools. Several studies have emphasized their positive effects on oil biodegradation, but recent studies have claimed that dispersants may actually inhibit the oil biodegradation process. In this study, biodegradation of oil dispersions in natural seawater at low temperature (5°C) was compared, using oil without dispersant, and oil premixed with different concentrations of Slickgone NS, a widely used oil spill dispersant in Europe. Saturates (nC10-nC36 alkanes), naphthalenes and 2- to 5-ring polycyclic aromatic hydrocarbons (PAH) were biotransformed at comparable rates in all dispersions, both with and without dispersant. Microbial communities differed primarily between samples with or without oil, and they were not significantly affected by increasing dispersant concentrations. Our data therefore showed that a common oil spill dispersant did not inhibit biodegradation of oil at dispersant concentrations relevant for response operations.
Collapse
Affiliation(s)
- Odd G Brakstad
- SINTEF Ocean, Dept. Environmental Technology, Brattørkaia 17C, 7010 Trondheim, Norway.
| | - Deni Ribicic
- The Norwegian University of Science and Technology, Dept. Cancer Research and Molecular Medicine, 7491 Trondheim, Norway
| | - Anika Winkler
- Bielefeld University, Centre for Biotechnology (CeBiTec), 33501 Bielefeld, Germany
| | - Roman Netzer
- SINTEF Ocean, Dept. Environmental Technology, Brattørkaia 17C, 7010 Trondheim, Norway
| |
Collapse
|
20
|
Omrani R, Spini G, Puglisi E, Saidane D. Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation. Biodegradation 2018; 29:187-209. [DOI: 10.1007/s10532-018-9823-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/23/2018] [Indexed: 02/06/2023]
|
21
|
Espínola F, Dionisi HM, Borglin S, Brislawn CJ, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lozada M. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. MICROBIAL ECOLOGY 2018; 75:123-139. [PMID: 28702706 DOI: 10.1007/s00248-017-1028-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023]
Abstract
In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.
Collapse
Affiliation(s)
- Fernando Espínola
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina
| | - Sharon Borglin
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colin J Brislawn
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Walter P Mac Cormack
- Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina
- Instituto Antártico Argentino, Buenos Aires, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
| |
Collapse
|
22
|
Sampaio DS, Almeida JRB, de Jesus HE, Rosado AS, Seldin L, Jurelevicius D. Distribution of Anaerobic Hydrocarbon-Degrading Bacteria in Soils from King George Island, Maritime Antarctica. MICROBIAL ECOLOGY 2017; 74:810-820. [PMID: 28484799 DOI: 10.1007/s00248-017-0973-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
Anaerobic diesel fuel Arctic (DFA) degradation has already been demonstrated in Antarctic soils. However, studies comparing the distribution of anaerobic bacterial groups and of anaerobic hydrocarbon-degrading bacteria in Antarctic soils containing different concentrations of DFA are scarce. In this study, functional genes were used to study the diversity and distribution of anaerobic hydrocarbon-degrading bacteria (bamA, assA, and bssA) and of sulfate-reducing bacteria (SRB-apsR) in highly, intermediate, and non-DFA-contaminated soils collected during the summers of 2009, 2010, and 2011 from King George Island, Antarctica. Signatures of bamA genes were detected in all soils analyzed, whereas bssA and assA were found in only 4 of 10 soils. The concentration of DFA was the main factor influencing the distribution of bamA-containing bacteria and of SRB in the analyzed soils, as shown by PCR-DGGE results. bamA sequences related to genes previously described in Desulfuromonas, Lautropia, Magnetospirillum, Sulfuritalea, Rhodovolum, Rhodomicrobium, Azoarcus, Geobacter, Ramlibacter, and Gemmatimonas genera were dominant in King George Island soils. Although DFA modulated the distribution of bamA-hosting bacteria, DFA concentration was not related to bamA abundance in the soils studied here. This result suggests that King George Island soils show functional redundancy for aromatic hydrocarbon degradation. The results obtained in this study support the hypothesis that specialized anaerobic hydrocarbon-degrading bacteria have been selected by hydrocarbon concentrations present in King George Island soils.
Collapse
Affiliation(s)
- Dayanna Souza Sampaio
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Hugo E de Jesus
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Alexandre S Rosado
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucy Seldin
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Diogo Jurelevicius
- Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
- Laboratório de Genética Microbiana, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes (IMPPG), Universidade Federal do Rio de Janeiro, Centro de Ciências da Saúde, Bloco I, Ilha do Fundão, Rio de Janeiro, 21941-590, Brazil.
| |
Collapse
|
23
|
Meng L, Liu H, Bao M, Sun P. Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters. MARINE POLLUTION BULLETIN 2016; 111:203-212. [PMID: 27485782 DOI: 10.1016/j.marpolbul.2016.07.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/04/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
This study tracked structure shifts of bacterial compositions before, during and after invading by crude oil to determine the microbial response and explore how temperature, dispersants and nutrients affect the composition of microbial communities or their activities of biodegradation in artificial marine environment. During petroleum hydrocarbons exposed, the composition and functional dynamics of marine microbial communities were altered, favoring bacteria that could utilize this rich carbon source such as the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes phyla. Low temperature as a dominant factor decreased bacterial richness and catabolic diversity due to abated enzymes activities in correlation with the process of biodegradation. Dispersants exerted no negative consequences on microbial composition, however, bacterial composition by the Chloroflexi, TM6, OP8, Cyanobacteria and Gemmatimonadetes phyla increased. It seemed that more frequent fertilizer application could be equally safe to bacteria and increased significantly the abundance of bacterial strains but Actinobacteria phyla decreased.
Collapse
Affiliation(s)
- Long Meng
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Han Liu
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Mutai Bao
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao 266100, China; College of Chemistry & Chemical Engineering, Ocean University of China, Qingdao 266100, China.
| | - Peiyan Sun
- Key Laboratory of Marine Spill Oil Identification and Damage Assessment Technology, North China Sea Environmental Monitoring Center, State Oceanic Administration, Qingdao 266033, China
| |
Collapse
|
24
|
Matos MN, Lozada M, Anselmino LE, Musumeci MA, Henrissat B, Jansson JK, Mac Cormack WP, Carroll J, Sjöling S, Lundgren L, Dionisi HM. Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments. Environ Microbiol 2016; 18:4471-4484. [PMID: 27348213 DOI: 10.1111/1462-2920.13433] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/23/2016] [Indexed: 12/20/2022]
Abstract
Alginates are abundant polysaccharides in brown algae that constitute an important energy source for marine heterotrophic bacteria. Despite the key role of alginate degradation processes in the marine carbon cycle, little information is available on the bacterial populations involved in these processes. The aim of this work was to gain a better understanding of alginate utilization capabilities in cold coastal environments. Sediment metagenomes from four high-latitude regions of both Hemispheres were interrogated for alginate lyase gene homologue sequences and their genomic context. Sediments contained highly abundant and diverse bacterial assemblages with alginolytic potential, including members of Bacteroidetes and Proteobacteria, as well as several poorly characterized taxa. The microbial communities in Arctic and Antarctic sediments exhibited the most similar alginolytic profiles, whereas brackish sediments showed distinct structures with a higher proportion of novel genes. Examination of the gene neighbourhood of the alginate lyase homologues revealed distinct patterns depending on the potential lineage of the scaffolds, with evidence of evolutionary relationships among alginolytic gene clusters from Bacteroidetes and Proteobacteria. This information is relevant for understanding carbon fluxes in cold coastal environments and provides valuable information for the development of biotechnological applications from brown algae biomass.
Collapse
Affiliation(s)
- Marina N Matos
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Mariana Lozada
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Luciano E Anselmino
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Matías A Musumeci
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France.,INRA, USC 1408 AFMB, Marseille, F-13288, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Janet K Jansson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Walter P Mac Cormack
- Instituto Antártico Argentino, Ciudad Autónoma de Buenos Aires, C1064ABR, Argentina.,Instituto Nanobiotec, CONICET - Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, C1113AAC, Argentina
| | - JoLynn Carroll
- Akvaplan-niva, Fram - High North Research Centre for Climate and the Environment, Tromsø, NO-9296, Norway.,CAGE - Centre for Arctic Gas Hydrate, Environment and Climate, UiT The Arctic University of Norway, Tromsø, N-9037, Norway
| | - Sara Sjöling
- School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, 141 89, Sweden
| | | | - Hebe M Dionisi
- Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Puerto Madryn, U9120ACD, Argentina
| |
Collapse
|