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Dong H, Wang Y, Zhi T, Guo H, Guo Y, Liu L, Yin Y, Shi J, He B, Hu L, Jiang G. Construction of protein-protein interaction network in sulfate-reducing bacteria: Unveiling of global response to Hg. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 351:124048. [PMID: 38714230 DOI: 10.1016/j.envpol.2024.124048] [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: 01/28/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024]
Abstract
Sulfate-reducing bacteria (SRB) play pivotal roles in the biotransformation of mercury (Hg). However, unrevealed global responses of SRB to Hg have restricted our understanding of details of Hg biotransformation processes. The absence of protein-protein interaction (PPI) network under Hg stimuli has been a bottleneck of proteomic analysis for molecular mechanisms of Hg transformation. This study constructed the first comprehensive PPI network of SRB in response to Hg, encompassing 67 connected nodes, 26 independent nodes, and 121 edges, covering 93% of differentially expressed proteins from both previous studies and this study. The network suggested that proteomic changes of SRB in response to Hg occurred globally, including microbial metabolism in diverse environments, carbon metabolism, nucleic acid metabolism and translation, nucleic acid repair, transport systems, nitrogen metabolism, and methyltransferase activity, partial of which could cover the known knowledge. Antibiotic resistance was the original response revealed by this network, providing insights into of Hg biotransformation mechanisms. This study firstly provided the foundational network for a comprehensive understanding of SRB's responses to Hg, convenient for exploration of potential targets for Hg biotransformation. Furthermore, the network indicated that Hg enhances the metabolic activities and modification pathways of SRB to maintain cellular activities, shedding light on the influences of Hg on the carbon, nitrogen, and sulfur cycles at the cellular level.
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Affiliation(s)
- Hongzhe Dong
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Danish Centre for Education and Research, Beijing, 100049, China
| | - Yuchuan Wang
- Hebei Key Laboratory for Chronic Diseases, School of Basic Medical Sciences, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Tingting Zhi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Hua Guo
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Yingying Guo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Lihong Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment and Health, Jianghan University, Wuhan, 430056, China
| | - Bin He
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Danish Centre for Education and Research, Beijing, 100049, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
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2
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Lawruk-Desjardins C, Storck V, Ponton DE, Amyot M, Walsh DA. A genome catalogue of mercury-methylating bacteria and archaea from sediments of a boreal river facing human disturbances. Environ Microbiol 2024; 26:e16669. [PMID: 38922750 DOI: 10.1111/1462-2920.16669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/23/2024] [Indexed: 06/28/2024]
Abstract
Methyl mercury, a toxic compound, is produced by anaerobic microbes and magnifies in aquatic food webs, affecting the health of animals and humans. The exploration of mercury methylators based on genomes is still limited, especially in the context of river ecosystems. To address this knowledge gap, we developed a genome catalogue of potential mercury-methylating microorganisms. This was based on the presence of hgcAB from the sediments of a river affected by two run-of-river hydroelectric dams, logging activities and a wildfire. Through the use of genome-resolved metagenomics, we discovered a unique and diverse group of mercury methylators. These were dominated by members of the metabolically versatile Bacteroidota and were particularly rich in microbes that ferment butyrate. By comparing the diversity and abundance of mercury methylators between sites subjected to different disturbances, we found that ongoing disturbances, such as the input of organic matter related to logging activities, were particularly conducive to the establishment of a mercury-methylating niche. Finally, to gain a deeper understanding of the environmental factors that shape the diversity of mercury methylators, we compared the mercury-methylating genome catalogue with the broader microbial community. The results suggest that mercury methylators respond to environmental conditions in a manner similar to the overall microbial community. Therefore, it is crucial to interpret the diversity and abundance of mercury methylators within their specific ecological context.
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Affiliation(s)
| | - Veronika Storck
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Dominic E Ponton
- Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - Marc Amyot
- Département de sciences biologiques, Université de Montréal, Montreal, Quebec, Canada
| | - David A Walsh
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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3
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Pereira-Garcia C, Sanz-Sáez I, Sánchez P, Coutinho FH, Bravo AG, Sánchez O, Acinas SG. Genomic and transcriptomic characterization of methylmercury detoxification in a deep ocean Alteromonas mediterranea ISS312. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123725. [PMID: 38467369 DOI: 10.1016/j.envpol.2024.123725] [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: 10/03/2023] [Revised: 01/12/2024] [Accepted: 03/04/2024] [Indexed: 03/13/2024]
Abstract
Methylmercury (MeHg) is one of the most worrisome pollutants in marine systems. MeHg detoxification is mediated by merB and merA genes, responsible for the demethylation of MeHg and the reduction of inorganic mercury, respectively. Little is known about the biological capacity to detoxify this compound in marine environments, and even less the bacterial transcriptional changes during MeHg detoxification. This study provides the genomic and transcriptomic characterization of the deep ocean bacteria Alteromonas mediterranea ISS312 with capacity for MeHg degradation. Its genome sequence revealed four mer operons containing three merA gene and two merB gene copies, that could be horizontally transferred among distant related genomes by mobile genetic elements. The transcriptomic profiling in the presence of 5 μM MeHg showed that merA and merB genes are within the most expressed genes, although not all mer genes were equally transcribed. Besides, we aimed to identify functional orthologous genes that displayed expression profiles highly similar or identical to those genes within the mer operons, which could indicate they are under the same regulatory controls. We found contrasting expression profiles for each mer operon that were positively correlated with a wide array of functions mostly related to amino acid metabolism, but also to flagellar assembly or two component systems. Also, this study highlights that all merAB genes of the four operons were globally distributed across oceans layers with higher transcriptional activity in the mesopelagic deeper waters. Our study provides new insights about the transcriptional patterns related to the capacity of marine bacteria to detoxify MeHg, with important implications for the understanding of this process in marine ecosystems.
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Affiliation(s)
- Carla Pereira-Garcia
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Catalunya, Spain.
| | - Isabel Sanz-Sáez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain; Department of Environmental Chemistry, IDAEA-CSIC, Barcelona, Catalunya, Spain
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Felipe H Coutinho
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Andrea G Bravo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
| | - Olga Sánchez
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Catalunya, Spain
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain.
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4
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Rincón-Tomás B, Lanzén A, Sánchez P, Estupiñán M, Sanz-Sáez I, Bilbao ME, Rojo D, Mendibil I, Pérez-Cruz C, Ferri M, Capo E, Abad-Recio IL, Amouroux D, Bertilsson S, Sánchez O, Acinas SG, Alonso-Sáez L. Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133120. [PMID: 38101011 DOI: 10.1016/j.jhazmat.2023.133120] [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: 08/31/2023] [Revised: 10/10/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.
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Affiliation(s)
- Blanca Rincón-Tomás
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain; Grupo Inv. Geología Aplicada a Recursos Marinos y Ambientes Extremos, Instituto Geológico y Minero de España (IGME-CSIC), 28003 Madrid, Spain.
| | - Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Pablo Sánchez
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Mónica Estupiñán
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Isabel Sanz-Sáez
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - M Elisabete Bilbao
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Diana Rojo
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Carla Pérez-Cruz
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - Marta Ferri
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Eric Capo
- Dep. Ecology and Environmental Science, Umeå University, 907 36 Umeå, Sweden
| | - Ion L Abad-Recio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain
| | - David Amouroux
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les matériaux (IPREM), Pau, France
| | - Stefan Bertilsson
- Dep. Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Olga Sánchez
- Dep. Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona (UAB), 08192 Bellaterra, Spain
| | - Silvia G Acinas
- Dep. Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM-CSIC), 08003 Barcelona, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, 48395 Sukarrieta, Spain.
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5
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Vigneron A, Guyoneaud R, Goñi-Urriza M. Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:1551-1562. [PMID: 38197744 DOI: 10.1021/acs.est.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.
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Affiliation(s)
- Adrien Vigneron
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
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6
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Liu S, Hu R, Peng N, Zhou Z, Chen R, He Z, Wang C. Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments. THE ISME JOURNAL 2023; 17:2313-2325. [PMID: 37880540 PMCID: PMC10689504 DOI: 10.1038/s41396-023-01544-4] [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: 04/24/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023]
Abstract
Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.
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Affiliation(s)
- Songfeng Liu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruiwen Hu
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Nenglong Peng
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhengyuan Zhou
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Ruihan Chen
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhili He
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China
| | - Cheng Wang
- Environmental Microbiomics Research Center, School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, 510006, China.
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7
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Cabrol L, Capo E, van Vliet DM, von Meijenfeldt FAB, Bertilsson S, Villanueva L, Sánchez-Andrea I, Björn E, G. Bravo A, Heimburger Boavida LE. Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea. mSystems 2023; 8:e0053723. [PMID: 37578240 PMCID: PMC10469668 DOI: 10.1128/msystems.00537-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/16/2023] [Indexed: 08/15/2023] Open
Abstract
In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc+) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc+ microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc+ microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc+) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc+ microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.
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Affiliation(s)
- Léa Cabrol
- Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
- Institute of Ecology and Biodiversity (IEB), University of Chile, Santiago, Chile
| | - Eric Capo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
- Wageningen Food and Biobased Research, Wageningen, the Netherlands
| | - F. A. Bastiaan von Meijenfeldt
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, Utrecht, the Netherlands
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Erik Björn
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Andrea G. Bravo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, Spain
| | - Lars-Eric Heimburger Boavida
- Aix Marseille University, Univ. Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
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8
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Hillyer KE, Raes E, Bissett A, Beale DJ. Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 318:120857. [PMID: 36513173 DOI: 10.1016/j.envpol.2022.120857] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO2 fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.
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Affiliation(s)
- Katie E Hillyer
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia
| | - Eric Raes
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia; Flourishing Oceans, Minderoo Foundation, Broadway, Nedlands, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, CSIRO, Battery Point, Hobart, TAS, Australia
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Ecosciences Precinct, Dutton Park, QLD, Australia.
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Vigneron A, Cruaud P, Guyoneaud R, Goñi-Urriza M. Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations. Front Microbiol 2023; 13:1073483. [PMID: 36699594 PMCID: PMC9868632 DOI: 10.3389/fmicb.2022.1073483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023] Open
Abstract
Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.
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Affiliation(s)
- Adrien Vigneron
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Rémy Guyoneaud
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
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10
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Frey B, Rast BM, Qi W, Stierli B, Brunner I. Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance. Front Microbiol 2022; 13:1034138. [PMID: 36274742 PMCID: PMC9581213 DOI: 10.3389/fmicb.2022.1034138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg–1 dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg–1 dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg–1 dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.
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Affiliation(s)
- Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
- *Correspondence: Beat Frey,
| | - Basil M. Rast
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Weihong Qi
- FGCZ Functional Genomics Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
- SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Beat Stierli
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
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11
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Capo E, Feng C, Bravo AG, Bertilsson S, Soerensen AL, Pinhassi J, Buck M, Karlsson C, Hawkes J, Björn E. Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13119-13130. [PMID: 36069707 PMCID: PMC9494745 DOI: 10.1021/acs.est.2c03784] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved HgII-sulfide species were strong predictors of both the HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc+ microorganisms by reconstructing their genomes from metagenomes (i.e., hgc+ MAGs), which highlighted the versatility of putative HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.
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Affiliation(s)
- Eric Capo
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
- Department
of Aquatic Sciences and Assessment, Swedish
University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Caiyan Feng
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | - Andrea G. Bravo
- Department
of Marine Biology and Oceanography, Institute of Marine Sciences, Spanish National Research Council (CSIC), Barcelona 08003, Spain
| | - Stefan Bertilsson
- Department
of Aquatic Sciences and Assessment, Swedish
University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Anne L. Soerensen
- Department
of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm 104 05, Sweden
| | - Jarone Pinhassi
- Centre
for Ecology and Evolution in Microbial Model Systems—EEMiS, Linnaeus University, Kalmar 391 82, Sweden
| | - Moritz Buck
- Department
of Aquatic Sciences and Assessment, Swedish
University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Camilla Karlsson
- Centre
for Ecology and Evolution in Microbial Model Systems—EEMiS, Linnaeus University, Kalmar 391 82, Sweden
| | - Jeffrey Hawkes
- Department
of Chemistry, Uppsala University, Uppsala 751 23, Sweden
| | - Erik Björn
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
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12
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Gao Z, Zheng W, Li Y, Liu Y, Wu M, Li S, Li P, Liu G, Fu X, Wang S, Wang F, Cai Y, Feng X, Gu B, Zhong H, Yin Y. Mercury transformation processes in nature: Critical knowledge gaps and perspectives for moving forward. J Environ Sci (China) 2022; 119:152-165. [PMID: 35934460 DOI: 10.1016/j.jes.2022.07.013] [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: 06/25/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The transformation of mercury (Hg) in the environment plays a vital role in the cycling of Hg and its risk to the ecosystem and human health. Of particular importance are Hg oxidation/reduction and methylation/demethylation processes driven or mediated by the dynamics of light, microorganisms, and organic carbon, among others. Advances in understanding those Hg transformation processes determine our capacity of projecting and mitigating Hg risk. Here, we provide a critical analysis of major knowledge gaps in our understanding of Hg transformation in nature, with perspectives on approaches moving forward. Our analysis focuses on Hg transformation processes in the environment, as well as emerging methodology in exploring these processes. Future avenues for improving the understanding of Hg transformation processes to protect ecosystem and human health are also explored.
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Affiliation(s)
- Zhiyuan Gao
- Centre for Earth Observation Science, and Department of Environment and Geography, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Wang Zheng
- Institute of Surface-Earth System Science, Tianjin University, Tianjin 300192, China
| | - Yanbin Li
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Yurong Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengjie Wu
- School of the Environment, Nanjing University, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing 210023, China
| | - Shouying Li
- School of the Environment, Nanjing University, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing 210023, China
| | - Ping Li
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Guangliang Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Xuewu Fu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Shuxiao Wang
- School of Environment and State Key Joint Laboratory of Environment Simulation and Pollution Control, Tsinghua University, Beijing 100084, China
| | - Feiyue Wang
- Centre for Earth Observation Science, and Department of Environment and Geography, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Yong Cai
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Xinbin Feng
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Huan Zhong
- School of the Environment, Nanjing University, State Key Laboratory of Pollution Control and Resource Reuse, Nanjing 210023, China; Environmental and Life Sciences Program (EnLS), Trent University, Peterborough, Ontario K9L 0G2, Canada.
| | - Yongguang Yin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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