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Yadav S, Koenen M, Bale NJ, Reitsma W, Engelmann JC, Stefanova K, Damsté JSS, Villanueva L. Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria. MICROBIOME 2024; 12:98. [PMID: 38797849 PMCID: PMC11129491 DOI: 10.1186/s40168-024-01816-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/15/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea. RESULTS We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea. CONCLUSIONS This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.
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Affiliation(s)
- Subhash Yadav
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Wietse Reitsma
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Julia C Engelmann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
| | - Kremena Stefanova
- Institute of Oceanology "Fridtjof Nansen", Bulgarian Academy of Sciences, Varna, Bulgaria
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797AB Den Burg, P.O. Box 59, Texel, The Netherlands.
- Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.021, 3508 TA, Utrecht, The Netherlands.
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Medina-Ruiz A, Jiménez-Millán J, Abad I, Gálvez A, Grande MJ, Jiménez-Espinosa R. Aragonite crystallization in a sulfate-rich hypersaline wetland under dry Mediterranean climate (Laguna Honda, eastern Guadalquivir basin, S Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171362. [PMID: 38428615 DOI: 10.1016/j.scitotenv.2024.171362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
This research investigates the influence of water composition, the presence of seasonal algal mats, detrital inputs and the activity of microorganisms on the crystallization of aragonite in the sediments deposited in the hypersaline Laguna Honda wetland (S of Spain). The high alkaline and hypersaline waters (pH > 9.2 and C.E. > 70 mS/cm) of the wetland lake are rich in SO42- (>24,000 mg/l), Cl- (>21,000 mg/l), Na+ (>11,000 mg/l) Mg2+ (>8400 mg/l) and Ca2+ (>1000 mg/l), and are supersaturated for dolomite, calcite and aragonite. Sediments have lower pH values than column waters, oscillating from 8.54 in the low Eh (up to -80.9 mV) central deep sediments and 6.33 in the shallower higher Eh (around -13.6 mV) shore sediments. Erosion of the surrounding olive groves soils produced detrital silicates rich sediments with concretions of carbonate or sulfate. Aragonite (up to 19 %) and pyrite (up to 13 %) are mainly concentrated in the organic matter rich samples from the upper part of the sediment cores, whereas gypsum is preferably concentrated in low organic matter content samples. Mineral crusts containing a MgAl silicate phase, epsomite, halite and gypsum are precipitated on the floating algal mats covering the wetland waters. Floating algal mats deposit increased the organic matter content of the upper sediments which promoted the presence of fermentative microorganisms, sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) communities and variations of Eh that influence the authigenesis of carbonate and S-bearing minerals. Replacement of poorly crystalline MgSi phases infilling algal cells by aragonite was favored in the organic matter rich sediments with low Eh values and important SRB communities that promoted sulfate bioreduction processes to form pyrite. Aragonite precipitation was favored by the increase of carbonate and bicarbonate concentration produced by the SRB oxidation of organic matter, the CO2 degassing by high summer temperatures and the CO2 uptake by photosynthesis of the algal mats.
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Affiliation(s)
- Antonio Medina-Ruiz
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Juan Jiménez-Millán
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain.
| | - Isabel Abad
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Antonio Gálvez
- Microbiology Division, Department of Health Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - María José Grande
- Microbiology Division, Department of Health Sciences, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Rosario Jiménez-Espinosa
- Department of Geology and CEACTEMA, University of Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
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Demin KA, Prazdnova EV, Minkina TM, Gorovtsov AV. Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments. Appl Environ Microbiol 2024; 90:e0139023. [PMID: 38551370 PMCID: PMC11022543 DOI: 10.1128/aem.01390-23] [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] [Indexed: 04/18/2024] Open
Abstract
Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.
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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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Yin X, Zhou G, Wang H, Han D, Maeke M, Richter-Heitmann T, Wunder LC, Aromokeye DA, Zhu QZ, Nimzyk R, Elvert M, Friedrich MW. Unexpected carbon utilization activity of sulfate-reducing microorganisms in temperate and permanently cold marine sediments. THE ISME JOURNAL 2024; 18:wrad014. [PMID: 38365251 PMCID: PMC10811731 DOI: 10.1093/ismejo/wrad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 02/18/2024]
Abstract
Significant amounts of organic carbon in marine sediments are degraded, coupled with sulfate reduction. However, the actual carbon and energy sources used in situ have not been assigned to each group of diverse sulfate-reducing microorganisms (SRM) owing to the microbial and environmental complexity in sediments. Here, we probed microbial activity in temperate and permanently cold marine sediments by using potential SRM substrates, organic fermentation products at very low concentrations (15-30 μM), with RNA-based stable isotope probing. Unexpectedly, SRM were involved only to a minor degree in organic fermentation product mineralization, whereas metal-reducing microbes were dominant. Contrastingly, distinct SRM strongly assimilated 13C-DIC (dissolved inorganic carbon) with H2 as the electron donor. Our study suggests that canonical SRM prefer autotrophic lifestyle, with hydrogen as the electron donor, while metal-reducing microorganisms are involved in heterotrophic organic matter turnover, and thus regulate carbon fluxes in an unexpected way in marine sediments.
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Affiliation(s)
- Xiuran Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Guowei Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- School of Resources and Environmental Engineering, Anhui University, 111 Jiulong Road, Hefei, Anhui 230601, China
| | - Haihua Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, 58 Renmin Avenue, Haikou 570228, China
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- College of Urban and Environmental Sciences, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Dukki Han
- Department of Marine Bioscience, Gangneung-Wonju National University, 7 Jukheon-gil, Gangneung-si 25457, Republic of Korea
| | - Mara Maeke
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - Tim Richter-Heitmann
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Lea C Wunder
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen D-28359, Germany
| | - David A Aromokeye
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Qing-Zeng Zhu
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
| | - Rolf Nimzyk
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Strasse 2-4, Bremen D-28359, Germany
| | - Michael W Friedrich
- Faculty of Biology/Chemistry, University of Bremen, Leobener Strasse 3, Bremen D-28359, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, Bremen D-28359, Germany
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Shakeri Yekta S, Svensson BH, Skyllberg U, Schnürer A. Sulfide in engineered methanogenic systems - Friend or foe? Biotechnol Adv 2023; 69:108249. [PMID: 37666371 DOI: 10.1016/j.biotechadv.2023.108249] [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: 05/02/2023] [Revised: 07/27/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Sulfide ions are regarded to be toxic to microorganisms in engineered methanogenic systems (EMS), where organic substances are anaerobically converted to products such as methane, hydrogen, alcohols, and carboxylic acids. A vast body of research has addressed solutions to mitigate process disturbances associated with high sulfide levels, yet the established paradigm has drawn the attention away from the multifaceted sulfide interactions with minerals, organics, microbial interfaces and their implications for performance of EMS. This brief review brings forward sulfide-derived pathways other than toxicity and with potential significance for anaerobic organic matter degradation. Available evidence on sulfide reactions with organic matter, interventions with key microbial metabolisms, and interspecies electron transfer are critically synthesized as a guidance for comprehending the sulfide effects on EMS apart from the microbial toxicity. The outcomes identify existing knowledge gaps and specify future research needs as a step forward towards realizing the potential of sulfide-derived mechanisms in diversifying and optimizing EMS applications.
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Affiliation(s)
- Sepehr Shakeri Yekta
- Department of Thematic Studies - Environmental Change, Linköping University, 58183 Linköping, Sweden; Biogas Solutions Research Center, Linköping University, 58183 Linköping, Sweden.
| | - Bo H Svensson
- Department of Thematic Studies - Environmental Change, Linköping University, 58183 Linköping, Sweden; Biogas Solutions Research Center, Linköping University, 58183 Linköping, Sweden
| | - Ulf Skyllberg
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Anna Schnürer
- Biogas Solutions Research Center, Linköping University, 58183 Linköping, Sweden; Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala BioCenter, 75007 Uppsala, Sweden
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Adam-Beyer N, Laufer-Meiser K, Fuchs S, Schippers A, Indenbirken D, Garbe-Schönberg D, Petersen S, Perner M. Microbial ecosystem assessment and hydrogen oxidation potential of newly discovered vent systems from the Central and South-East Indian Ridge. Front Microbiol 2023; 14:1173613. [PMID: 37886064 PMCID: PMC10598711 DOI: 10.3389/fmicb.2023.1173613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
In order to expand the knowledge of microbial ecosystems from deep-sea hydrothermal vent systems located on the Central and South-East Indian Ridge, we sampled hydrothermal fluids, massive sulfides, ambient water and sediments of six distinct vent fields. Most of these vent sites were only recently discovered in the course of the German exploration program for massive sulfide deposits and no previous studies of the respective microbial communities exist. Apart from typically vent-associated chemosynthetic members of the orders Campylobacterales, Mariprofundales, and Thiomicrospirales, high numbers of uncultured and unspecified Bacteria were identified via 16S rRNA gene analyses in hydrothermal fluid and massive sulfide samples. The sampled sediments however, were characterized by an overall lack of chemosynthetic Bacteria and the presence of high proportions of low abundant bacterial groups. The archaeal communities were generally less diverse and mostly dominated by members of Nitrosopumilales and Woesearchaeales, partly exhibiting high proportions of unassigned Archaea. Correlations with environmental parameters were primarily observed for sediment communities and for microbial species (associated with the nitrogen cycle) in samples from a recently identified vent field, which was geochemically distinct from all other sampled sites. Enrichment cultures of diffuse fluids demonstrated a great potential for hydrogen oxidation coupled to the reduction of various electron-acceptors with high abundances of Hydrogenovibrio and Sulfurimonas species. Overall, given the large number of currently uncultured and unspecified microorganisms identified in the vent communities, their respective metabolic traits, ecosystem functions and mediated biogeochemical processes have still to be resolved for estimating consequences of potential environmental disturbances by future mining activities.
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Affiliation(s)
- Nicole Adam-Beyer
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Katja Laufer-Meiser
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sebastian Fuchs
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Axel Schippers
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | | | | | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Mirjam Perner
- Marine Geosystems, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
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Polymenakou PN, Nomikou P, Hannington M, Petersen S, Kilias SP, Anastasiou TI, Papadimitriou V, Zaka E, Kristoffersen JB, Lampridou D, Wind S, Heinath V, Lange S, Magoulas A. Taxonomic diversity of microbial communities in sub-seafloor hydrothermal sediments of the active Santorini-Kolumbo volcanic field. Front Microbiol 2023; 14:1188544. [PMID: 37455712 PMCID: PMC10345502 DOI: 10.3389/fmicb.2023.1188544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Active hydrothermal vents of volcanic origin provide a remarkable manifestation of life on Earth under extreme conditions, which may have consequences for our understanding of habitability on other terrestrial bodies as well. Methods Here, we performed for the first time Illumina sequencing of bacterial and archaeal communities on sub-seafloor samples collected from the Santorini-Kolumbo volcanic field. A total of 19 (3-m long) gravity corers were collected and processed for microbial community analysis. Results From a total of 6,46,671 produced V4 sequences for all samples, a total of 10,496 different Operational Taxonomic Units (OTUs) were identified that were assigned to 40 bacterial and 9 archaeal phyla and 14 candidate divisions. On average, the most abundant phyla in all samples were Chloroflexi (Chloroflexota) (24.62%), followed by Proteobacteria (Pseudomonadota) (11.29%), Firmicutes (Bacillota) (10.73%), Crenarchaeota (Thermoproteota) (8.55%), and Acidobacteria (Acidobacteriota) (8.07%). At the genus level, a total of 286 known genera and candidate genera were mostly dominated by members of Bacillus, Thermoflexus, Desulfatiglans, Pseudoalteromonas, and Pseudomonas. Discussion In most of the stations, the Chao1 values at the deeper layers were comparable to the surface sediment samples denoting the high diversity in the subsurface of these ecosystems. Heatmap analysis based on the 100 most abundant OTUs, grouped the sampling stations according to their geographical location, placing together the two hottest stations (up to 99°C). This result indicates that this specific area within the active Kolumbo crater create a distinct niche, where microorganisms with adaptation strategies to withstand heat stresses can thrive, such as the endospore-forming Firmicutes.
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Affiliation(s)
- Paraskevi N. Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Paraskevi Nomikou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Mark Hannington
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Stephanos P. Kilias
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Thekla I. Anastasiou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Vasiliki Papadimitriou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Eleutheria Zaka
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Jon Bent Kristoffersen
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
| | - Danai Lampridou
- Faculty of Geology and Geoenvironment, National and Kapodistrian University of Athens, Athens, Greece
| | - Sandra Wind
- Department of Earth and Environmental Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Verena Heinath
- Institute of Geosciences, University of Kiel (CAU), Kiel, Germany
| | - Sabine Lange
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Antonios Magoulas
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology, and Aquaculture, Heraklion, Greece
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Nagar S, Bharti M, Negi RK. Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring. Appl Microbiol Biotechnol 2023; 107:3273-3289. [PMID: 37052633 DOI: 10.1007/s00253-023-12503-6] [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: 10/28/2022] [Revised: 03/18/2023] [Accepted: 03/25/2023] [Indexed: 04/14/2023]
Abstract
The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.
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Affiliation(s)
- Shekhar Nagar
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
- Department of Zoology, Deshbandhu College, Kalkaji, New Delhi, India
| | - Meghali Bharti
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007, India.
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Gómez-Acata ES, Teutli C, Falcón LI, García-Maldonado JQ, Prieto-Davó A, Yanez-Montalvo A, Cadena S, Chiappa-Carrara X, Herrera-Silveira JA. Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico. PeerJ 2023; 11:e14587. [PMID: 36785710 PMCID: PMC9921989 DOI: 10.7717/peerj.14587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/28/2022] [Indexed: 02/11/2023] Open
Abstract
Mangroves are unique coastal ecosystems, which have many important ecological functions, as they are a reservoir of many marine species well adapted to saline conditions and are fundamental as sites of carbon storage. Although the microbial contribution to nutrient cycling in these ecosystems has been well recognized, there is a lack of information regarding the microbial composition and structure of different ecological types of mangrove forests. In this study, we characterized the microbial community (Bacteria and Archaea) in sediments associated with five ecological types of mangrove forests in a coastal lagoon dominated by Avicennia germinans and Rhizophora mangle, through 16S rRNA-V4 gene sequencing. Overall, Proteobacteria (51%), Chloroflexi (12%), Gemmatimonadetes (5%) and Planctomycetes (6%) were the most abundant bacterial phyla, while Thaumarchaeota (30%), Bathyarchaeota (21%) and Nanoarchaeaeota (18%) were the dominant archaeal phyla. The microbial composition associated with basin mangroves dominated by Avicennia germinans was significantly different from the other ecological types, which becomes relevant for restoration strategies.
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Affiliation(s)
| | - Claudia Teutli
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México
| | | | - José Q. García-Maldonado
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | | | | | - Santiago Cadena
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
| | - Xavier Chiappa-Carrara
- Escuela Nacional de Estudios Superiores, Mérida, Yucatán, México,Unidad Multidisciplinaria de Docencia e Investigación, Unidad Sisal, Universidad Nacional Autónoma de México, Sisal, Yucatán, México
| | - Jorge A. Herrera-Silveira
- Laboratorio Nacional de Resiliencia Costera (LANRESC), Sisal, Yucatán, México,Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México
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11
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Calvo-Martin E, Teira E, Álvarez-Salgado XA, Rocha C, Jiang S, Justel-Díez M, Ibánhez JSP. On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries. Environ Microbiol 2022; 24:5859-5881. [PMID: 36054689 PMCID: PMC10087554 DOI: 10.1111/1462-2920.16160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/02/2022] [Indexed: 01/12/2023]
Abstract
Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.
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Affiliation(s)
- Elisa Calvo-Martin
- Organic Geochemistry Lab, Department of Oceanography, Instituto de Investigacións Mariñas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain.,PhD Program in Marine Science, Technology and Management, Universidade de Vigo, Vigo, Spain
| | - Eva Teira
- Departamento de Ecología y Biología Animal, Universidade de Vigo, Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Vigo, Spain
| | - Xosé Antón Álvarez-Salgado
- Organic Geochemistry Lab, Department of Oceanography, Instituto de Investigacións Mariñas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Carlos Rocha
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
| | - Shan Jiang
- School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland.,State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Maider Justel-Díez
- Departamento de Ecología y Biología Animal, Universidade de Vigo, Centro de Investigación Mariña da Universidade de Vigo (CIM-UVigo), Vigo, Spain
| | - Juan Severino Pino Ibánhez
- Organic Geochemistry Lab, Department of Oceanography, Instituto de Investigacións Mariñas, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain.,School of Natural Sciences, Trinity College Dublin, Dublin 2, Ireland
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12
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Liau P, Kim C, Saxton MA, Malkin SY. Microbial succession in a marine sediment: Inferring interspecific microbial interactions with marine cable bacteria. Environ Microbiol 2022; 24:6348-6364. [PMID: 36178156 PMCID: PMC10092204 DOI: 10.1111/1462-2920.16230] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/27/2022] [Indexed: 01/12/2023]
Abstract
Cable bacteria are long, filamentous, multicellular bacteria that grow in marine sediments and couple sulfide oxidation to oxygen reduction over centimetre-scale distances via long-distance electron transport. Cable bacteria can strongly modify biogeochemical cycling and may affect microbial community networks. Here we examine interspecific interactions with marine cable bacteria (Ca. Electrothrix) by monitoring the succession of 16S rRNA amplicons (DNA and RNA) and cell abundance across depth and time, contrasting sediments with and without cable bacteria growth. In the oxic zone, cable bacteria activity was positively associated with abundant predatory bacteria (Bdellovibrionota, Myxococcota, Bradymonadales), indicating putative predation on cathodic cells. At suboxic depths, cable bacteria activity was positively associated with sulfate-reducing and magnetotactic bacteria, consistent with cable bacteria functioning as ecosystem engineers that modify their local biogeochemical environment, benefitting certain microbes. Cable bacteria activity was negatively associated with chemoautotrophic sulfur-oxidizing Gammaproteobacteria (Thiogranum, Sedimenticola) at oxic depths, suggesting competition, and positively correlated with these taxa at suboxic depths, suggesting syntrophy and/or facilitation. These observations are consistent with chemoautotrophic sulfur oxidizers benefitting from an oxidizing potential imparted by cable bacteria at suboxic depths, possibly by using cable bacteria as acceptors for electrons or electron equivalents, but by an as yet enigmatic mechanism.
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Affiliation(s)
- Pinky Liau
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Carol Kim
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
| | - Matthew A Saxton
- Department of Biological Sciences, Miami University, Middletown, Ohio, USA
| | - Sairah Y Malkin
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, Maryland, USA
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13
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Roth HK, Nelson AR, McKenna AM, Fegel TS, Young RB, Rhoades CC, Wilkins MJ, Borch T. Impact of beaver ponds on biogeochemistry of organic carbon and nitrogen along a fire-impacted stream. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2022; 24:1661-1677. [PMID: 36004537 DOI: 10.1039/d2em00184e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wildfires, which are increasing in frequency and severity in the western U.S., impact water quality through increases in erosion, and transport of nutrients and metals. Meanwhile, beaver populations have been increasing since the early 1900s, and the ponds they create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). However, it remains unknown how the presence of beaver ponds in burned watersheds may impact retention and transformation of chemical constituents originating in burned uplands (e.g., pyrogenic dissolved organic matter; pyDOM) and the consequences for downstream water quality. Here, we investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments. The chemistry and microbiology of surface water and sediment changed along a stream sequence starting upstream of fire and flowing through multiple beaver ponds and interconnecting stream reaches within a burned high-elevation forest watershed. The relative abundance of N-containing compounds increased in surface water of the burned beaver ponds, which corresponded to lower C/N and O/C, and higher aromaticity as characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The resident microbial communities lack the capacity to process such aromatic pyDOM, though genomic analyses demonstrate their potential to metabolize various compounds in the anaerobic sediments of the beaver ponds. Collectively, this work highlights the role of beaver ponds as biological "hotspots" with unique biogeochemistry in fire-impacted systems.
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Affiliation(s)
- Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- National High Magnetic Field Laboratory, Ion Cyclotron Resonance Facility, Florida State University, FL, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis & Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
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14
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Begmatov S, Beletsky AV, Dedysh SN, Mardanov AV, Ravin NV. Genome analysis of the candidate phylum MBNT15 bacterium from a boreal peatland predicted its respiratory versatility and dissimilatory iron metabolism. Front Microbiol 2022; 13:951761. [PMID: 35992725 PMCID: PMC9386147 DOI: 10.3389/fmicb.2022.951761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
Uncultured bacteria of the candidate phylum MBNT15, distantly related to Desulfobacterota, have been identified in a broad range of mostly organic-rich aquatic environments. We assembled a near-complete genome of a member of MBNT15 from a boreal peatland metagenome and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated SHF-111, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Genome-based phylogenetic analysis supported the phylum-level classification of the MBNT15 lineage. Genome annotation and metabolic reconstruction revealed the presence of the Embden-Meyerhof, Entner-Doudoroff and pentose phosphate pathways, as well as the complete tricarboxylic acid (TCA) cycle, and suggested a facultatively anaerobic chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, fatty acids and simple sugars, and completely oxidize these substrates through aerobic and anaerobic respiration. The SHF-111 genome encodes multiple multiheme c-type cytochromes that probably enable dissimilatory iron reduction. Consistently, the relative abundance of MBNT15 in peatlands positively correlated with iron concentration. Apparently, in the wetland ecosystem, MBNT15 representatives play the role of scavengers, carrying out the complete mineralization of low molecular weight organic substances formed as a result of microbial degradation of complex polymeric substrates. Comparative genome analysis of the MBNT15 phylum revealed that vast majority of its members are capable of aerobic respiration and dissimilatory iron reduction and some species also can reduce sulfur and nitrogen compounds, but not sulfate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Deferrimicrobium borealis, within a candidate phylum Deferrimicrobiota.
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Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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15
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Zhang C, Atashgahi S, Bosma TNP, Peng P, Smidt H. Organohalide respiration potential in marine sediments from Aarhus Bay. FEMS Microbiol Ecol 2022; 98:6605901. [PMID: 35689665 PMCID: PMC9303371 DOI: 10.1093/femsec/fiac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/09/2022] [Accepted: 06/08/2022] [Indexed: 11/14/2022] Open
Abstract
Organohalide respiration (OHR), catalysed by reductive dehalogenases (RDases), plays an important role in halogen cycling. Natural organohalides and putative RDase-encoding genes have been reported in Aarhus Bay sediments, however, OHR has not been experimentally verified. Here we show that sediments of Aarhus Bay can dehalogenate a range of organohalides, and different organohalides differentially affected microbial community compositions. PCE-dechlorinating cultures were further examined by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing. Known organohalide-respiring bacteria (OHRB) including Dehalococcoides, Dehalobacter and Desulfitobacterium decreased in abundance during transfers and serial dilutions, suggesting the importance of yet uncharacterized OHRB in these cultures. Switching from PCE to 2,6-DBP led to its complete debromination to phenol in cultures with and without sulfate. 2,6-DBP debrominating cultures differed in microbial composition from PCE-dechlorinating cultures. Desulfobacterota genera recently verified to include OHRB, including Desulfovibrio and Desulfuromusa, were enriched in all microcosms, whereas Halodesulfovibrio was only enriched in cultures without sulfate. Hydrogen and methane were detected in cultures without sulfate. Hydrogen likely served as electron donor for OHR and methanogenesis. This study shows that OHR can occur in marine environments mediated by yet unknown OHRB, suggesting their role in natural halogen cycling.
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Affiliation(s)
- Chen Zhang
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Tom N P Bosma
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peng Peng
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109-2125, United States
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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16
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Zhang N, Wu M, Che Y, Kong Y, Shu F, Wang Q, Sha W, Gong Z, Zhou J. Effects of shining pondweed (Potamogeton lucens) on bacterial communities in water and rhizosphere sediments in Nansi Lake, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:51665-51673. [PMID: 35249194 DOI: 10.1007/s11356-022-19516-0] [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: 09/17/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
Submerged macrophytes and microbial communities are important parts of lake ecosystems. In this study, the bacterial community composition in rhizosphere sediments and water from areas cultivated with (PL) and without (CK) shining pondweed (Potamogeton lucens Linn.) was investigated to determine the effects of P. lucens Linn. on the structure of the bacterial communities in Nansi Lake, China. Molecular techniques, including Illumina MiSeq and qPCR targeting of the 16S rRNA gene, were used to analyze the composition and abundance of the bacterial community. We found that bacterial alpha diversity was higher in PL water than in CK water, and the opposite trend was observed in sediment. In addition, 16S rRNA gene copy number in sediment was lower in PL than in CK. We found 30 (e.g., Desulfatiglans) and 29 (e.g., Limnohabitans) significantly different genera in sediment and water, respectively. P. lucens Linn. can change chemical properties in sediment and water and thereby affect the bacterial community. At the genus level, members of bacterial community clustered according to source (water/sediment) and area (PL/CK). Our study demonstrated that submerged macrophytes can affect the bacterial community composition in both sediment and water, suggesting that submerged macrophytes affect the transportation and cycling of nutrients in lake ecosystems.
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Affiliation(s)
- Nianxin Zhang
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Mengmeng Wu
- Shandong Freshwater Fisheries Research Institute, Jinan, 250013, China
| | - Yuying Che
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Yong Kong
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Fengyue Shu
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Qingfeng Wang
- Eco-Environmental Protection Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, People's Republic of China
| | - Weilai Sha
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Zhijin Gong
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China
| | - Jing Zhou
- School of Life Sciences, Qufu Normal University, Jining, 273 165, China.
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17
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Chen M, Zhang YQ, Krumholz LR, Zhao LY, Yan ZS, Yang YJ, Li ZH, Hayat F, Chen HB, Huang R. Black blooms-induced adaptive responses of sulfate reduction bacteria in a shallow freshwater lake. ENVIRONMENTAL RESEARCH 2022; 209:112732. [PMID: 35077715 DOI: 10.1016/j.envres.2022.112732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Decomposing cyanobacterial bloom-induced black blooms been seen as an issue in the management of freshwater ecosystems, but its effect on sulfate-reducing bacteria (SRB) in shallow freshwater lakes is not clear. The objective of this study is to present an in-depth investigation of black bloom effects on the activities and composition of SRB, as well as the interactions between SRB and other bacteria. Water and surface sediments samples were collected from a shallow freshwater lake during black and non-black blooms. Sulfate reduction rates (SRRs) in the water column were determined from the linear regression of sulfate depletion with time. Quantitative real-time polymerase chain reactions (qPCRs), targeting the dsrA gene and Illumina sequencing of 16S rDNA, were used to estimate the SRB population and SRB community structures, respectively. Our data indicate that although a higher abundance of SRB was responsible for the higher SRR in the bottom water (34.09 ± 2.37 nmol mL-1 day-1) than in the surface water (14.57 ± 2.91 nmol mL-1 day-1) during black blooms, cell-specific sulfate reduction rates (csSRRs) in the distinct water layers were not significantly different (P = 0.95), with the value of approximately 0.017 fmol cell-1 day-1. Additionally, Desulfomicrobium and Desulfovibrio were the two main genera of SRB in the water column during black bloom season, while Desulfobulbus, Desulfobacca and Desulfatiglans genera were identified in the sediments of both the black and non-black blooms in genera pools. Each SRB genus preferentially associated with bacteria for specific functions in the bacterial co-occurrence network, regardless of whether black booms occurred or not. These results extend our knowledge on the importance of SRB during black blooms and the adaptation of SRB to environmental changes in freshwater lakes.
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Affiliation(s)
- Mo Chen
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China.
| | - Ya-Qing Zhang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
| | - Lee R Krumholz
- Department of Botany & Microbiology, University of Oklahoma, Norman, OK, USA
| | - Li-Ya Zhao
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Zai-Sheng Yan
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yu-Jing Yang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Zhao-Hua Li
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Faisal Hayat
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
| | - Hong-Bing Chen
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China; Hubei Engineering Research Center for Rural Drinking Water Security, Hubei University, Wuhan, 430062, China
| | - Ran Huang
- Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Sciences, Hubei University, Wuhan, 430062, China
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18
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Edgcomb VP, Teske AP, Mara P. Microbial Hydrocarbon Degradation in Guaymas Basin-Exploring the Roles and Potential Interactions of Fungi and Sulfate-Reducing Bacteria. Front Microbiol 2022; 13:831828. [PMID: 35356530 PMCID: PMC8959706 DOI: 10.3389/fmicb.2022.831828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Hydrocarbons are degraded by specialized types of bacteria, archaea, and fungi. Their occurrence in marine hydrocarbon seeps and sediments prompted a study of their role and their potential interactions, using the hydrocarbon-rich hydrothermal sediments of Guaymas Basin in the Gulf of California as a model system. This sedimented vent site is characterized by localized hydrothermal circulation that introduces seawater sulfate into methane- and hydrocarbon-rich sediments, and thus selects for diverse hydrocarbon-degrading communities of which methane, alkane- and aromatics-oxidizing sulfate-reducing bacteria and archaea have been especially well-studied. Current molecular and cultivation surveys are detecting diverse fungi in Guaymas Basin hydrothermal sediments, and draw attention to possible fungal-bacterial interactions. In this Hypothesis and Theory article, we report on background, recent results and outcomes, and underlying hypotheses that guide current experiments on this topic in the Edgcomb and Teske labs in 2021, and that we will revisit during our ongoing investigations of bacterial, archaeal, and fungal communities in the deep sedimentary subsurface of Guaymas Basin.
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Affiliation(s)
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Paraskevi Mara
- Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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19
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Suter EA, Pachiadaki M, Taylor GT, Edgcomb VP. Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters. Front Microbiol 2022; 12:764605. [PMID: 35069470 PMCID: PMC8770914 DOI: 10.3389/fmicb.2021.764605] [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] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 01/04/2023] Open
Abstract
Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.
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Affiliation(s)
- Elizabeth A Suter
- Biology, Chemistry & Environmental Studies Department, Center for Environmental Research and Coastal Oceans Monitoring, Molloy College, Rockville Centre, NY, United States.,School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Maria Pachiadaki
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Gordon T Taylor
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, United States
| | - Virginia P Edgcomb
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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20
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Pierce CE, Furman OS, Nicholas SL, Wasik JC, Gionfriddo CM, Wymore AM, Sebestyen SD, Kolka RK, Mitchell CPJ, Griffiths NA, Elias DA, Nater EA, Toner BM. Role of Ester Sulfate and Organic Disulfide in Mercury Methylation in Peatland Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:1433-1444. [PMID: 34979084 DOI: 10.1021/acs.est.1c04662] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We examined the composition and spatial correlation of sulfur and mercury pools in peatland soil profiles by measuring sulfur speciation by 1s X-ray absorption near-edge structure spectrocopy and mercury concentrations by cold vapor atomic fluorescence spectroscopy. Also investigated were the methylation/demethylation rate constants and the presence of hgcAB genes with depth. Methylmercury (MeHg) concentration and organic disulfide were spatially correlated and had a significant positive correlation (p < 0.05). This finding is consistent with these species being products of dissimilatory sulfate reduction. Conversely, a significant negative correlation between organic monosulfides and MeHg was observed, which is consistent with a reduction in Hg(II) bioavailability via complexation reactions. Finally, a significant positive correlation between ester sulfate and instantaneous methylation rate constants was observed, which is consistent with ester sulfate being a substrate for mercury methylation via dissimilatory sulfate reduction. Our findings point to the importance of organic sulfur species in mercury methylation processes, as substrates and products, as well as potential inhibitors of Hg(II) bioavailability. For a peatland system with sub-μmol L-1 porewater concentrations of sulfate and hydrogen sulfide, our findings indicate that the solid-phase sulfur pools, which have a much larger sulfur concentration range, may be accessible to microbial activity or exchanging with the porewater.
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Affiliation(s)
- Caroline E Pierce
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Olha S Furman
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Sarah L Nicholas
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Jill Coleman Wasik
- Plant and Earth Science Department, University of Wisconsin River Falls, River Falls, Wisconsin 54022, United States
| | - Caitlin M Gionfriddo
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Ann M Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephen D Sebestyen
- USDA Forest Service, Northern Research Station, Grand Rapids, Minnesota 55744, United States
| | - Randall K Kolka
- USDA Forest Service, Northern Research Station, Grand Rapids, Minnesota 55744, United States
| | - Carl P J Mitchell
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Scarborough, Ontario M1C 1A4, Canada
| | - Natalie A Griffiths
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Dwayne A Elias
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Edward A Nater
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota 55108, United States
| | - Brandy M Toner
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota 55108, United States
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21
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Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. THE ISME JOURNAL 2022; 16:307-320. [PMID: 34331018 PMCID: PMC8692467 DOI: 10.1038/s41396-021-01057-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.
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22
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Marlow J, Spietz R, Kim K, Ellisman M, Girguis P, Hatzenpichler R. Spatially resolved correlative microscopy and microbial identification reveal dynamic depth- and mineral-dependent anabolic activity in salt marsh sediment. Environ Microbiol 2021; 23:4756-4777. [PMID: 34346142 PMCID: PMC8456820 DOI: 10.1111/1462-2920.15667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/08/2021] [Indexed: 01/04/2023]
Abstract
Coastal salt marshes are key sites of biogeochemical cycling and ideal systems in which to investigate the community structure of complex microbial communities. Here, we clarify structural-functional relationships among microorganisms and their mineralogical environment, revealing previously undescribed metabolic activity patterns and precise spatial arrangements within salt marsh sediment. Following 3.7-day in situ incubations with a non-canonical amino acid that was incorporated into new biomass, samples were resin-embedded and analysed by correlative fluorescence and electron microscopy to map the microscale arrangements of anabolically active and inactive organisms alongside mineral grains. Parallel sediment samples were examined by fluorescence-activated cell sorting and 16S rRNA gene sequencing to link anabolic activity to taxonomic identity. Both approaches demonstrated a rapid decline in the proportion of anabolically active cells with depth into salt marsh sediment, from ~60% in the top centimetre to 9.4%-22.4% between 2 and 10 cm. From the top to the bottom, the most prominent active community members shifted from sulfur cycling phototrophic consortia, to putative sulfate-reducing bacteria likely oxidizing organic compounds, to fermentative lineages. Correlative microscopy revealed more abundant (and more anabolically active) organisms around non-quartz minerals including rutile, orthoclase and plagioclase. Microbe-mineral relationships appear to be dynamic and context-dependent arbiters of biogeochemical cycling.
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Affiliation(s)
- Jeffrey Marlow
- Department of Organismic and Evolutionary BiologyHarvard University16 Divinity AveCambridgeMassachusetts02138USA
| | - Rachel Spietz
- Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Thermal Biology Institute, and Center for Biofilm EngineeringMontana State UniversityBozemanMontana59717USA
| | - Keun‐Young Kim
- Department of NeurosciencesUniversity of California at San Diego School of Medicine and National Center for Microscopy and Imaging Research, University of CaliforniaSan DiegoLa JollaCalifornia92093USA
| | - Mark Ellisman
- Department of NeurosciencesUniversity of California at San Diego School of Medicine and National Center for Microscopy and Imaging Research, University of CaliforniaSan DiegoLa JollaCalifornia92093USA
- Department of PharmacologyUniversity of CaliforniaSan DiegoLa JollaCalifornia92161USA
| | - Peter Girguis
- Department of Organismic and Evolutionary BiologyHarvard University16 Divinity AveCambridgeMassachusetts02138USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Thermal Biology Institute, and Center for Biofilm EngineeringMontana State UniversityBozemanMontana59717USA
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23
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Kong Y, Lei H, Zhang Z, Cheng W, Wang B, Pan F, Huang F, Huang F, Li W. Depth profiles of geochemical features, geochemical activities and biodiversity of microbial communities in marine sediments from the Shenhu area, the northern South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146233. [PMID: 34030248 DOI: 10.1016/j.scitotenv.2021.146233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The biogeochemical processes, anaerobic oxidation of methane (AOM) and methanogenesis, control methane emission and create distinct geochemical profiles with depth in marine sediments. Correlating the capacities and biodiversity of the microbial communities in marine sediments remains challenging. We therefore investigated the geochemical constituents and the capabilities and diversity of microbial communities in sediments at different depths in two cores from the Shenhu area in the northern South China Sea, which is characterized by underlying gas hydrates. The geochemical features, sulfate concentration decreased linearly and the acid volatile sulfur accumulated from 4 m below the seafloor (mbsf) to the bottom, indicating significant sulfate reduction. However, the methane concentration was relatively low and showed irregular trends, indicating that our study cores did not reach the sulfate-methane transition zone (SMTZ). Nevertheless, incubation experiments showed that the microbial groups in sediments performed AOM and methanogenesis in the region where sulfate decreased linearly above the SMTZ. We mapped the diversity and abundance of microbial communities in sediments with depth using high-throughput sequencing. A small proportion of known methanogens (<0.3%) may have been responsible for the methanogenesis during incubation. No classical archaeal anaerobic methanotroph (ANME) sequences were detected across all samples; only a small amount of SEEP-SRB1 were detected, and their abundance did not increase with increasing depth. Thus, unknown or unconventional phylotypes may have participated in AOM during the incubation, and the dominant phylum Bathyarchaeota or the small number of detected methanogens are the most likely performers of AOM.
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Affiliation(s)
- Yuan Kong
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Huaiyan Lei
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China.
| | - Zilian Zhang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Weidong Cheng
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Bin Wang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fulong Pan
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanfan Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Fanli Huang
- Department of Geological Oceanography, College of Ocean & Earth Science, Xiamen University, Xiamen 361102, PR China
| | - Wenqing Li
- Key Laboratory of Mineral Resources Evaluation in Northeast China, Ministry of Land and Resources, Changchun 130061, PR China
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Carbonate-hosted microbial communities are prolific and pervasive methane oxidizers at geologically diverse marine methane seep sites. Proc Natl Acad Sci U S A 2021; 118:2006857118. [PMID: 34161255 PMCID: PMC8237665 DOI: 10.1073/pnas.2006857118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Methane is a strong greenhouse gas that plays a key role in Earth’s climate. At methane seeps, large amounts of methane move upward through the seafloor, where microbial communities consume much of it. A full accounting of methane’s sources and sinks has evaded researchers—in part, perhaps, because key habitats including carbonate rock mounds have been largely neglected. We sampled seven methane seeps representing four geological settings and found that all sites had rock-hosted microbes capable of consuming methane; in lab-based incubations, some did so at the highest rates reported to date. We demonstrate several factors that help determine a sample’s methane-consuming potential and propose that carbonate rocks at methane seeps may represent a methane sink of far-reaching importance. At marine methane seeps, vast quantities of methane move through the shallow subseafloor, where it is largely consumed by microbial communities. This process plays an important role in global methane dynamics, but we have yet to identify all of the methane sinks in the deep sea. Here, we conducted a continental-scale survey of seven geologically diverse seafloor seeps and found that carbonate rocks from all sites host methane-oxidizing microbial communities with substantial methanotrophic potential. In laboratory-based mesocosm incubations, chimney-like carbonates from the newly described Point Dume seep off the coast of Southern California exhibited the highest rates of anaerobic methane oxidation measured to date. After a thorough analysis of physicochemical, electrical, and biological factors, we attribute this substantial metabolic activity largely to higher cell density, mineral composition, kinetic parameters including an elevated Vmax, and the presence of specific microbial lineages. Our data also suggest that other features, such as electrical conductance, rock particle size, and microbial community alpha diversity, may influence a sample’s methanotrophic potential, but these factors did not demonstrate clear patterns with respect to methane oxidation rates. Based on the apparent pervasiveness within seep carbonates of microbial communities capable of performing anaerobic oxidation of methane, as well as the frequent occurrence of carbonates at seeps, we suggest that rock-hosted methanotrophy may be an important contributor to marine methane consumption.
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25
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Suominen S, Dombrowski N, Sinninghe Damsté JS, Villanueva L. A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone. Environ Microbiol 2021; 23:2709-2728. [PMID: 31858660 PMCID: PMC8359207 DOI: 10.1111/1462-2920.14902] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 11/27/2022]
Abstract
Organic matter degradation in marine environments is essential for the recycling of nutrients, especially under conditions of anoxia where organic matter tends to accumulate. However, little is known about the diversity of the microbial communities responsible for the mineralization of organic matter in the absence of oxygen, as well as the factors controlling their activities. Here, we determined the active heterotrophic prokaryotic community in the sulphidic water column of the Black Sea, an ideal model system, where a tight coupling between carbon, nitrogen and sulphur cycles is expected. Active microorganisms degrading both dissolved organic matter (DOM) and protein extracts were determined using quantitative DNA stable isotope probing incubation experiments. These results were compared with the metabolic potential of metagenome-assembled genomes obtained from the water column. Organic matter incubations showed that groups like Cloacimonetes and Marinimicrobia are generalists degrading DOM. Based on metagenomic profiles the degradation proceeds in a potential interaction with members of the Deltaproteobacteria and Chloroflexi Dehalococcoidia. On the other hand, microbes with small genomes like the bacterial phyla Parcubacteria, Omnitrophica and of the archaeal phylum Woesearchaeota, were the most active, especially in protein-amended incubations, revealing the potential advantage of streamlined microorganisms in highly reduced conditions.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht UniversityUtrechtThe Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryNIOZ Royal Netherlands Institute for Sea Research and Utrecht UniversityDen HoornThe Netherlands
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26
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van Vliet DM, von Meijenfeldt FB, Dutilh BE, Villanueva L, Sinninghe Damsté JS, Stams AJ, Sánchez‐Andrea I. The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environ Microbiol 2021; 23:2834-2857. [PMID: 33000514 PMCID: PMC8359478 DOI: 10.1111/1462-2920.15265] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 09/03/2020] [Accepted: 09/28/2020] [Indexed: 01/29/2023]
Abstract
Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
| | | | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for LifeUtrecht University, Padualaan 8, 3584 CHUtrechtNetherlands
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Landsdiep 4, 1797 SZ, 'tHorntje (Texel)Netherlands
- Department of Earth Sciences, Faculty of GeosciencesUtrecht University, Princetonlaan 8A, 3584 CBUtrechtNetherlands
| | - Alfons J.M. Stams
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de Gualtar, 4710‐057BragaPortugal
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University and Research, Stippeneng 4, 6708WEWageningenNetherlands
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27
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Suominen S, van Vliet DM, Sánchez-Andrea I, van der Meer MTJ, Sinninghe Damsté JS, Villanueva L. Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments. Front Microbiol 2021; 12:628301. [PMID: 34025597 PMCID: PMC8131844 DOI: 10.3389/fmicb.2021.628301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Abstract
Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.
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Affiliation(s)
- Saara Suominen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Daan M. van Vliet
- Wageningen Food and Biobased Research (WFBR), Bornse Weilanden 9, Wageningen, Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | | | - Marcel T. J. van der Meer
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
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28
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Sánchez-Soto MF, Cerqueda-García D, Alcántara-Hernández RJ, Falcón LI, Pech D, Árcega-Cabrera F, Aguirre-Macedo ML, García-Maldonado JQ. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. MICROBIAL ECOLOGY 2021; 81:908-921. [PMID: 33196853 DOI: 10.1007/s00248-020-01631-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, 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, Mexico
| | | | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Ma Leopoldina Aguirre-Macedo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico.
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México.
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29
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Fischer PQ, Sánchez‐Andrea I, Stams AJM, Villanueva L, Sousa DZ. Anaerobic microbial methanol conversion in marine sediments. Environ Microbiol 2021; 23:1348-1362. [PMID: 33587796 PMCID: PMC8048578 DOI: 10.1111/1462-2920.15434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/15/2023]
Abstract
Methanol is an ubiquitous compound that plays a role in microbial processes as a carbon and energy source, intermediate in metabolic processes or as end product in fermentation. In anoxic environments, methanol can act as the sole carbon and energy source for several guilds of microorganisms: sulfate-reducing microorganisms, nitrate-reducing microorganisms, acetogens and methanogens. In marine sediments, these guilds compete for methanol as their common substrate, employing different biochemical pathways. In this review, we will give an overview of current knowledge of the various ways in which methanol reaches marine sediments, the ecology of microorganisms capable of utilizing methanol and their metabolism. Furthermore, through a metagenomic analysis, we shed light on the unknown diversity of methanol utilizers in marine sediments which is yet to be explored.
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Affiliation(s)
- Peter Q. Fischer
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
| | - Irene Sánchez‐Andrea
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
| | - Alfons J. M. Stams
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
- Centre of Biological EngineeringUniversity of Minho, Campus de GualtarBraga4710‐057Portugal
| | - Laura Villanueva
- Department of Marine Microbiology and BiogeochemistryRoyal Netherlands Institute for Sea Research, P.O. Box 59Den BurgTexel7197 ABThe Netherlands
- Faculty of GeosciencesUtrecht University, Princetonlaan 8aUtrecht3584 CBThe Netherlands
| | - Diana Z. Sousa
- Laboratory of MicrobiologyWageningen University & Research, Stippeneng 4Wageningen6708 WEThe Netherlands
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30
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Teske A, Wegener G, Chanton JP, White D, MacGregor B, Hoer D, de Beer D, Zhuang G, Saxton MA, Joye SB, Lizarralde D, Soule SA, Ruff SE. Microbial Communities Under Distinct Thermal and Geochemical Regimes in Axial and Off-Axis Sediments of Guaymas Basin. Front Microbiol 2021; 12:633649. [PMID: 33643265 PMCID: PMC7906980 DOI: 10.3389/fmicb.2021.633649] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/12/2021] [Indexed: 01/04/2023] Open
Abstract
Cold seeps and hydrothermal vents are seafloor habitats fueled by subsurface energy sources. Both habitat types coexist in Guaymas Basin in the Gulf of California, providing an opportunity to compare microbial communities with distinct physiologies adapted to different thermal regimes. Hydrothermally active sites in the southern Guaymas Basin axial valley, and cold seep sites at Octopus Mound, a carbonate mound with abundant methanotrophic cold seep fauna at the Central Seep location on the northern off-axis flanking regions, show consistent geochemical and microbial differences between hot, temperate, cold seep, and background sites. The changing microbial actors include autotrophic and heterotrophic bacterial and archaeal lineages that catalyze sulfur, nitrogen, and methane cycling, organic matter degradation, and hydrocarbon oxidation. Thermal, biogeochemical, and microbiological characteristics of the sampling locations indicate that sediment thermal regime and seep-derived or hydrothermal energy sources structure the microbial communities at the sediment surface.
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Affiliation(s)
- Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Gunter Wegener
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany.,MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Jeffrey P Chanton
- Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, United States
| | - Dylan White
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Barbara MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Department of Earth and Environmental Sciences, University of Minnesota, St. Paul, MI, United States
| | - Daniel Hoer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States.,United States Environmental Protection Agency, Research Triangle Park, NC, United States
| | - Dirk de Beer
- Max-Planck-Institute for Marine Microbiology, Bremen, Germany
| | - Guangchao Zhuang
- Frontiers Science Centre for Deep Ocean Multispheres and Earth System (FDOMES)/Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Ocean University of China, Qingdao, China.,Department of Marine Sciences, University of Georgia, Athens, GA, United States
| | - Matthew A Saxton
- Department of Marine Sciences, University of Georgia, Athens, GA, United States.,Department of Biological Sciences, Miami University, Oxford, OH, United States
| | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, United States
| | - Daniel Lizarralde
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - S Adam Soule
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - S Emil Ruff
- Marine Biological Laboratory, The Ecosystems Center, Woods Hole, MA, United States.,Marine Biological Laboratory, The Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Woods Hole, MA, United States
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31
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Guo C, Zhang X, Luan S, Zhou H, Liu L, Qu Y. Diversity and structure of soil bacterial community in intertidal zone of Daliao River estuary, Northeast China. MARINE POLLUTION BULLETIN 2021; 163:111965. [PMID: 33450443 DOI: 10.1016/j.marpolbul.2020.111965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Soil samples from the intertidal zone of Daliao River, Northeast China, were collected in three seasons (autumn, L1; winter, L2; and spring, L3) to evaluate the diversity and structure of bacterial community using high-throughput sequencing. Soil physicochemical characteristics varied greatly with seasons, and the potential nitrification rates were detected in the range of 1.04-2.71 μg NO3--N·g-1 dry soil·h-1 with the highest rate in spring (L3). Soil bacterial communities also differed seasonally, and nitrogen nutrients were the important variables affecting the bacterial communities as demonstrated by distance-based redundancy analysis and Mantel tests. Proteobacteria was the predominant phylum in soils showing a descending trend from L1 to L3. Woeseia and Ignatzschineria, both affiliating with Gammaproteobacteria, were the two most dominant genera, but they exerted different seasonal variations. The predicted functional profiles revealed 6 major nitrogen cycling processes, and the functional genes in relation to denitrification process were dominant in intertidal soils.
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Affiliation(s)
- Chaochen Guo
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China.
| | - Shimeng Luan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China
| | - Lifen Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Dalian University of Technology, Panjin 124221, China; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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32
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Zhou C, Miao T, Jiang L, Zhang H, Zhang Y, Zhang X. Conditions that promote the formation of black bloom in aquatic microcosms and its effects on sediment bacteria related to iron and sulfur cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141869. [PMID: 32882542 DOI: 10.1016/j.scitotenv.2020.141869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Black bloom occurs frequently in eutrophic waters. We investigated the conditions promoted the formation of black bloom via in-situ measurement in two aquatic microcosms and the effects of black bloom on the bacterial community composition. Although larger changes in dissolved oxygen (DO) were detected in the Hydrilla verticillata-dominated microcosm over the 90-day simulation, black bloom occurred more readily in the phytoplankton-dominated than macrophyte-dominated microcosm under conditions of O2 depletion and temperature above 30 °C. The sediment bacterial community composition shifted after black bloom; the relative abundance of Thiobacillus and Sideroxydans, which oxidize iron (Fe) and sulfur (S), decreased by 47% and 48%, respectively, in the phytoplankton-dominated microcosm and by 18% and 20% in the macrophyte-dominated microcosm. By contrast, Desulfatiglans increased by 13% and 19%, respectively, after black bloom. Furthermore, inter-taxa correlations remarkably changed according to co-occurrence network analysis. Thirty-six different taxa from the phylum to the genus level were identified as biomarkers of sediments collected before and after the black bloom event. Most of these biomarkers are related to Fe/S cycling in aquatic ecosystems.
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Affiliation(s)
- Chi Zhou
- Hubei Water Resources Research Institute, Hubei Water Resources and Hydropower Science and Technology Promotion Center, Wuhan 430070, PR China
| | - Teng Miao
- Hubei Water Resources Research Institute, Hubei Water Resources and Hydropower Science and Technology Promotion Center, Wuhan 430070, PR China
| | - Lai Jiang
- Hubei Water Resources Research Institute, Hubei Water Resources and Hydropower Science and Technology Promotion Center, Wuhan 430070, PR China
| | - Hang Zhang
- Hubei Water Resources Research Institute, Hubei Water Resources and Hydropower Science and Technology Promotion Center, Wuhan 430070, PR China
| | - Yi Zhang
- Hubei Water Resources Research Institute, Hubei Water Resources and Hydropower Science and Technology Promotion Center, Wuhan 430070, PR China
| | - Xu Zhang
- School of Resources and Environmental Science, Wuhan University, Wuhan 430079, PR China.
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Bin Hudari MS, Vogt C, Richnow HH. Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions. Front Microbiol 2021; 11:606565. [PMID: 33391229 PMCID: PMC7773710 DOI: 10.3389/fmicb.2020.606565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/23/2020] [Indexed: 01/04/2023] Open
Abstract
Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with 13C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.
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Affiliation(s)
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
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34
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Trueba-Santiso A, Wasmund K, Soder-Walz JM, Marco-Urrea E, Adrian L. Genome Sequence, Proteome Profile, and Identification of a Multiprotein Reductive Dehalogenase Complex in Dehalogenimonas alkenigignens Strain BRE15M. J Proteome Res 2020; 20:613-623. [PMID: 32975419 PMCID: PMC7786376 DOI: 10.1021/acs.jproteome.0c00569] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Bacteria
of the genus Dehalogenimonas respire
with vicinally halogenated alkanes via dihaloelimination.
We aimed to describe involved proteins and their supermolecular organization.
Metagenomic sequencing of a Dehalogenimonas-containing culture resulted in a 1.65 Mbp draft genome of Dehalogenimonas alkenigignens strain BRE15M. It contained
31 full-length reductive dehalogenase homologous genes (rdhA), but only eight had cognate rdhB gene coding for
membrane-anchoring proteins. Shotgun proteomics of cells grown with
1,2-dichloropropane as an electron acceptor identified 1152 proteins
representing more than 60% of the total proteome. Ten RdhA proteins
were detected, including a DcpA ortholog, which was the strongest
expressed RdhA. Blue native gel electrophoresis
(BNE) demonstrating maximum activity was localized in a protein complex
of 146–242 kDa. Protein mass spectrometry revealed the presence
of DcpA, its membrane-anchoring protein DcpB, two hydrogen uptake
hydrogenase subunits (HupL and HupS), an iron–sulfur protein
(HupX), and subunits of a redox protein with a molybdopterin-binding
motif (OmeA and OmeB) in the complex. BNE after protein solubilization
with different detergent concentrations revealed no evidence for an
interaction between the putative respiratory electron input module
(HupLS) and the OmeA/OmeB/HupX module. All detected RdhAs comigrated
with the organohalide respiration complex. Based on genomic and proteomic
analysis, we propose quinone-independent respiration in Dehalogenimonas.
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Affiliation(s)
- Alba Trueba-Santiso
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra 08193, Spain
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1010, Austria
| | - Jesica M Soder-Walz
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra 08193, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, Bellaterra 08193, Spain
| | - Lorenz Adrian
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig 04318, Germany.,Chair of Geobiotechnology, Technische Universität Berlin, Berlin 10623, Germany
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Savvichev AS, Kadnikov VV, Rusanov II, Beletsky AV, Krasnova ED, Voronov DA, Kallistova AY, Veslopolova EF, Zakharova EE, Kokryatskaya NM, Losyuk GN, Demidenko NA, Belyaev NA, Sigalevich PA, Mardanov AV, Ravin NV, Pimenov NV. Microbial Processes and Microbial Communities in the Water Column of the Polar Meromictic Lake Bol'shie Khruslomeny at the White Sea Coast. Front Microbiol 2020; 11:1945. [PMID: 32849486 PMCID: PMC7432294 DOI: 10.3389/fmicb.2020.01945] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2022] Open
Abstract
Microbiological, molecular ecological, biogeochemical, and isotope geochemical research was carried out at the polar Lake Bol'shie Khruslomeny at the coast of the Kandalaksha Bay, White Sea in March and September 2017. The uppermost mixolimnion was oxic, with low salinity (3-5%). The lower chemocline layer was brown-green colored, with very high content of particulate organic matter (up to 11.8 mg C L-1). The lowermost monimolimnion had marine salinity (22-24%) and very high concentrations of sulfide (up to 18 mmol L-1) and CH4 (up to 1.8 mmol L-1). In the chemocline, total microbial abundance and the rate of anoxygenic photosynthesis were 8.8 × 106 cells mL-1 and 34.4 μmol C L-1 day-1, respectively. Both in March and September, sulfate reduction rate increased with depth, peaking (up to 0.6-1.1 μmol S L-1 day-1) in the lower chemocline. Methane oxidation rates in the chemocline were up to 85 and 180 nmol CH4 L-1 day-1 in March and September, respectively; stimulation of this process by light was observed in September. The percentages of cyanobacteria and methanotrophs in the layer where light-induced methane oxidation occurred were similar, ∼2.5% of the microbial community. Light did not stimulate methane oxidation in deeper layers. The carbon isotope composition of particulate organic matter (δ13C-Corg), dissolved carbonates (δ13C-DIC), and methane (δ13C- CH4) indicated high microbial activity in the chemocline. Analysis of the 16S rRNA gene sequences revealed predominance of Cyanobium cyanobacteria (order Synechococcales) in the mixolimnion. Green sulfur bacteria Chlorobium phaeovibrioides capable of anoxygenic photosynthesis constituted ∼20% of the chemocline community both in March and in September. Methyloprofundus gammaptoteobacteria (family Methylomonaceae) were present in the upper chemocline, where active methane oxidation occurred. During winter, cyanobacteria were less abundant in the chemocline, while methanotrophs occurred in higher horizons, including the under-ice layer. Chemolithotrophic gammaproteobacteria of the genus Thiomicrorhabdus, oxidizing reduced sulfur compounds at low oxygen concentrations, were revealed in the chemocline in March. Both in March and September archaea constituted up to 50% of all microorganisms in the hypolimnion. The percentage of putative methanogens in the archaeal community was low, and they occurred mainly in near-bottom horizons.
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Affiliation(s)
- Alexander S. Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Igor I. Rusanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena D. Krasnova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A. Voronov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Yu. Kallistova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena F. Veslopolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Elena E. Zakharova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nataliya M. Kokryatskaya
- N. Laverov Federal Center for Integrated Arctic Research, Ural Branch, Russian Academy of Sciences, Moscow, Russia
| | - Galina N. Losyuk
- N. Laverov Federal Center for Integrated Arctic Research, Ural Branch, Russian Academy of Sciences, Moscow, Russia
| | | | - Nikolai A. Belyaev
- Shirshov Institute of Oceanology, Russian Academy of Sciences, Moscow, Russia
| | - Pavel A. Sigalevich
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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36
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Lanzén A, Mendibil I, Borja Á, Alonso-Sáez L. A microbial mandala for environmental monitoring: Predicting multiple impacts on estuarine prokaryote communities of the Bay of Biscay. Mol Ecol 2020; 30:2969-2987. [PMID: 32479653 DOI: 10.1111/mec.15489] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/08/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023]
Abstract
Routine monitoring of benthic biodiversity is critical for managing and understanding the anthropogenic impacts on marine, transitional and freshwater ecosystems. However, traditional reliance on morphological identification generally makes it cost-prohibitive to increase the scale of monitoring programmes. Metabarcoding of environmental DNA has clear potential to overcome many of the problems associated with traditional monitoring, with prokaryotes and other microorganisms showing particular promise as bioindicators. However, due to the limited knowledge regarding the ecological roles and responses of environmental microorganisms to different types of pressure, the use of de novo approaches is necessary. Here, we use two such approaches for the prediction of multiple impacts present in estuaries and coastal areas of the Bay of Biscay based on microbial communities. The first (Random Forests) is a machine learning method while the second (Threshold Indicator Taxa Analysis and quantile regression splines) is based on de novo identification of bioindicators. Our results show that both methods overlap considerably in the indicator taxa identified, but less for sequence variants. Both methods also perform well in spite of the complexity of the studied ecosystem, providing predictive models with strong correlation to reference values and fair to good agreement with ecological status groups. The ability to predict several specific types of pressure is especially appealing. The cross-validated models and biotic indices developed can be directly applied to predict the environmental status of estuaries in the same geographical region, although more work is needed to evaluate and improve them for use in new regions or habitats.
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Affiliation(s)
- Anders Lanzén
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Iñaki Mendibil
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Ángel Borja
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Pasaia, Gipuzkoa, Spain
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37
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Atashgahi S. Discovered by genomics: putative reductive dehalogenases with N-terminus transmembrane helixes. FEMS Microbiol Ecol 2020; 95:5426821. [PMID: 30942854 PMCID: PMC6797604 DOI: 10.1093/femsec/fiz048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Attempts for bioremediation of toxic organohalogens resulted in the identification of organohalide-respiring bacteria harbouring reductive dehalogenases (RDases) enzymes. RDases consist of the catalytic subunit (RdhA, encoded by rdhA) that does not have membrane-integral domains, and a small putative membrane anchor (RdhB, encoded by rdhB) that (presumably) locates the A subunit to the outside of the cytoplasmic membrane. Recent genomic studies identified a putative rdh gene in an uncultured deltaproteobacterial genome that was not accompanied by an rdhB gene, but contained transmembrane helixes in N-terminus. Therefore, rather than having a separate membrane anchor protein, this putative RDase is likely a hybrid of RdhA and RdhB, and directly connected to the membrane with transmembrane helixes. However, functionality of the hybrid putative RDase remains unknown. Further analysis showed that the hybrid putative rdh genes are present in the genomes of pure cultures and uncultured members of Bacteriodetes and Deltaproteobacteria, but also in the genomes of the candidate divisions. The encoded hybrid putative RDases have cytoplasmic or exoplasmic C-terminus localization, and cluster phylogenetically separately from the existing RDase groups. With increasing availability of (meta)genomes, more diverse and likely novel rdh genes are expected, but questions regarding their functionality and ecological roles remain open.
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Affiliation(s)
- Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,Department of Microbiology, IWWR, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,Soehngen Institute of Anaerobic Microbiology, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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38
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Taylor HB, Kurtz HD. Microbial community structure shows differing levels of temporal stability in intertidal beach sands of the grand strand region of South Carolina. PLoS One 2020; 15:e0229387. [PMID: 32106250 PMCID: PMC7046189 DOI: 10.1371/journal.pone.0229387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/05/2020] [Indexed: 11/18/2022] Open
Abstract
Studies of microbial community structure in intertidal and supratidal beach sands along the California and Gulf of Mexico coasts have begun to reveal geographical patterns in microbial diversity through the use of next generation sequencing technology. Only a few studies have targeted communities along the Eastern seaboard, leaving a variety of microbial ecosystems uncharacterized. In this study, we examine the microbial community structure within three South Carolina beaches along the Grand Strand via sequencing of the V4 region of the 16S rRNA gene to discern relationships between diversity and temporal or regional factors. Gammaproteobacteria, Planctomycetes, Acidobacteria, and Actinobacteria dominated the composition of these beaches. Diversity analyses revealed that highly diverse communities were similar in overall composition and diversity but showed different levels of community structure stability over time. The community structure in Pawleys Island sands showed no significant change over time, while Garden City experienced significant shifts between each sampling date. Community structure also differed between beaches and, to a lesser degree, sampling date. These data provide evidence of the high microbial diversity within these beach sands and suggest that even though beaches of the same geographic region can show similarity in composition and diversity at a particular timepoint, the nature of their community structure and underlying diversity may differ comparatively and over time.
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Affiliation(s)
- Harrison B. Taylor
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
| | - Harry D. Kurtz
- Department of Biological Sciences, Clemson University, Clemson, SC, United States of America
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39
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Organohalide-respiring Desulfoluna species isolated from marine environments. ISME JOURNAL 2020; 14:815-827. [PMID: 31896791 PMCID: PMC7031245 DOI: 10.1038/s41396-019-0573-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
The genus Desulfoluna comprises two anaerobic sulfate-reducing strains, D. spongiiphila AA1T and D. butyratoxydans MSL71T, of which only the former was shown to perform organohalide respiration (OHR). Here we isolated a third strain, designated D. spongiiphila strain DBB, from marine intertidal sediment using 1,4-dibromobenzene and sulfate as the electron acceptors and lactate as the electron donor. Each strain harbors three reductive dehalogenase gene clusters (rdhABC) and corrinoid biosynthesis genes in their genomes, and dehalogenated brominated but not chlorinated organohalogens. The Desulfoluna strains maintained OHR in the presence of 20 mM sulfate or 20 mM sulfide, which often negatively affect other organohalide-respiring bacteria. Strain DBB sustained OHR with 2% oxygen in the gas phase, in line with its genetic potential for reactive oxygen species detoxification. Reverse transcription-quantitative PCR revealed differential induction of rdhA genes in strain DBB in response to 1,4-dibromobenzene or 2,6-dibromophenol. Proteomic analysis confirmed expression of rdhA1 with 1,4-dibromobenzene, and revealed a partially shared electron transport chain from lactate to 1,4-dibromobenzene and sulfate, which may explain accelerated OHR during concurrent sulfate reduction. Versatility in using electron donors, de novo corrinoid biosynthesis, resistance to sulfate, sulfide and oxygen, and concurrent sulfate reduction and OHR may confer an advantage to marine Desulfoluna strains.
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40
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Pelikan C, Jaussi M, Wasmund K, Seidenkrantz MS, Pearce C, Kuzyk ZZA, Herbold CW, Røy H, Kjeldsen KU, Loy A. Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments. Front Microbiol 2019; 10:2558. [PMID: 31787951 PMCID: PMC6853847 DOI: 10.3389/fmicb.2019.02558] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Marine fjords with active glacier outlets are hot spots for organic matter burial in the sediments and subsequent microbial mineralization. Here, we investigated controls on microbial community assembly in sub-arctic glacier-influenced (GI) and non-glacier-influenced (NGI) marine sediments in the Godthåbsfjord region, south-western Greenland. We used a correlative approach integrating 16S rRNA gene and dissimilatory sulfite reductase (dsrB) amplicon sequence data over six meters of depth with biogeochemistry, sulfur-cycling activities, and sediment ages. GI sediments were characterized by comparably high sedimentation rates and had "young" sediment ages of <500 years even at 6 m sediment depth. In contrast, NGI stations reached ages of approximately 10,000 years at these depths. Sediment age-depth relationships, sulfate reduction rates (SRR), and C/N ratios were strongly correlated with differences in microbial community composition between GI and NGI sediments, indicating that age and diagenetic state were key drivers of microbial community assembly in subsurface sediments. Similar bacterial and archaeal communities were present in the surface sediments of all stations, whereas only in GI sediments were many surface taxa also abundant through the whole sediment core. The relative abundance of these taxa, including diverse Desulfobacteraceae members, correlated positively with SRRs, indicating their active contributions to sulfur-cycling processes. In contrast, other surface community members, such as Desulfatiglans, Atribacteria, and Chloroflexi, survived the slow sediment burial at NGI stations and dominated in the deepest sediment layers. These taxa are typical for the energy-limited marine deep biosphere and their relative abundances correlated positively with sediment age. In conclusion, our data suggests that high rates of sediment accumulation caused by glacier runoff and associated changes in biogeochemistry, promote persistence of sulfur-cycling activity and burial of a larger fraction of the surface microbial community into the deep subsurface.
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Affiliation(s)
- Claus Pelikan
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Marion Jaussi
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Marit-Solveig Seidenkrantz
- Palaeoceanography and Palaeoclimate Group, Arctic Research Centre, and iClimate Interdisciplinary Centre for Climate Change, Department of Geoscience, Aarhus University, Aarhus, Denmark
| | - Christof Pearce
- Palaeoceanography and Palaeoclimate Group, Arctic Research Centre, and iClimate Interdisciplinary Centre for Climate Change, Department of Geoscience, Aarhus University, Aarhus, Denmark
| | - Zou Zou Anna Kuzyk
- Department of Geological Sciences, Centre for Earth Observation Science, University of Manitoba, Winnipeg, MB, Canada
| | - Craig W. Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Hans Røy
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper Urup Kjeldsen
- Center for Geomicrobiology, Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
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41
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Teske A, McKay LJ, Ravelo AC, Aiello I, Mortera C, Núñez-Useche F, Canet C, Chanton JP, Brunner B, Hensen C, Ramírez GA, Sibert RJ, Turner T, White D, Chambers CR, Buckley A, Joye SB, Soule SA, Lizarralde D. Characteristics and Evolution of sill-driven off-axis hydrothermalism in Guaymas Basin - the Ringvent site. Sci Rep 2019; 9:13847. [PMID: 31554864 PMCID: PMC6761151 DOI: 10.1038/s41598-019-50200-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/09/2019] [Indexed: 01/17/2023] Open
Abstract
The Guaymas Basin spreading center, at 2000 m depth in the Gulf of California, is overlain by a thick sedimentary cover. Across the basin, localized temperature anomalies, with active methane venting and seep fauna exist in response to magma emplacement into sediments. These sites evolve over thousands of years as magma freezes into doleritic sills and the system cools. Although several cool sites resembling cold seeps have been characterized, the hydrothermally active stage of an off-axis site was lacking good examples. Here, we present a multidisciplinary characterization of Ringvent, an ~1 km wide circular mound where hydrothermal activity persists ~28 km northwest of the spreading center. Ringvent provides a new type of intermediate-stage hydrothermal system where off-axis hydrothermal activity has attenuated since its formation, but remains evident in thermal anomalies, hydrothermal biota coexisting with seep fauna, and porewater biogeochemical signatures indicative of hydrothermal circulation. Due to their broad potential distribution, small size and limited life span, such sites are hard to find and characterize, but they provide critical missing links to understand the complex evolution of hydrothermal systems.
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Affiliation(s)
- Andreas Teske
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA.
| | - Luke J McKay
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA.,Montana State University, Center for Biofilm Engineering, Bozeman, USA
| | - Ana Christina Ravelo
- University of California at Santa Cruz, Department of Ocean Sciences, Santa Cruz, USA
| | - Ivano Aiello
- San Jose State University, Moss Landing Marine Laboratory, Moss Landing, USA
| | - Carlos Mortera
- Universidad Nacional Autónoma de México, Instituto de Geofísica, Mexico City, Mexico
| | | | - Carles Canet
- Universidad Nacional Autónoma de México, Instituto de Geofísica, Mexico City, Mexico.,Universidad Nacional Autónoma de México, Centro de Ciencias de la Atmósfera, Mexico City, Mexico
| | - Jeffrey P Chanton
- Florida State University, Department of Earth, Ocean and Atmospheric Sciences, Tallahassee, USA
| | - Benjamin Brunner
- The University of Texas at El Paso, Department of Geological Sciences, El Paso, USA
| | | | - Gustavo A Ramírez
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Ryan J Sibert
- University of Georgia, Department of Marine Sciences, Athens, USA
| | - Tiffany Turner
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Dylan White
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Christopher R Chambers
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Andrew Buckley
- University of North Carolina at Chapel Hill, Department of Marine Sciences, Chapel Hill, USA
| | - Samantha B Joye
- University of Georgia, Department of Marine Sciences, Athens, USA
| | - S Adam Soule
- Woods Hole Oceanographic Institution, Geology & Geophysics Department, Woods Hole, USA
| | - Daniel Lizarralde
- Woods Hole Oceanographic Institution, Geology & Geophysics Department, Woods Hole, USA
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42
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Ben Salem F, Ben Said O, Cravo-Laureau C, Mahmoudi E, Bru N, Monperrus M, Duran R. Bacterial community assemblages in sediments under high anthropogenic pressure at Ichkeul Lake/Bizerte Lagoon hydrological system, Tunisia. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:644-656. [PMID: 31185353 DOI: 10.1016/j.envpol.2019.05.146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Bacterial communities inhabiting sediments in coastal areas endure the effect of strong anthropogenic pressure characterized by the presence of multiple contaminants. Understanding the effect of pollutants on the organization of bacterial communities is of paramount importance in order to unravel bacterial assemblages colonizing specific ecological niches. Here, chemical and molecular approaches were combined to investigate the bacterial communities inhabiting the sediments of the Ichkeul Lake/Bizerte Lagoon, a hydrological system under anthropogenic pressure. Although the microbial community of the Ichkeul Lake sediment was different to that of the Bizerte Lagoon, common bacterial genera were identified suggesting a lake-lagoon continuum probably due to the hydrology of the system exchanging waters according to the season. These genera represent bacterial "generalists" maintaining probably general biogeochemical functions. Linear discriminant analysis effect size (LEfSe) showed significant differential abundance distribution of bacterial genera according to the habitat, the pollution type and level. Further, correlation analyses identified specific bacterial genera which abundance was linked with pesticides concentrations in the lake, while in the lagoon the abundance of specific bacterial genera was found linked with the concentrations of PAHs (Polycyclic aromatic hydrocarbons) and organic forms of Sn. As well, bacterial genera which abundance was not correlated with the concentrations of pollutants were identified in both lake and lagoon. These findings represent valuable information, pointing out specific bacterial genera associated with pollutants, which represent assets for developing bacterial tools for the implementation, the management, and monitoring of bioremediation processes to mitigate the effect of pollutants in aquatic ecosystems.
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Affiliation(s)
- Fida Ben Salem
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia; MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Olfa Ben Said
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia; MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Cristiana Cravo-Laureau
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Ezzeddine Mahmoudi
- Laboratoire de Biosurveillance de l'Environment, Faculté des Sciences de Bizerte, Tunisia
| | - Noëlle Bru
- Laboratoire de Mathématiques et de leurs Applications, PAU UMR CNRS 5142, Université de Pau et des Pays de l'Adour, E2S-UPPA, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Mathilde Monperrus
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France
| | - Robert Duran
- MELODY Group, Université de Pau et des Pays de l'Adour, E2S-UPPA, IPREM UMR CNRS 5254, BP 1155, Pau Cedex, 64013, France; Fédération de recherche MIRA, Université de Pau et des Pays de l'Adour, E2S-UPPA, France.
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43
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Environmental filtering determines family-level structure of sulfate-reducing microbial communities in subsurface marine sediments. ISME JOURNAL 2019; 13:1920-1932. [PMID: 30894690 DOI: 10.1038/s41396-019-0387-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/22/2019] [Accepted: 02/28/2019] [Indexed: 01/09/2023]
Abstract
Recent work has shown that subsurface microbial communities assemble by selective survival of surface community members during sediment burial, but it remains unclear to what extent the compositions of the subsurface communities are a product of their founding population at the sediment surface or of the changing geochemical conditions during burial. Here we investigate this question for communities of sulfate-reducing microorganisms (SRMs). We collected marine sediment samples from the upper 3-5 m at four geochemically contrasting sites in the Skagerrak and Baltic Sea and measured SRM abundance (quantitative PCR of dsrB), metabolic activity (radiotracer rate measurements), and community composition (Illumina sequencing of dsrB amplicons). These data showed that SRM abundance, richness, and phylogenetic clustering as determined by the nearest taxon index peaked below the bioturbation zone and above the depth of sulfate depletion. Minimum cell-specific rates of sulfate reduction did not vary substantially between sites. SRM communities at different sites were best distinguished based on their composition of amplicon sequence variants (ASVs), while communities in different geochemical zones were best distinguished based on their composition of SRM families. This demonstrates environmental filtering of SRM communities in sediment while a site-specific fingerprint of the founding community is retained.
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