1
|
Hörstmann C, Hattermann T, Thomé PC, Buttigieg PL, Morel I, Waite AM, John U. Biogeographic gradients of picoplankton diversity indicate increasing dominance of prokaryotes in warmer Arctic fjords. Commun Biol 2024; 7:256. [PMID: 38431695 PMCID: PMC10908816 DOI: 10.1038/s42003-024-05946-8] [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: 04/14/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Climate change is opening the Arctic Ocean to increasing human impact and ecosystem changes. Arctic fjords, the region's most productive ecosystems, are sustained by a diverse microbial community at the base of the food web. Here we show that Arctic fjords become more prokaryotic in the picoplankton (0.2-3 µm) with increasing water temperatures. Across 21 fjords, we found that Arctic fjords had proportionally more trophically diverse (autotrophic, mixotrophic, and heterotrophic) picoeukaryotes, while subarctic and temperate fjords had relatively more diverse prokaryotic trophic groups. Modeled oceanographic connectivity between fjords suggested that transport alone would create a smooth gradient in beta diversity largely following the North Atlantic Current and East Greenland Current. Deviations from this suggested that picoeukaryotes had some strong regional patterns in beta diversity that reduced the effect of oceanographic connectivity, while prokaryotes were mainly stopped in their dispersal if strong temperature differences between sites were present. Fjords located in high Arctic regions also generally had very low prokaryotic alpha diversity. Ultimately, warming of Arctic fjords could induce a fundamental shift from more trophic diverse eukaryotic- to prokaryotic-dominated communities, with profound implications for Arctic ecosystem dynamics including their productivity patterns.
Collapse
Affiliation(s)
- Cora Hörstmann
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany.
- Aix Marseille Univ, Universite de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
- Turing Center for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | - Tore Hattermann
- Norwegian Polar Institute, iC3: Centre for Ice, Cryosphere, Carbon and Climate, Framsenteret, Hjalmar Johansens gate 14, 9296, Tromsø, Norway
- Complex Systems Group, Department of Mathematics and Statistics, The Arctic University - University of Tromsø, Hansine Hansens veg 18, 9019, Tromsø, Norway
| | - Pauline C Thomé
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587, Berlin, Germany
| | - Pier Luigi Buttigieg
- Helmholtz Metadata Collaboration, GEOMAR, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Isidora Morel
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Anya M Waite
- Ocean Frontier Institute, Dalhousie University, 1355 Oxford Street, Halifax, NS, Canada
| | - Uwe John
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstraße 231, 26129, Oldenburg, Germany
| |
Collapse
|
2
|
Kachiprath B, Solomon S, Gopi J, Jayachandran PR, Thajudeen J, Sarasan M, Mohan AS, Puthumana J, Chaithanya ER, Philip R. Exploring bacterial diversity in Arctic fjord sediments: a 16S rRNA-based metabarcoding portrait. Braz J Microbiol 2024; 55:499-513. [PMID: 38175355 PMCID: PMC10920534 DOI: 10.1007/s42770-023-01217-6] [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: 07/21/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
The frosty polar environment houses diverse habitats mostly driven by psychrophilic and psychrotolerant microbes. Along with traditional cultivation methods, next-generation sequencing technologies have become common for exploring microbial communities from various extreme environments. Investigations on glaciers, ice sheets, ponds, lakes, etc. have revealed the existence of numerous microorganisms while details of microbial communities in the Arctic fjords remain incomplete. The current study focuses on understanding the bacterial diversity in two Arctic fjord sediments employing the 16S rRNA gene metabarcoding and its comparison with previous studies from various Arctic habitats. The study revealed that Proteobacteria was the dominant phylum from both the fjord samples followed by Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Chloroflexi and Chlamydiae. A significant proportion of unclassified reads derived from bacteria was also detected. Psychrobacter, Pseudomonas, Acinetobacter, Aeromonas, Photobacterium, Flavobacterium, Gramella and Shewanella were the major genera in both the fjord sediments. The above findings were confirmed by the comparative analysis of fjord metadata with the previously reported (secondary metadata) Arctic samples. This study demonstrated the potential of 16S rRNA gene metabarcoding in resolving bacterial composition and diversity thereby providing new in situ insights into Arctic fjord systems.
Collapse
Affiliation(s)
- Bhavya Kachiprath
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Solly Solomon
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
- Fishery Survey of India, Cochin Zonal Base, Kochangadi Road, Kochi, Kerala, 682005, India
| | - Jayanath Gopi
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - P R Jayachandran
- Applied Research Center for Environment and Marine Studies, King Fahd University of Petroleum and Minerals, Dhahran, 31261, Kingdom of Saudi Arabia
| | - Jabir Thajudeen
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403804, India
| | - Manomi Sarasan
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Anjali S Mohan
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Jayesh Puthumana
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - E R Chaithanya
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India
| | - Rosamma Philip
- Dept. of Marine Biology, Microbiology & Biochemistry, Cochin University of Science and Technology, Cochin, Kerala, 682016, India.
| |
Collapse
|
3
|
Handler ER, Andersen SDJ, Gradinger R, McGovern M, Vader A, Poste AE. Seasonality in land-ocean connectivity and local processes control sediment bacterial community structure and function in a High Arctic tidal flat. FEMS Microbiol Ecol 2024; 100:fiad162. [PMID: 38111220 PMCID: PMC10799726 DOI: 10.1093/femsec/fiad162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 10/26/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
Climate change is altering patterns of precipitation, cryosphere thaw, and land-ocean influxes, affecting understudied Arctic estuarine tidal flats. These transitional zones between terrestrial and marine systems are hotspots for biogeochemical cycling, often driven by microbial processes. We investigated surface sediment bacterial community composition and function from May to September along a river-intertidal-subtidal-fjord gradient. We paired metabarcoding of in situ communities with in vitro carbon-source utilization assays. Bacterial communities differed in space and time, alongside varying environmental conditions driven by local seasonal processes and riverine inputs, with salinity emerging as the dominant structuring factor. Terrestrial and riverine taxa were found throughout the system, likely transported with runoff. In vitro assays revealed sediment bacteria utilized a broader range of organic matter substrates when incubated in fresh and brackish water compared to marine water. These results highlight the importance of salinity for ecosystem processes in these dynamic tidal flats, with the highest potential for utilization of terrestrially derived organic matter likely limited to tidal flat areas (and times) where sediments are permeated by freshwater. Our results demonstrate that intertidal flats must be included in future studies on impacts of increased riverine discharge and transport of terrestrial organic matter on coastal carbon cycling in a warming Arctic.
Collapse
Affiliation(s)
- Eleanor R Handler
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Sebastian D J Andersen
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| | - Anna Vader
- Department of Arctic Biology, The University Centre in Svalbard, P.O. Box 156, 9171 Longyearbyen, Norway
| | - Amanda E Poste
- Department of Arctic and Marine Biology, UiT – The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
- Norwegian Institute for Water Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
- Norwegian Institute for Nature Research, Fram Centre for High North Research, Hjalmar Johansensgate 14, 9007 Tromsø, Norway
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Hoover RL, Keffer JL, Polson SW, Chan CS. Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms. mSystems 2023; 8:e0003823. [PMID: 37882557 PMCID: PMC10734462 DOI: 10.1128/msystems.00038-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study, we show the Gallionellaceae FeOB genomes encode both characterized iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it would be advantageous for them to have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.
Collapse
Affiliation(s)
- Rene L. Hoover
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Keffer
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
| | - Shawn W. Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, USA
| | - Clara S. Chan
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
| |
Collapse
|
6
|
Coon GR, Duesing PD, Paul R, Baily JA, Lloyd KG. Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC. Front Microbiol 2023; 14:1268361. [PMID: 37869653 PMCID: PMC10587565 DOI: 10.3389/fmicb.2023.1268361] [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: 07/27/2023] [Accepted: 09/14/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Anaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate. Methods 16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina. Results We found that methane began to accumulate while sulfate is still abundant (6-8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES). Discussion We conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the co-occurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations.
Collapse
|
7
|
von Friesen LW, Paulsen ML, Müller O, Gründger F, Riemann L. Glacial meltwater and seasonality influence community composition of diazotrophs in Arctic coastal and open waters. FEMS Microbiol Ecol 2023; 99:fiad067. [PMID: 37349965 DOI: 10.1093/femsec/fiad067] [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: 02/03/2023] [Revised: 04/29/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023] Open
Abstract
The Arctic Ocean is particularly affected by climate change with unknown consequences for primary productivity. Diazotrophs-prokaryotes capable of converting atmospheric nitrogen to ammonia-have been detected in the often nitrogen-limited Arctic Ocean but distribution and community composition dynamics are largely unknown. We performed amplicon sequencing of the diazotroph marker gene nifH from glacial rivers, coastal, and open ocean regions and identified regionally distinct Arctic communities. Proteobacterial diazotrophs dominated all seasons, epi- to mesopelagic depths and rivers to open waters and, surprisingly, Cyanobacteria were only sporadically identified in coastal and freshwaters. The upstream environment of glacial rivers influenced diazotroph diversity, and in marine samples putative anaerobic sulphate-reducers showed seasonal succession with highest prevalence in summer to polar night. Betaproteobacteria (Burkholderiales, Nitrosomonadales, and Rhodocyclales) were typically found in rivers and freshwater-influenced waters, and Delta- (Desulfuromonadales, Desulfobacterales, and Desulfovibrionales) and Gammaproteobacteria in marine waters. The identified community composition dynamics, likely driven by runoff, inorganic nutrients, particulate organic carbon, and seasonality, imply diazotrophy a phenotype of ecological relevance with expected responsiveness to ongoing climate change. Our study largely expands baseline knowledge of Arctic diazotrophs-a prerequisite to understand underpinning of nitrogen fixation-and supports nitrogen fixation as a contributor of new nitrogen in the rapidly changing Arctic Ocean.
Collapse
Affiliation(s)
- Lisa W von Friesen
- Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
| | - Maria L Paulsen
- Department of Biology, Aarhus University, Ny Munkegade 114-116, DK-8000 Aarhus, Denmark
| | - Oliver Müller
- Department of Biological Sciences, University of Bergen, Thormøhlens gate 53A, NO-5006 Bergen, Norway
| | - Friederike Gründger
- Department of Biology, Aarhus University, Ny Munkegade 114-116, DK-8000 Aarhus, Denmark
| | - Lasse Riemann
- Department of Biology, University of Copenhagen, Strandpromenaden 5, DK-3000 Helsingør, Denmark
| |
Collapse
|
8
|
Baloza M, Henkel S, Kasten S, Holtappels M, Molari M. The Impact of Sea Ice Cover on Microbial Communities in Antarctic Shelf Sediments. Microorganisms 2023; 11:1572. [PMID: 37375074 DOI: 10.3390/microorganisms11061572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The area around the Antarctic Peninsula (AP) is facing rapid climatic and environmental changes, with so far unknown impacts on the benthic microbial communities of the continental shelves. In this study, we investigated the impact of contrasting sea ice cover on microbial community compositions in surface sediments from five stations along the eastern shelf of the AP using 16S ribosomal RNA (rRNA) gene sequencing. Redox conditions in sediments with long ice-free periods are characterized by a prevailing ferruginous zone, whereas a comparatively broad upper oxic zone is present at the heavily ice-covered station. Low ice cover stations were highly dominated by microbial communities of Desulfobacterota (mostly Sva1033, Desulfobacteria, and Desulfobulbia), Myxococcota, and Sva0485, whereas Gammaproteobacteria, Alphaproteobacteria, Bacteroidota, and NB1-j prevail at the heavy ice cover station. In the ferruginous zone, Sva1033 was the dominant member of Desulfuromonadales for all stations and, along with eleven other taxa, showed significant positive correlations with dissolved Fe concentrations, suggesting a significant role in iron reduction or an ecological relationship with iron reducers. Our results indicate that sea ice cover and its effect on organic carbon fluxes are the major drivers for changes in benthic microbial communities, favoring potential iron reducers at stations with increased organic matter fluxes.
Collapse
Affiliation(s)
- Marwa Baloza
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty 2 Biology/Chemistry, University of Bremen, Leobener Str., 28359 Bremen, Germany
| | - Susann Henkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Sabine Kasten
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Klagenfurter Str., 28359 Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Moritz Holtappels
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Massimiliano Molari
- HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| |
Collapse
|
9
|
Varliero G, Lebre PH, Frey B, Fountain AG, Anesio AM, Cowan DA. Glacial Water: A Dynamic Microbial Medium. Microorganisms 2023; 11:1153. [PMID: 37317127 DOI: 10.3390/microorganisms11051153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/15/2023] [Accepted: 04/19/2023] [Indexed: 06/16/2023] Open
Abstract
Microbial communities and nutrient dynamics in glaciers and ice sheets continuously change as the hydrological conditions within and on the ice change. Glaciers and ice sheets can be considered bioreactors as microbiomes transform nutrients that enter these icy systems and alter the meltwater chemistry. Global warming is increasing meltwater discharge, affecting nutrient and cell export, and altering proglacial systems. In this review, we integrate the current understanding of glacial hydrology, microbial activity, and nutrient and carbon dynamics to highlight their interdependence and variability on daily and seasonal time scales, as well as their impact on proglacial environments.
Collapse
Affiliation(s)
- Gilda Varliero
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Andrew G Fountain
- Departments of Geology and Geography, Portland State University, Portland, OR 97212, USA
| | - Alexandre M Anesio
- Department of Environmental Science, iClimate, Aarhus University, DK-4000 Roskilde, Denmark
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| |
Collapse
|
10
|
Venkatachalam S, Gopinath A, Krishnan KP. Fjords of the western and northern regions of Svalbard harbour distinct bacterioplankton community structures. World J Microbiol Biotechnol 2022; 39:57. [PMID: 36572813 DOI: 10.1007/s11274-022-03493-0] [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: 09/20/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022]
Abstract
Fjords are highly dynamic ecosystems that are known to be sentinels to climate change due to increased glaciomarine interactions. The convergence and mixing of warm Atlantic water (AtW) and cold Arctic water (ArW) is known to influence the hydrodynamics and ecology of the Arctic fjords. However, most past studies were limited to single-fjord ecosystems, determining the baseline knowledge of inter-fjord comparison on bacterioplankton diversity and distribution patterns. In the present study, we investigated the bacterial diversity and community composition across three Arctic fjords located in the western and northern regions of Svalbard. Our observations show that the bacterial community structure varied significantly among the fjords, while abundant Operational Taxonomic Units (OTUs) were widespread (n = 100) between all the samples and rare OTUs (n = 2221) mainly contributed to these differences. Phylogenetic classification revealed that Alpha (27.3-55%) and Gamma-proteobacteria (16-51.3%), followed by Bacteroidota (17-35.7%) were dominant in the St.Jonsfjorden and Magdalenefjorden, while Verrucomicrobiota (up to 84.19%) and Actinobacteriota (up to 76.5%) were predominant in the Raudfjorden. Temperature, dissolved inorganic phosphate (DIP) and depth were found to significantly influence the community composition of abundant bacterial groups, whereas the rare bacterial groups were affected by temperature, DIP, dissolved inorganic nitrate (DIN), ammonium and depth. A comparative meta-analysis along with Kongsfjorden and Krossfjorden also showed that each fjord had a significantly different bacterioplankton community structure.
Collapse
Affiliation(s)
- Siddarthan Venkatachalam
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India
| | - Anu Gopinath
- Department of Aquatic Environment Management, Kerala University of Fisheries and Ocean Studies (KUFOS), Madavana, Kerala, India
| | - Kottekkatu Padinchati Krishnan
- Arctic Ecology and Biogeochemistry Division, National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Govt. of India), Vasco-da-Gama, Goa, India.
| |
Collapse
|
11
|
Liang L, Vigderovich H, Sivan O, Hou J, Niu M, Yorshansky O, Zhang T, Bosco-Santos A, Wang F. Iron (oxyhydr)oxides shift the methanogenic community in deep sea methanic sediment - insights from long-term high-pressure incubations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157590. [PMID: 35901888 DOI: 10.1016/j.scitotenv.2022.157590] [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: 05/10/2022] [Revised: 07/03/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Intermittent increases of dissolved ferrous iron concentrations have been observed in deep marine methanic sediments which is different from the traditional diagenetic electron acceptor cascade, where iron reduction precedes methanogenesis. Here we aimed to gain insight into the mechanism of iron reduction and the associated microbial processes in deep sea methanic sediment by setting up long-term high-pressure incubation experiments supplemented with ferrihydrite and methane. Continuous iron reduction was observed during the entire incubation period. Intriguingly, ferrihydrite addition shifted the archaeal community from the dominance of hydrogenotrophic methanogens (Methanogenium) to methylotrophic methanogens (Methanococcoides). The enriched samples were then amended with 13C-labeled methane and different iron (oxyhydr)oxides in batch slurries to test the mechanism of iron reduction. Intensive iron reduction was observed, the highest rates with ferrihydrite, followed by hematite and then magnetite, however, no anaerobic oxidation of methane (AOM) was observed in any treatment. Further tests on the enriched slurry showed that the addition of molybdate decreased iron reduction, suggesting a link between iron reduction with sulfur cycling. This was accompanied by the enrichment of microbes capable of dissimilatory sulfate reduction and sulfur/thiosulfate oxidation, which indicates the presence of a cryptic sulfur cycle in the incubation system with the addition of iron (oxyhydr)oxides. Our work suggests that under low sulfate conditions, the presence of iron (oxyhydr)oxides would trigger a cascade of microbial reactions, and iron reduction could link with the microbial sulfur cycle, changing the kinetics of the methanogenesis process in methanic sediment.
Collapse
Affiliation(s)
- Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hanni Vigderovich
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Orit Sivan
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Omer Yorshansky
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Taoliang Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Alice Bosco-Santos
- Department of Earth and Environmental Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; Institute of Earth Surface Dynamics, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China.
| |
Collapse
|
12
|
Scicchitano D, Lo Martire M, Palladino G, Nanetti E, Fabbrini M, Dell’Anno A, Rampelli S, Corinaldesi C, Candela M. Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea). Sci Rep 2022; 12:16670. [PMID: 36198901 PMCID: PMC9535000 DOI: 10.1038/s41598-022-21182-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractBecause of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules—and taxa—were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance.
Collapse
|
13
|
Aldeguer-Riquelme B, Rubio-Portillo E, Álvarez-Rogel J, Giménez-Casalduero F, Otero XL, Belando MD, Bernardeau-Esteller J, García-Muñoz R, Forcada A, Ruiz JM, Santos F, Antón J. Factors structuring microbial communities in highly impacted coastal marine sediments (Mar Menor lagoon, SE Spain). Front Microbiol 2022; 13:937683. [PMID: 36160249 PMCID: PMC9491240 DOI: 10.3389/fmicb.2022.937683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/27/2022] [Indexed: 11/21/2022] Open
Abstract
Coastal marine lagoons are environments highly vulnerable to anthropogenic pressures such as agriculture nutrient loading or runoff from metalliferous mining. Sediment microorganisms, which are key components in the biogeochemical cycles, can help attenuate these impacts by accumulating nutrients and pollutants. The Mar Menor, located in the southeast of Spain, is an example of a coastal lagoon strongly altered by anthropic pressures, but the microbial community inhabiting its sediments remains unknown. Here, we describe the sediment prokaryotic communities along a wide range of environmental conditions in the lagoon, revealing that microbial communities were highly heterogeneous among stations, although a core microbiome was detected. The microbiota was dominated by Delta- and Gammaproteobacteria and members of the Bacteroidia class. Additionally, several uncultured groups such as Asgardarchaeota were detected in relatively high proportions. Sediment texture, the presence of Caulerpa or Cymodocea, depth, and geographic location were among the most important factors structuring microbial assemblages. Furthermore, microbial communities in the stations with the highest concentrations of potentially toxic elements (Fe, Pb, As, Zn, and Cd) were less stable than those in the non-contaminated stations. This finding suggests that bacteria colonizing heavily contaminated stations are specialists sensitive to change.
Collapse
Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Esther Rubio-Portillo
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - José Álvarez-Rogel
- Department of Agricultural Engineering of the Escuela Técnica Superior Ingeniería Agronómica (ETSIA) & Soil Ecology and Biotechnology Unit of the Institute of Plant Biotechnology, Technical University of Cartagena, Cartagena, Spain
| | | | - Xose Luis Otero
- Cross-Research in Environmental Technologies (CRETUS), Departamento de Edafoloxía e Química Agrícola, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - María-Dolores Belando
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Jaime Bernardeau-Esteller
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Rocío García-Muñoz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Aitor Forcada
- Department of Marine Science and Applied Biology, University of Alicante, Alicante, Spain
| | - Juan M. Ruiz
- Seagrass Ecology Group, Spanish Oceanography Institute of the Spanish National Research Council, Oceanography Center of Murcia, Murcia, Spain
| | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, Spain
- Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, Spain
- *Correspondence: Josefa Antón,
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Phylogenetic diversity in sulphate-reducing bacterial communities from oxidised and reduced bottom sediments of the Barents Sea. Antonie van Leeuwenhoek 2022; 115:801-820. [DOI: 10.1007/s10482-022-01733-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/22/2022] [Indexed: 11/25/2022]
|
16
|
Sipes K, Paul R, Fine A, Li P, Liang R, Boike J, Onstott TC, Vishnivetskaya TA, Schaeffer S, Lloyd KG. Permafrost Active Layer Microbes From Ny Ålesund, Svalbard (79°N) Show Autotrophic and Heterotrophic Metabolisms With Diverse Carbon-Degrading Enzymes. Front Microbiol 2022; 12:757812. [PMID: 35185810 PMCID: PMC8851200 DOI: 10.3389/fmicb.2021.757812] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/24/2021] [Indexed: 02/02/2023] Open
Abstract
The active layer of permafrost in Ny Ålesund, Svalbard (79°N) around the Bayelva River in the Leirhaugen glacier moraine is measured as a small net carbon sink at the brink of becoming a carbon source. In many permafrost-dominating ecosystems, microbes in the active layers have been shown to drive organic matter degradation and greenhouse gas production, creating positive feedback on climate change. However, the microbial metabolisms linking the environmental geochemical processes and the populations that perform them have not been fully characterized. In this paper, we present geochemical, enzymatic, and isotopic data paired with 10 Pseudomonas sp. cultures and metagenomic libraries of two active layer soil cores (BPF1 and BPF2) from Ny Ålesund, Svalbard, (79°N). Relative to BPF1, BPF2 had statistically higher C/N ratios (15 ± 1 for BPF1 vs. 29 ± 10 for BPF2; n = 30, p < 10–5), statistically lower organic carbon (2% ± 0.6% for BPF1 vs. 1.6% ± 0.4% for BPF2, p < 0.02), statistically lower nitrogen (0.1% ± 0.03% for BPF1 vs. 0.07% ± 0.02% for BPF2, p < 10–6). The d13C values for inorganic carbon did not correlate with those of organic carbon in BPF2, suggesting lower heterotrophic respiration. An increase in the δ13C of inorganic carbon with depth either reflects an autotrophic signal or mixing between a heterotrophic source at the surface and a lithotrophic source at depth. Potential enzyme activity of xylosidase and N-acetyl-β-D-glucosaminidase increases twofold at 15°C, relative to 25°C, indicating cold adaptation in the cultures and bulk soil. Potential enzyme activity of leucine aminopeptidase across soils and cultures was two orders of magnitude higher than other tested enzymes, implying that organisms use leucine as a nitrogen and carbon source in this nutrient-limited environment. Besides demonstrating large variability in carbon compositions of permafrost active layer soils only ∼84 m apart, results suggest that the Svalbard active layer microbes are often limited by organic carbon or nitrogen availability and have adaptations to the current environment, and metabolic flexibility to adapt to the warming climate.
Collapse
Affiliation(s)
- Katie Sipes
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Raegan Paul
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Aubrey Fine
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Peibo Li
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Renxing Liang
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Julia Boike
- Alfred Wegener Institute, Potsdam, Germany.,Geography Department, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tatiana A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sean Schaeffer
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, Knoxville, TN, United States
| |
Collapse
|
17
|
Wunder LC, Aromokeye DA, Yin X, Richter-Heitmann T, Willis-Poratti G, Schnakenberg A, Otersen C, Dohrmann I, Römer M, Bohrmann G, Kasten S, Friedrich MW. Iron and sulfate reduction structure microbial communities in (sub-)Antarctic sediments. THE ISME JOURNAL 2021; 15:3587-3604. [PMID: 34155335 PMCID: PMC8630232 DOI: 10.1038/s41396-021-01014-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/30/2022]
Abstract
Permanently cold marine sediments are heavily influenced by increased input of iron as a result of accelerated glacial melt, weathering, and erosion. The impact of such environmental changes on microbial communities in coastal sediments is poorly understood. We investigated geochemical parameters that shape microbial community compositions in anoxic surface sediments of four geochemically differing sites (Annenkov Trough, Church Trough, Cumberland Bay, Drygalski Trough) around South Georgia, Southern Ocean. Sulfate reduction prevails in Church Trough and iron reduction at the other sites, correlating with differing local microbial communities. Within the order Desulfuromonadales, the family Sva1033, not previously recognized for being capable of dissimilatory iron reduction, was detected at rather high relative abundances (up to 5%) while other members of Desulfuromonadales were less abundant (<0.6%). We propose that Sva1033 is capable of performing dissimilatory iron reduction in sediment incubations based on RNA stable isotope probing. Sulfate reducers, who maintain a high relative abundance of up to 30% of bacterial 16S rRNA genes at the iron reduction sites, were also active during iron reduction in the incubations. Thus, concurrent sulfate reduction is possibly masked by cryptic sulfur cycling, i.e., reoxidation or precipitation of produced sulfide at a small or undetectable pool size. Our results show the importance of iron and sulfate reduction, indicated by ferrous iron and sulfide, as processes that shape microbial communities and provide evidence for one of Sva1033's metabolic capabilities in permanently cold marine sediments.
Collapse
Affiliation(s)
- Lea C Wunder
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - David A Aromokeye
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| | - Xiuran Yin
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Graciana Willis-Poratti
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Instituto Antártico Argentino, Buenos Aires, Argentina
- Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Annika Schnakenberg
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Carolin Otersen
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Ingrid Dohrmann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Miriam Römer
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Gerhard Bohrmann
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Sabine Kasten
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM - Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| |
Collapse
|
18
|
Begmatov S, Savvichev AS, Kadnikov VV, Beletsky AV, Rusanov II, Klyuvitkin AA, Novichkova EA, Mardanov AV, Pimenov NV, Ravin NV. Microbial Communities Involved in Methane, Sulfur, and Nitrogen Cycling in the Sediments of the Barents Sea. Microorganisms 2021; 9:2362. [PMID: 34835487 PMCID: PMC8625253 DOI: 10.3390/microorganisms9112362] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
A combination of physicochemical and radiotracer analysis, high-throughput sequencing of the 16S rRNA, and particulate methane monooxygenase subunit A (pmoA) genes was used to link a microbial community profile with methane, sulfur, and nitrogen cycling processes. The objects of study were surface sediments sampled at five stations in the northern part of the Barents Sea. The methane content in the upper layers (0-5 cm) ranged from 0.2 to 2.4 µM and increased with depth (16-19 cm) to 9.5 µM. The rate of methane oxidation in the oxic upper layers varied from 2 to 23 nmol CH4 L-1 day-1 and decreased to 0.3 nmol L-1 day-1 in the anoxic zone at a depth of 16-19 cm. Sulfate reduction rates were much higher, from 0.3 to 2.8 µmol L-1 day-1. In the surface sediments, ammonia-oxidizing Nitrosopumilaceae were abundant; the subsequent oxidation of nitrite to nitrate can be carried out by Nitrospira sp. Aerobic methane oxidation could be performed by uncultured deep-sea cluster 3 of gamma-proteobacterial methanotrophs. Undetectable low levels of methanogenesis were consistent with a near complete absence of methanogens. Anaerobic methane oxidation in the deeper sediments was likely performed by ANME-2a-2b and ANME-2c archaea in consortium with sulfate-reducing Desulfobacterota. Sulfide can be oxidized by nitrate-reducing Sulfurovum sp. Thus, the sulfur cycle was linked with the anaerobic oxidation of methane and the nitrogen cycle, which included the oxidation of ammonium to nitrate in the oxic zone and denitrification coupled to the oxidation of sulfide in the deeper sediments. Methane concentrations and rates of microbial biogeochemical processes in sediments in the northern part of the Barents Sea were noticeably higher than in oligotrophic areas of the Arctic Ocean, indicating that an increase in methane concentration significantly activates microbial processes.
Collapse
Affiliation(s)
- Shahjahon Begmatov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexander S. Savvichev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Vitaly V. Kadnikov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Alexey V. Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Igor I. Rusanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
| | - Alexey A. Klyuvitkin
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Ekaterina A. Novichkova
- Shirshov Institute of Oceanology of the Russian Academy of Sciences, 117997 Moscow, Russia; (A.A.K.); (E.A.N.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| | - Nikolai V. Pimenov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.S.S.); (I.I.R.); (N.V.P.)
- Il’ichev Pacific Institute of Oceanology, Far East Branch of the Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Nikolai V. Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (S.B.); (V.V.K.); (A.V.B.); (A.V.M.)
| |
Collapse
|
19
|
Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG, Loy A, Wasmund K. Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. THE ISME JOURNAL 2021; 15:3159-3180. [PMID: 33981000 PMCID: PMC8528874 DOI: 10.1038/s41396-021-00992-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/05/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023]
Abstract
Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.
Collapse
Affiliation(s)
- Mathias Flieder
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Joy Buongiorno
- grid.411461.70000 0001 2315 1184Department of Microbiology, University of Tennessee, Knoxville, TN USA ,grid.421147.50000 0000 8528 5498Present Address: Division of Natural Sciences, Maryville College, Maryville, TN USA
| | - Craig W. Herbold
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- grid.10420.370000 0001 2286 1424Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Karen G. Lloyd
- grid.411461.70000 0001 2315 1184Department of Microbiology, University of Tennessee, Knoxville, TN USA
| | - Alexander Loy
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria ,grid.465498.2Austrian Polar Research Institute, Vienna, Austria
| | - Kenneth Wasmund
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.465498.2Austrian Polar Research Institute, Vienna, Austria ,grid.5117.20000 0001 0742 471XCenter for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| |
Collapse
|
20
|
Guo Y, Aoyagi T, Hori T. Comparative insights into genome signatures of ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains. BMC Genomics 2021; 22:475. [PMID: 34171987 PMCID: PMC8235581 DOI: 10.1186/s12864-021-07809-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Halotolerant Fe (III) oxide reducers affiliated in the family Desulfuromonadaceae are ubiquitous and drive the carbon, nitrogen, sulfur and metal cycles in marine subsurface sediment. Due to their possible application in bioremediation and bioelectrochemical engineering, some of phylogenetically close Desulfuromonas spp. strains have been isolated through enrichment with crystalline Fe (III) oxide and anode. The strains isolated using electron acceptors with distinct redox potentials may have different abilities, for instance, of extracellular electron transport, surface recognition and colonization. The objective of this study was to identify the different genomic signatures between the crystalline Fe (III) oxide-stimulated strain AOP6 and the anode-stimulated strains WTL and DDH964 by comparative genome analysis. RESULTS The AOP6 genome possessed the flagellar biosynthesis gene cluster, as well as diverse and abundant genes involved in chemotaxis sensory systems and c-type cytochromes capable of reduction of electron acceptors with low redox potentials. The WTL and DDH964 genomes lacked the flagellar biosynthesis cluster and exhibited a massive expansion of transposable gene elements that might mediate genome rearrangement, while they were deficient in some of the chemotaxis and cytochrome genes and included the genes for oxygen resistance. CONCLUSIONS Our results revealed the genomic signatures distinctive for the ferric iron oxide- and anode-stimulated Desulfuromonas spp. strains. These findings highlighted the different metabolic abilities, such as extracellular electron transfer and environmental stress resistance, of these phylogenetically close bacterial strains, casting light on genome evolution of the subsurface Fe (III) oxide reducers.
Collapse
Affiliation(s)
- Yong Guo
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| |
Collapse
|
21
|
Thomas FA, Mohan M, Krishnan KP. Bacterial diversity and their metabolic profiles in the sedimentary environments of Ny-Ålesund, Arctic. Antonie van Leeuwenhoek 2021; 114:1339-1360. [PMID: 34148162 DOI: 10.1007/s10482-021-01604-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/01/2021] [Indexed: 11/26/2022]
Abstract
Sedimentary environments in the Arctic are known to harbor diverse microbial communities playing a crucial role in the remineralization of organic matter and associated biogeochemical cycles. In this study, we used a combination of culture-dependent and culture-independent approaches to understanding the bacterial community composition associated with the sediments of a terrestrial versus fjord system in the Svalbard Arctic. Community-level metabolic profiling and growth response of retrieved bacterial isolates towards different carbon substrates at varying temperatures were also studied to assess the metabolic response of communities and isolates in the system. Bacterial species belonging to Cryobacterium and Psychrobacter dominated the terrestrial and fjord sediment retrievable fraction. Amplicon sequencing analysis revealed higher bacterial diversity in the terrestrial sediments (Shannon index; 8.135 and 7.935) as compared to the fjord sediments (4.5-5.37). Phylum Proteobacteria and Bacteroidetes dominated both terrestrial and fjord sediments. Phylum Verrucomicrobia and Cyanobacteria were abundant in terrestrial sediments while Epsilonbacteraeota and Fusobacteriia dominated the fjord sediments. Significant differences were observed in the carbon substrate utilization profiles between the terrestrial and fjord sediments at both 4 °C and 20 °C incubations (p < 0.005). Utilization of N-acetyl-D-glucosamine, D-mannitol and Tween-80 by the sediment communities and bacterial isolates from both systems, irrespective of their temperature incubations implies the affinity of bacteria for such substrates as energy sources and for their survival in cold environments. Our results suggest the ability of sediment bacterial communities to adjust their substrate utilization profiles according to condition changes in the ecosystems and are found to be less influenced by their phylogenetic relatedness.
Collapse
Affiliation(s)
- Femi Anna Thomas
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau Goa, 403206, India
| | - Mahesh Mohan
- School of Environmental Sciences, Mahatma Gandhi University, Kottayam, Kerala, 686560, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Headland Sada, Vasco da Gama, Goa, 403804, India.
| |
Collapse
|
22
|
Wasmund K, Pelikan C, Schintlmeister A, Wagner M, Watzka M, Richter A, Bhatnagar S, Noel A, Hubert CRJ, Rattei T, Hofmann T, Hausmann B, Herbold CW, Loy A. Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments. Nat Microbiol 2021; 6:885-898. [PMID: 34127845 PMCID: PMC8289736 DOI: 10.1038/s41564-021-00917-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse ‘Candidatus Izemoplasma’, Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse ‘Candidatus Izemoplasmatales’ (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed. Using microcosms, stable isotope probing, genome-resolved metagenomics and NanoSIMS, the authors identify diverse bacterial taxa that can degrade extracellular DNA in marine sediments, including ‘Candidatus Izemoplasma’, which encode numerous extracellular nucleases.
Collapse
Affiliation(s)
- Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria. .,Austrian Polar Research Institute, Vienna, Austria. .,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
| | - Claus Pelikan
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Austrian Polar Research Institute, Vienna, Austria
| | - Arno Schintlmeister
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Margarete Watzka
- Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Austrian Polar Research Institute, Vienna, Austria.,Division of Terrestrial Ecosystem Research, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Srijak Bhatnagar
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Amy Noel
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Casey R J Hubert
- Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Thomas Rattei
- Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thilo Hofmann
- Division of Environmental Geosciences, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Craig W Herbold
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,Austrian Polar Research Institute, Vienna, Austria.,Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
| |
Collapse
|
23
|
Zhang Y, Yao P, Sun C, Li S, Shi X, Zhang XH, Liu J. Vertical diversity and association pattern of total, abundant and rare microbial communities in deep-sea sediments. Mol Ecol 2021; 30:2800-2816. [PMID: 33960545 PMCID: PMC8251536 DOI: 10.1111/mec.15937] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/16/2022]
Abstract
Microbial abundance and community composition in marine sediments have been widely explored. However, high‐resolution vertical changes of benthic microbial diversity and co‐occurrence patterns are poorly described. The ecological contributions of abundant and rare species in sediments also remain largely unknown. Here, by analysing microbial populations at 14 depth layers of 10 subseafloor sediment cores (water depth 1,250–3,530 m) obtained in the South China Sea, we provided the vertical profiles of microbial β‐diversity and co‐occurrence influenced by subcommunities of different abundance. These 134 sediment samples were clustered into four groups according to sediment depth (1–2, 6–10, 30–90 and 190–790 cm) with obvious shifts in microbial community compositions. The vertical succession of microorganisms was consistent with redox zonation and influenced by terrestrial inputs. Partitioning of vertical β‐diversity showed extremely high species replacement between deep layers and the surface layer, indicating selection‐induced loss of rare species and dispersal of dormant cells and spores. By contrast, for horizontal β‐diversity, richness of rare species became increasingly significant in deep sediments. Accompanying this β‐diversity profile were clear changes in the association pattern, with microorganisms being less connected in deeper sediment layers, probably reflecting reduced syntrophic interactions. Rare species accounted for an indispensable proportion in the co‐occurrence network, and tended to form complex “small worlds.” The rare subcommunity also responded differently to various environmental factors compared with the abundant subcommunity. Our findings expand current knowledge on vertical changes of marine benthic microbial diversity and their association patterns, emphasizing the potential roles of rare species.
Collapse
Affiliation(s)
- Yunhui Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Chuang Sun
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Sanzhong Li
- Key Laboratory of Submarine Geosciences and Prospecting Techniques, Ministry of Education/College of Marine Geosciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Geology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaochong Shi
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Jiwen Liu
- College of Marine Life Sciences, Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, China
| |
Collapse
|
24
|
Minerals Determined a Special Ecological Niche and Selectively Enriched Microbial Species from Bulk Water Communities in Hot Springs. Microorganisms 2021; 9:microorganisms9051020. [PMID: 34068582 PMCID: PMC8151621 DOI: 10.3390/microorganisms9051020] [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] [Received: 04/04/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/21/2022] Open
Abstract
Minerals provide physical niches and supply nutrients or serve as electron donors/acceptors for microorganism survival and growth, and thus minerals and microbes co-evolved. Yet, little is known about how sediment minerals impact microbial community assembly in hot springs and to what extent mineralogical composition influences microbial community composition and diversity. Here the influences of minerals on thermophiles in Tengchong hot springs were revealed by network analysis of field samples, as well as in-situ microcosm experiments with minerals. A molecular ecological network was constructed based on high throughput sequencing data of 16S rRNA gene, with a combination of water geochemistry and sedimentary mineralogical compositions. Six modules were identified and this highly modular network structure represents the microbial preference to different abiotic factors, consequently resulting in niche partitioning in sedimentary communities in hot springs. Diverse mineralogical compositions generated special niches for microbial species. Subsequently, the in-situ microcosm experiments with four minerals (aragonite, albite, K-feldspar, and quartz) and spring water were conducted in a silicate-hosted alkaline spring (i.e., Gmq) and a carbonate-hosted neutral hot spring (i.e., Gxs) for 70 days. Different microbial preferences were observed among different mineral types (carbonate versus silicate). Aragonite microcosms in Gmq spring enriched archaeal genera Sulfophobococcus and Aeropyrum within the order Desulfurococcales by comparison with both in-situ water and silicate microcosms. Sulfophobococcus was also accumulated in Gxs aragonite microcosms, but the contribution to overall dissimilarity is much lower than that in Gmq spring. Besides, Caldimicrobium was a bacterial genus enriched in Gxs aragonite microcosms, in contrast to in-situ water and silicate microcosms, whereas Candidatus Kryptobacter and Thermus were more abundant in silicate microcosms. The differences in microbial accumulations among different mineral types in the same spring implied that mineral chemistry may exert extra deterministic selective pressure in drawing certain species from the bulk water communities, in addition to stochastic absorption on mineral surface. Taken together, our results highlight the special niche partitioning determined by mineralogical compositions and further confirm that minerals could be used as “fishing bait” to enrich certain rare microbial species.
Collapse
|
25
|
Jabir T, Vipindas PV, Krishnan KP, Mohamed Hatha AA. Abundance and diversity of diazotrophs in the surface sediments of Kongsfjorden, an Arctic fjord. World J Microbiol Biotechnol 2021; 37:41. [PMID: 33544264 DOI: 10.1007/s11274-020-02993-1] [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: 06/15/2020] [Accepted: 12/27/2020] [Indexed: 10/22/2022]
Abstract
Diazotrophy in the Arctic environment is poorly understood compared to tropical and subtropical regions. Hence in this study, we report the abundance and diversity of diazotrophs in Arctic fjord sediments and elucidate the role of environmental factors on the distribution of diazotrophs. The study was conducted during the boreal summer in the Kongsfjorden, an Arctic fjord situated in the western coast of Spitsbergen. The abundance of nifH gene was measured through quantitative real-time PCR and the diversity of diazotrophs was assessed by nifH targeted clone library and next generation sequence analysis. Results revealed that the abundance of nifH gene in the surface sediments ranged from 2.3 × 106 to 3.7 × 107 copies g- 1. The δ-proteobacterial diazotrophs (71% of total sequence) were the dominant class observed in this study. Major genera retrieved from the sequence analysis were Desulfovibrionaceae (25% of total sequence), Desulfuromonadaceae (18% of total sequence) and Desulfobacteriaceae (10% of total sequence); these are important diazotrophic iron and sulfur-reducing bacterial clade in the Kongsfjorden sediments. The abundance of nifH gene showed a significant positive correlation TOC/TN ratio (r2 = 0.96, p ≤ 0.05) and total organic carbon (p ≤ 0.05) content in the fjord sediments. The higher TOC/TN ratio (4.24-14.5) indicated low nitrogen content organic matter in the fjord sediments through glacier runoff, which enhances the abundance and diversity of nitrogen fixing microorganisms.
Collapse
Affiliation(s)
- T Jabir
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403 804, India
| | - P V Vipindas
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403 804, India
| | - K P Krishnan
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences (Government of India), Headland Sada, Vasco-da-Gama, Goa, 403 804, India. .,CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi, 682 016, India.
| | - A A Mohamed Hatha
- Department of Marine Biology, Microbiology, Biochemistry, School of Marine Sciences, Cochin University of Science and Technology (CUSAT), Kochi, 682 016, India.,CUSAT-NCPOR Centre for Polar Sciences, Cochin University of Science and Technology (CUSAT), Kochi, 682 016, India
| |
Collapse
|
26
|
Walker AM, Leigh MB, Mincks SL. Patterns in Benthic Microbial Community Structure Across Environmental Gradients in the Beaufort Sea Shelf and Slope. Front Microbiol 2021; 12:581124. [PMID: 33584606 PMCID: PMC7876419 DOI: 10.3389/fmicb.2021.581124] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
The paradigm of tight pelagic-benthic coupling in the Arctic suggests that current and future fluctuations in sea ice, primary production, and riverine input resulting from global climate change will have major impacts on benthic ecosystems. To understand how these changes will affect benthic ecosystem function, we must characterize diversity, spatial distribution, and community composition for all faunal components. Bacteria and archaea link the biotic and abiotic realms, playing important roles in organic matter (OM) decomposition, biogeochemical cycling, and contaminant degradation, yet sediment microbial communities have rarely been examined in the North American Arctic. Shifts in microbial community structure and composition occur with shifts in OM inputs and contaminant exposure, with implications for shifts in ecological function. Furthermore, the characterization of benthic microbial communities provides a foundation from which to build focused experimental research. We assessed diversity and community structure of benthic prokaryotes in the upper 1 cm of sediments in the southern Beaufort Sea (United States and Canada), and investigated environmental correlates of prokaryotic community structure over a broad spatial scale (spanning 1,229 km) at depths ranging from 17 to 1,200 m. Based on hierarchical clustering, we identified four prokaryotic assemblages from the 85 samples analyzed. Two were largely delineated by the markedly different environmental conditions in shallow shelf vs. upper continental slope sediments. A third assemblage was mainly comprised of operational taxonomic units (OTUs) shared between the shallow shelf and upper slope assemblages. The fourth assemblage corresponded to sediments receiving heavier OM loading, likely resulting in a shallower anoxic layer. These sites may also harbor microbial mats and/or methane seeps. Substructure within these assemblages generally reflected turnover along a longitudinal gradient, which may be related to the quantity and composition of OM deposited to the seafloor; bathymetry and the Mackenzie River were the two major factors influencing prokaryote distribution on this scale. In a broader geographical context, differences in prokaryotic community structure between the Beaufort Sea and Norwegian Arctic suggest that benthic microbes may reflect regional differences in the hydrography, biogeochemistry, and bathymetry of Arctic shelf systems.
Collapse
Affiliation(s)
- Alexis M Walker
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK, United States
| | - Sarah L Mincks
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, United States
| |
Collapse
|
27
|
Yu X, Zhou J, Song W, Xu M, He Q, Peng Y, Tian Y, Wang C, Shu L, Wang S, Yan Q, Liu J, Tu Q, He Z. SCycDB: A curated functional gene database for metagenomic profiling of sulphur cycling pathways. Mol Ecol Resour 2020. [DOI: 10.1111/1755-0998.13306] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Xiaoli Yu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Jiayin Zhou
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Wen Song
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Mengzhao Xu
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Qiang He
- Department of Civil and Environmental Engineering The University of Tennessee Knoxville TN USA
| | - Yisheng Peng
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems School of Life Sciences Xiamen University Xiamen China
| | - Cheng Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Longfei Shu
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Shanquan Wang
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Qingyun Yan
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
| | - Jihua Liu
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Qichao Tu
- Institute of Marine Science and Technology Shandong University Qingdao China
| | - Zhili He
- Environmental Microbiomics Research Center School of Environmental Science and Engineering Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) Sun Yat‐sen University Guangzhou China
- College of Agronomy Hunan Agricultural University Changsha China
| |
Collapse
|
28
|
Stevenson MA, Faust JC, Andrade LL, Freitas FS, Gray ND, Tait K, Hendry KR, Hilton RG, Henley SF, Tessin A, Leary P, Papadaki S, Ford A, März C, Abbott GD. Transformation of organic matter in a Barents Sea sediment profile: coupled geochemical and microbiological processes. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20200223. [PMID: 32862813 PMCID: PMC7481670 DOI: 10.1098/rsta.2020.0223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Process-based, mechanistic investigations of organic matter transformation and diagenesis directly beneath the sediment-water interface (SWI) in Arctic continental shelves are vital as these regions are at greatest risk of future change. This is in part due to disruptions in benthic-pelagic coupling associated with ocean current change and sea ice retreat. Here, we focus on a high-resolution, multi-disciplinary set of measurements that illustrate how microbial processes involved in the degradation of organic matter are directly coupled with inorganic and organic geochemical sediment properties (measured and modelled) as well as the extent/depth of bioturbation. We find direct links between aerobic processes, reactive organic carbon and highest abundances of bacteria and archaea in the uppermost layer (0-4.5 cm depth) followed by dominance of microbes involved in nitrate/nitrite and iron/manganese reduction across the oxic-anoxic redox boundary (approx. 4.5-10.5 cm depth). Sulfate reducers dominate in the deeper (approx. 10.5-33 cm) anoxic sediments which is consistent with the modelled reactive transport framework. Importantly, organic matter reactivity as tracked by organic geochemical parameters (n-alkanes, n-alkanoic acids, n-alkanols and sterols) changes most dramatically at and directly below the SWI together with sedimentology and biological activity but remained relatively unchanged across deeper changes in sedimentology. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.
Collapse
Affiliation(s)
- Mark A. Stevenson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- e-mail:
| | - Johan C. Faust
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Luiza L. Andrade
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Felipe S. Freitas
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
| | - Neil D. Gray
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Karen Tait
- Plymouth Marine Laboratory, Prospect Place, Plymouth PL1 3DH, UK
| | | | - Robert G. Hilton
- Department of Geography, Science Laboratories, Durham University, South Road, Durham DH1 3LE, UK
| | - Sian F. Henley
- School of GeoSciences, University of Edinburgh, James Hutton Road, Edinburgh EH9 3FE, UK
| | - Allyson Tessin
- Department of Geology, Kent State University, Kent, OH 44240, USA
| | - Peter Leary
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Sonia Papadaki
- School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK
| | - Ailbe Ford
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Christian März
- School of Earth and Environment, University of Leeds, Leeds LS2 9JT, UK
| | - Geoffrey D. Abbott
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| |
Collapse
|
29
|
Quan X, Zhang H, Liu H, Chen L, Li N. Remediation of nitrogen polluted water using Fe-C microelectrolysis and biofiltration under mixotrophic conditions. CHEMOSPHERE 2020; 257:127272. [PMID: 32534299 DOI: 10.1016/j.chemosphere.2020.127272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 05/28/2020] [Accepted: 05/30/2020] [Indexed: 06/11/2023]
Abstract
A hybrid biofilter was established on Fe-C supported carriers aimed to enhance nitrogen removal from polluted water of low Carbon/Nitrogen (C/N) ratio. Effects of organic loadings, hydraulic retention time (HRT), additional electron donor (Fe2+) supplementation and operation mode on the performance of the biofilter were investigated. Results showed that up-flow operation mode was better than down-flow mode in terms of nitrate and total nitrogen (TN) removal at low COD/N. The average removal of NO3--N, NH4+ -N and TN attained 83.1%, 84.7% and 81.2%, respectively, under the conditions of influent COD/NO3--N = 1.5-3.6, HRT = 10 h and up-flow operation. When the biofilter was operated under autotrophic conditions without organic compounds in influent as electron donors, the biofilter achieved a NO3--N removal of 46% and TN removal of 56% depending on the innate electron donors provided by the Fe-C carriers. Supplementation of Fe2+ in influent further promoted autotrophic denitrifying process, and the removal of NO3--N and TN increased to 96.3% and 84.7%, respectively, at the mol ratio of Fe2+/NO3- = 10 and HRT = 10 h. The microbial community was analyzed for the biofilm samples enriched under heterotrophic and autotrophic conditions. The Fe-C biofilter boosted the growth of a large population of mixotrophic denitrifying bacteria including Gallionella, heterotrophic denitrifying bacteria Denitratisoma, and autotrophic denitrifying bacteria Thiobacillus and Thioalkalispira. On the whole, the biofilter coupled with Fe-C micro-electrolysis provides a novel strategy to treat polluted water of low C/N under both heterotrophic and autotrophic conditions.
Collapse
Affiliation(s)
- Xiangchun Quan
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China.
| | - Haifeng Zhang
- School of Chemical Engineering, Northeast Electric Power University, Jinlin, 132012, Jinlin Province, China
| | - Hezun Liu
- School of Chemical Engineering, Northeast Electric Power University, Jinlin, 132012, Jinlin Province, China
| | - Liang Chen
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| | - Naiyu Li
- Key Laboratory of Water and Sediment Sciences of Ministry of Education, State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, 100875, China
| |
Collapse
|
30
|
Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd KG. Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PLoS One 2020; 15:e0234839. [PMID: 32853201 PMCID: PMC7451513 DOI: 10.1371/journal.pone.0234839] [Citation(s) in RCA: 5] [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: 06/01/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.
Collapse
Affiliation(s)
- Joy Buongiorno
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Karen G. Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|