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Wang W, Tao J, Liu H, Li P, Chen S, Wang P, Zhang C. Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary. AMB Express 2020; 10:16. [PMID: 31970539 PMCID: PMC6975606 DOI: 10.1186/s13568-020-0950-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 01/27/2023] Open
Abstract
Microbial community structure and metabolic activities have profound impacts on biogeochemical processes in marine sediments. Functional bacteria such as nitrate- and sulfate-reducing bacteria respond to redox gradients by coupling specific reactions amenable to relevant energy metabolisms. However, similar functional patterns have not been observed for sedimentary archaea (except for anaerobic methanotrophs and methanogens). We coupled taxonomic composition with comprehensive geochemical species to investigate the participation of distinct bacteria and archaea in sedimentary geochemical cycles in a sediment core (300 cm) from Pearl River Estuary (PRE). Geochemical properties (NO3−, dissolved Mn and Fe, SO42+, NH4+; dissolved inorganic carbon (DIC), δ13CDIC, dissolved organic carbon (DOC), total organic carbon (TOC), δ13CTOC, and fluorescent dissolved organic matter (FDOM)) exhibited strong depth variability of different trends. Bacterial 16S rRNA- and dsrB gene abundance decreased sharply with depth while archaeal and bathyarchaeotal 16S rRNA gene copies were relatively constant. This resulted in an increase in relative abundance of archaea from surface (11.6%) to bottom (42.8%). Network analysis showed that bacterial groups of Desulfobacterales, Syntrophobacterales and Gammaproteobacteria were significantly (P < 0.0001) associated with SO42− and dissolved Mn while archaeal groups of Bathyarchaeota, Group C3 and Marine Benthic Group D (MBGD) showed close positive correlations (P < 0.0001) with NH4+, δ13CTOC values and humic-like FDOM. Our study suggested that these bacterial groups dominated in redox processes relevant to sulfate or metal oxides, while the archaeal groups are more like to degrade recalcitrant organic compounds in anaerobic sediments.
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Kinetics and Identities of Extracellular Peptidases in Subsurface Sediments of the White Oak River Estuary, North Carolina. Appl Environ Microbiol 2019; 85:AEM.00102-19. [PMID: 31324636 PMCID: PMC6752024 DOI: 10.1128/aem.00102-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 07/14/2019] [Indexed: 11/20/2022] Open
Abstract
Anoxic subsurface sediments contain communities of heterotrophic microorganisms that metabolize organic carbon at extraordinarily low rates. In order to assess the mechanisms by which subsurface microorganisms access detrital sedimentary organic matter, we measured kinetics of a range of extracellular peptidases in anoxic sediments of the White Oak River Estuary, NC. Nine distinct peptidase substrates were enzymatically hydrolyzed at all depths. Potential peptidase activities (V max) decreased with increasing sediment depth, although V max expressed on a per-cell basis was approximately the same at all depths. Half-saturation constants (Km ) decreased with depth, indicating peptidases that functioned more efficiently at low substrate concentrations. Potential activities of extracellular peptidases acting on molecules that are enriched in degraded organic matter (d-phenylalanine and l-ornithine) increased relative to enzymes that act on l-phenylalanine, further suggesting microbial community adaptation to access degraded organic matter. Nineteen classes of predicted, exported peptidases were identified in genomic data from the same site, of which genes for class C25 (gingipain-like) peptidases represented more than 40% at each depth. Methionine aminopeptidases, zinc carboxypeptidases, and class S24-like peptidases, which are involved in single-stranded-DNA repair, were also abundant. These results suggest a subsurface heterotrophic microbial community that primarily accesses low-quality detrital organic matter via a diverse suite of well-adapted extracellular enzymes.IMPORTANCE Burial of organic carbon in marine and estuarine sediments represents a long-term sink for atmospheric carbon dioxide. Globally, ∼40% of organic carbon burial occurs in anoxic estuaries and deltaic systems. However, the ultimate controls on the amount of organic matter that is buried in sediments, versus oxidized into CO2, are poorly constrained. In this study, we used a combination of enzyme assays and metagenomic analysis to identify how subsurface microbial communities catalyze the first step of proteinaceous organic carbon degradation. Our results show that microbial communities in deeper sediments are adapted to access molecules characteristic of degraded organic matter, suggesting that those heterotrophs are adapted to life in the subsurface.
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Comparative evaluation of three archaeal primer pairs for exploring archaeal communities in deep-sea sediments and permafrost soils. Extremophiles 2019; 23:747-757. [PMID: 31489482 DOI: 10.1007/s00792-019-01128-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
16S rRNA gene profiling is a powerful method for characterizing microbial communities; however, no universal primer pair can target all bacteria and archaea, resulting in different primer pairs which may impact the diversity profile obtained. Here, we evaluated three pairs of high-throughput sequencing primers for characterizing archaeal communities from deep-sea sediments and permafrost soils. The results show that primer pair Arch519/Arch915 (V4-V5 regions) produced the highest alpha diversity estimates, followed by Arch349f/Arch806r (V3-V4 regions) and A751f/AU1204r (V5-V7 regions) in both sample types. The archaeal taxonomic compositions and the relative abundance estimates of archaeal communities are influenced by the primer pairs. Beta diversity of the archaeal community detected by the three primer pairs reveals that primer pairs Arch349f/Arch806r and Arch519f/Arch915r are biased toward detection of Halobacteriales, Methanobacteriales and MBG-E/Hydrothermarchaeota, whereas the primer pairs Arch519f/Arch915r and A751f/UA1204r are biased to detect MBG-B/Lokiarchaeota, and the primers pairs Arch349f/Arch806r and A751f/UA1204r are biased to detect Methanomicrobiales and Methanosarcinales. The data suggest that the alpha and beta diversities of archaeal communities as well as the community compositions are influenced by the primer pair choice. This finding provides researchers with valuable experimental insight for selection of appropriate archaeal primer pairs to characterize archaeal communities.
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Yi XY, Yang YP, Yuan HY, Chen Z, Duan GL, Zhu YG. Coupling metabolisms of arsenic and iron with humic substances through microorganisms in paddy soil. JOURNAL OF HAZARDOUS MATERIALS 2019; 373:591-599. [PMID: 30952004 DOI: 10.1016/j.jhazmat.2019.03.113] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/20/2019] [Accepted: 03/26/2019] [Indexed: 05/12/2023]
Abstract
Humic acid (HA) and fulvic acid (FA) are dominating humic substances (HS) in soil. In this study, the effects of HA and FA addition (0.2%-1.5%) on arsenic (As) mobility and microbial community composition in paddy soil were investigated. FA significantly increased the concentrations of As (12-fold), iron (Fe; 20-fold), manganese (Mn; 3-fold) and acetic acid (3-fold) in soil porewater, and also caused significant enrichment of Desulfitobacterium (41-fold). Furthermore, the FA addition significantly increased the relative abundance of Bathyarchaeota (4-fold), a microorganism that is suggested to be important for FA degradation. In contrast, HA slightly increased As (1.2-fold) in porewater, had little effect on Fe, Mn and acetic acid, and 1.5% HA addition significantly decreased As in porewater at day 14 (45%). Both HA and FA addition promoted As methylation. HA increased dimethylarsenate concentration and FA increased monomethylarsenate concentration in porewater. These results highlight the contrasting effects of different (HA vs. FA) organic substances on As fate in paddy soil and advance our understanding of the associations among As, Fe and organic substances through microorganisms in paddy soil.
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Affiliation(s)
- Xing-Yun Yi
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yu-Ping Yang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Hai-Yan Yuan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zheng Chen
- Department of Health and Environmental Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, People's Republic of China
| | - Gui-Lan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China; University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, People's Republic of China
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Miettinen H, Bomberg M, Nyyssönen M, Reunamo A, Jørgensen KS, Vikman M. Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area. PLoS One 2019; 14:e0218834. [PMID: 31265451 PMCID: PMC6605675 DOI: 10.1371/journal.pone.0218834] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/10/2019] [Indexed: 11/19/2022] Open
Abstract
Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea.
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Affiliation(s)
- Hanna Miettinen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
- * E-mail:
| | - Malin Bomberg
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
| | - Mari Nyyssönen
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
| | - Anna Reunamo
- Marine Research Centre, Finnish Environment Institute SYKE, Helsinki, Finland
| | | | - Minna Vikman
- Solutions for Natural Resources and Environment, VTT Technical Research Centre of Finland Ltd, VTT, Finland
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Complex Microbial Communities Drive Iron and Sulfur Cycling in Arctic Fjord Sediments. Appl Environ Microbiol 2019; 85:AEM.00949-19. [PMID: 31076435 DOI: 10.1128/aem.00949-19] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 04/28/2019] [Indexed: 11/20/2022] Open
Abstract
Glacial retreat is changing biogeochemical cycling in the Arctic, where glacial runoff contributes iron for oceanic shelf primary production. We hypothesize that in Svalbard fjords, microbes catalyze intense iron and sulfur cycling in low-organic-matter sediments. This is because low organic matter limits sulfide generation, allowing iron mobility to the water column instead of precipitation as iron monosulfides. In this study, we tested this with high-depth-resolution 16S rRNA gene libraries in the upper 20 cm at two sites in Van Keulenfjorden, Svalbard. At the site closer to the glaciers, iron-reducing Desulfuromonadales, iron-oxidizing Gallionella and Mariprofundus, and sulfur-oxidizing Thiotrichales and Epsilonproteobacteria were abundant above a 12-cm depth. Below this depth, the relative abundances of sequences for sulfate-reducing Desulfobacteraceae and Desulfobulbaceae increased. At the outer station, the switch from iron-cycling clades to sulfate reducers occurred at shallower depths (∼5 cm), corresponding to higher sulfate reduction rates. Relatively labile organic matter (shown by δ13C and C/N ratios) was more abundant at this outer site, and ordination analysis suggested that this affected microbial community structure in surface sediments. Network analysis revealed more correlations between predicted iron- and sulfur-cycling taxa and with uncultured clades proximal to the glacier. Together, these results suggest that complex microbial communities catalyze redox cycling of iron and sulfur, especially closer to the glacier, where sulfate reduction is limited due to low availability of organic matter. Diminished sulfate reduction in upper sediments enables iron to flux into the overlying water, where it may be transported to the shelf.IMPORTANCE Glacial runoff is a key source of iron for primary production in the Arctic. In the fjords of the Svalbard archipelago, glacial retreat is predicted to stimulate phytoplankton blooms that were previously restricted to outer margins. Decreased sediment delivery and enhanced primary production have been hypothesized to alter sediment biogeochemistry, wherein any free reduced iron that could potentially be delivered to the shelf will instead become buried with sulfide generated through microbial sulfate reduction. We support this hypothesis with sequencing data that showed increases in the relative abundance of sulfate reducing taxa and sulfate reduction rates with increasing distance from the glaciers in Van Keulenfjorden, Svalbard. Community structure was driven by organic geochemistry, suggesting that enhanced input of organic material will stimulate sulfate reduction in interior fjord sediments as glaciers continue to recede.
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Wang S, Zheng X, Xia H, Shi D, Fan J, Wang P, Yan Z. Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing. PLoS One 2019; 14:e0218611. [PMID: 31226149 PMCID: PMC6588238 DOI: 10.1371/journal.pone.0218611] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
The differences in archaeal diversity and community composition in the sediments and waters of the Qinhuangdao coastal aquaculture zone were investigated. Furthermore, the associations between dominant archaeal taxa with geographic and environmental variables were evaluated. High-throughput sequencing of archaeal 16S rRNA genes yielded a total of 176,211 quality-filtered reads and 1,178 operational taxonomic units (OTUs) overall. The most abundant phylum and class among all communities were Thaumarchaeota and Nitrososphaeria, respectively. Beta diversity analysis indicated that community composition was divided into two groups according to the habitat type (i.e., sediments or waters). Only 9.8% OTUs were shared by communities from the two habitats, while 73.9% and 16.3% of the OTUs were unique to sediment or water communities, respectively. Furthermore, the relative abundances of the dominant OTUs differed with habitat type. Investigations of relationships between dominant OTUs and environmental variables indicated that some dominant OTUs were more sensitive to variation in environmental factors, which could be due to individual taxonomic differences in lifestyles and biological processes. Overall, the investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.
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Affiliation(s)
- Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xin Zheng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Huijuan Xia
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Di Shi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Juntao Fan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Pengyuan Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Zhenguang Yan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
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Bacterial and Archaeal Assemblages from Two Size Fractions in Submarine Groundwater Near an Industrial Zone. WATER 2019. [DOI: 10.3390/w11061261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nutrients and organic pollutants transported by submarine groundwater discharge (SGD) play a significant role in controlling water quality, and can lead to the concerned deleterious effects on marine ecosystems. Subterranean estuaries are complicated habitats of diverse microbial communities that mediate different biogeochemical processes. However, there is less information on how microorganisms mediate biogeochemical cycles in the submarine groundwater system. In this study, we investigated the changes in bacterial and archaeal assemblages from two size fractions (0.2–0.45 μm and >0.45 μm) in the submarine groundwater of Qinzhou Bay, China. Phylogenetic analysis showed that Bathyarchaeota was dominant in archaeal communities in the >0.45 μm size fraction, but was seldom in the 0.2–0.45 μm fraction. The co-occurrence of sequences belonging to Bathyarchaeota and Methanosaeta was found in the >0.45 μm size fraction. Since a gene encoding acetate kinase of Bathyarchaeota is involved in acetate production, and acetate is also a necessary growth factor for Methanosaeta, the acetate produced by Bathyarchaeota can provide food or energy sources for Methanosaeta in this very >0.45 μm size fraction. The most abundant bacterial sequences in the >0.45 μm size fraction was closely related to biomineral iron-oxidizing Gallionella spp., whereas the dominant bacterial sequences in the 0.2–0.45 μm fraction were affiliated with Limnohabitans spp., which can utilize dissolved organic matter as an important source of growth substrates. Notably, approximately 10% of the bacterial sequences in both of the two size fractions belonged to Novosphingobium spp., which plays an important role in the degradation of pollutants, especially aromatic compounds. Furthermore, the predictive functional profiling also revealed that the pathways involved in the degradation of aromatic compounds by both bacteria and archaea were identified. The presence of nutrients or pollutants in our study site provides different substrates for the growth of the specific microbial groups; in turn, these microbes may help to deplete pollutants to the ocean through submarine groundwater. We suggest that these specific microbial groups could be potential candidates for effective in situ bioremediation of groundwater ecosystems.
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Potts LD, Perez Calderon LJ, Gubry-Rangin C, Witte U, Anderson JA. Characterisation of microbial communities of drill cuttings piles from offshore oil and gas installations. MARINE POLLUTION BULLETIN 2019; 142:169-177. [PMID: 31232291 DOI: 10.1016/j.marpolbul.2019.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/03/2019] [Accepted: 03/08/2019] [Indexed: 06/09/2023]
Abstract
Drill cuttings (DC) are produced during hydrocarbon drilling operations and are composed of subsurface rock coated with hydrocarbons and drilling fluids. Historic disposal of DC at sea has resulted in the formation of large piles on the seabed that may be left in situ following infrastructure decommissioning. This study provides a first insight into the microbial abundance, diversity and community structure of two DC piles from North Sea oil and gas installations. The abundance of both bacteria and archaea was lower in DC than in surrounding natural sediments. Microbial diversity and richness within DC were low but increased with distance from the piles. Microbial community structure was significantly different in DC piles compared to nearby natural sediments. DC bacterial communities were dominated by Halomonas, Dietzia and Dethiobacter. The presence of such organisms suggests a potential function of hydrocarbon degradation ability and may play an active role in DC pile remediation.
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Affiliation(s)
- Lloyd D Potts
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom.
| | - Luis J Perez Calderon
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom; Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
| | - Cecile Gubry-Rangin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Ursula Witte
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - James A Anderson
- Chemical and Materials Engineering, School of Engineering, University of Aberdeen, Aberdeen, United Kingdom
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60
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Petro C, Zäncker B, Starnawski P, Jochum LM, Ferdelman TG, Jørgensen BB, Røy H, Kjeldsen KU, Schramm A. Marine Deep Biosphere Microbial Communities Assemble in Near-Surface Sediments in Aarhus Bay. Front Microbiol 2019; 10:758. [PMID: 31031732 PMCID: PMC6474314 DOI: 10.3389/fmicb.2019.00758] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/26/2019] [Indexed: 11/30/2022] Open
Abstract
Analyses of microbial diversity in marine sediments have identified a core set of taxa unique to the marine deep biosphere. Previous studies have suggested that these specialized communities are shaped by processes in the surface seabed, in particular that their assembly is associated with the transition from the bioturbated upper zone to the nonbioturbated zone below. To test this hypothesis, we performed a fine-scale analysis of the distribution and activity of microbial populations within the upper 50 cm of sediment from Aarhus Bay (Denmark). Sequencing and qPCR were combined to determine the depth distributions of bacterial and archaeal taxa (16S rRNA genes) and sulfate-reducing microorganisms (SRM) (dsrB gene). Mapping of radionuclides throughout the sediment revealed a region of intense bioturbation at 0-6 cm depth. The transition from bioturbated sediment to the subsurface below (7 cm depth) was marked by a shift from dominant surface populations to common deep biosphere taxa (e.g., Chloroflexi and Atribacteria). Changes in community composition occurred in parallel to drops in microbial activity and abundance caused by reduced energy availability below the mixed sediment surface. These results offer direct evidence for the hypothesis that deep subsurface microbial communities present in Aarhus Bay mainly assemble already centimeters below the sediment surface, below the bioturbation zone.
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Affiliation(s)
- Caitlin Petro
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Birthe Zäncker
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Piotr Starnawski
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Lara M. Jochum
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Timothy G. Ferdelman
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bo Barker Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U. Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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61
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Ma KL, Li XK, Bao LL. Influence of organic loading rate on purified terephthalic acid wastewater treatment in a temperature staged anaerobic treatment (TSAT) system: Performance and metagenomic characteristics. CHEMOSPHERE 2019; 220:1091-1099. [PMID: 33395796 DOI: 10.1016/j.chemosphere.2019.01.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 01/01/2019] [Accepted: 01/03/2019] [Indexed: 06/12/2023]
Abstract
In this study, a temperature staged anaerobic treatment (TSAT) system featured by thermophilic reactor (R1)-mesophilic reactor (R2) co-digestion was introduced to treat PTA wastewater. The process was successively conducted at three organic loading rates (OLRs): 3.34, 4.45, 6.68 kg COD/(m³·d), respectively (OLRs were R1 basis). The results indicated that TSAT system was highly efficient in PTA wastewater treatment at OLR lower than 4.45 kg COD/(m³·d). Miseq sequencing analysis demonstrated that R1 and R2 were predominated by hydrogenotrophic Methanolinea and acetotrophic Methanosaeta, separately. In addition, TA06, Caldisericia and Acetothermia associated groups were highly abundant in R1, whereas Chlorobiaceae and Syntrophobacteraceae were largely observed in R2. Tax4Fun analysis suggested that the important functional capabilities were significantly different between R1 and R2 (P < 0.05). The pathways related to aromatic compounds degradation mainly occurred in mesophilic stage, while the biosynthesis and metabolism pathways were more favored in thermophilic stage.
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Affiliation(s)
- Kai-Li Ma
- School of Environment, Henan Normal University, Xinxiang, 453007, China.
| | - Xiang-Kun Li
- School of Environment, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China; School of Civil and Transportation Engineering, Hebei University of Technology, Tianjin, 300000, China.
| | - Lin-Lin Bao
- School of Environment, Henan Normal University, Xinxiang, 453007, China
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Zhang Q, Li Y, Xing J, Brookes PC, Xu J. Soil available phosphorus content drives the spatial distribution of archaeal communities along elevation in acidic terrace paddy soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 658:723-731. [PMID: 30583167 DOI: 10.1016/j.scitotenv.2018.12.144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
Archaea play crucial roles in geochemical cycles and influence the emission of greenhouse gases in acidic soils. However, little is known about the distribution pattern of total archaeal diversity and community composition with increasing elevation, especially in acidic agricultural ecosystems. Terraces, characterized by vertical climate changes and unique hydrological properties, are "natural experiments" to explore the spatial distribution of microorganisms along elevation in paddy soils. Here we investigated the diversity and structure of soil archaeal communities in nine increasingly elevated acidic paddy soils of the Yunhe terrace, China. Archaeal communities were dominated by Methanomicrobia of Euryarchaeota (38.5%), Group 1.1a-associated cluster (SAGSCG-1) of Thaumarchaeota (22.0%) and Subgroup-6 (previously described as crenarchaeotal group 1.3b) of Bathyarchaeota (17.8%). The archaeal phylotype richness decreased with increasing elevation. Both the species richness and phylogenetic diversity of the archaeal communities were significantly negatively correlated with soil available phosphorus (AP) content according to linear regression analyses. The archaeal communities differed greatly between soils of increasing elevation, and were roughly clustered into three groups, mostly in relation to AP contents. A variation partitioning analysis further confirmed that edaphic factors including the content of AP (17.1%), nitrate (7.83%), soil organic carbon (4.69%), dissolved organic carbon (4.22%) and soil pH (4.07%) shaped the archaeal community. The variation of soil properties were probably induced by elevation. The co-occurrence network indicated a modular structure of the archaeal community. Overall, our results emphasized that soil AP content was the best predictor of archaeal diversity and community structure, and the impacts of elevation on soil archaeal communities were not diminished by long-term rice cultivation, although minor compared with the effects of soil properties.
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Affiliation(s)
- Qian Zhang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Yong Li
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Jiajia Xing
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Philip C Brookes
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.
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63
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Pan J, Chen Y, Wang Y, Zhou Z, Li M. Vertical Distribution of Bathyarchaeotal Communities in Mangrove Wetlands Suggests Distinct Niche Preference of Bathyarchaeota Subgroup 6. MICROBIAL ECOLOGY 2019; 77:417-428. [PMID: 30612184 DOI: 10.1007/s00248-018-1309-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/16/2018] [Indexed: 06/09/2023]
Abstract
Bathyarchaeota is a diverse, abundant, and widespread archaeal phylum that may play an important role in global carbon cycling. The vertical distribution of Bathyarchaeota and environmental impact on bathyarchaeotal community in deep-sea and lake sediments are known; however, little information is available on Bathyarchaeota in eutrophic and brackish environments, such as mangrove wetlands. In the current study, we investigated the bathyarchaeotal community in the mangrove ecosystem of Futian Nature Reserve, Shenzhen. By slicing the profile into 2-cm layers from the surface to bottom, 110 sediment samples were obtained from three mangrove and three mud flat profiles. High-throughput sequencing of archaeal 16S rRNA genes, quantification of bathyarchaeotal 16S rRNA genes with optimized quantitative primers, and the ensuing statistical analyses revealed the vertical distribution of Bathyarchaeota in the mangrove ecosystem, indicating that Bathyarchaeota was the dominant archaeal phylum therein, with Bathyarchaeota subgroups 6, 8, 15, and 17 as the most abundant subgroups. The abundance of Bathyarchaeota was higher in the mangrove than in the mud flat and other oligotrophic or freshwater habitats. Total organic carbon (TOC) and nitric oxide were significantly correlated with the abundance of Bathyarchaeota, and pH was the major factor shaping the community composition. Further, the data suggested that Bathyarchaeota subgroup 6 preferentially dwelled in slightly acidic, high TOC, and subsurface environments, indicating a potentially distinct role in the global geochemical cycle. These findings expand the knowledge of the distribution and niche preference of Bathyarchaeota, emphasizing the need for continuous characterization of bathyarchaeotal subgroups.
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Affiliation(s)
- Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yulian Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yongming Wang
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
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64
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An evolving view of methane metabolism in the Archaea. Nat Rev Microbiol 2019; 17:219-232. [DOI: 10.1038/s41579-018-0136-7] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 11/26/2018] [Indexed: 11/08/2022]
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65
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Sollai M, Villanueva L, Hopmans EC, Reichart G, Sinninghe Damsté JS. A combined lipidomic and 16S rRNA gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column. GEOBIOLOGY 2019; 17:91-109. [PMID: 30281902 PMCID: PMC6586073 DOI: 10.1111/gbi.12316] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/02/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2023]
Abstract
Archaea are important players in marine biogeochemical cycles, and their membrane lipids are useful biomarkers in environmental and geobiological studies. However, many archaeal groups remain uncultured and their lipid composition unknown. Here, we aim to expand the knowledge on archaeal lipid biomarkers and determine the potential sources of those lipids in the water column of the euxinic Black Sea. The archaeal community was evaluated by 16S rRNA gene amplicon sequencing and by quantitative PCR. The archaeal intact polar lipids (IPLs) were investigated by ultra-high-pressure liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed both a complex archaeal community and large changes with water depth in the IPL assemblages. In the oxic/upper suboxic waters (<105 m), the archaeal community was dominated by marine group (MG) I Thaumarchaeota, coinciding with a higher relative abundance of hexose phosphohexose crenarchaeol, a known marker for Thaumarchaeota. In the suboxic waters (80-110 m), MGI Nitrosopumilus sp. dominated and produced predominantly monohexose glycerol dibiphytanyl glycerol tetraethers (GDGTs) and hydroxy-GDGTs. Two clades of MGII Euryarchaeota were present in the oxic and upper suboxic zones in much lower abundances, preventing the detection of their specific IPLs. In the deep sulfidic waters (>110 m), archaea belonging to the DPANN Woesearchaeota, Bathyarchaeota, and ANME-1b clades dominated. Correlation analyses suggest that the IPLs GDGT-0, GDGT-1, and GDGT-2 with two phosphatidylglycerol (PG) head groups and archaeol with a PG, phosphatidylethanolamine, and phosphatidylserine head groups were produced by ANME-1b archaea. Bathyarchaeota represented 55% of the archaea in the deeper part of the euxinic zone and likely produces archaeol with phospho-dihexose and hexose-glucuronic acid head groups.
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Affiliation(s)
- Martina Sollai
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Laura Villanueva
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Ellen C. Hopmans
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
| | - Gert‐Jan Reichart
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
| | - Jaap S. Sinninghe Damsté
- Departments of Marine Microbiology and Biogeochemistry and Ocean SystemsNIOZ Royal Netherlands Institute for Sea Researchand Utrecht UniversityDen BurgThe Netherlands
- Department of Earth SciencesFaculty of GeosciencesUniversity of UtrechtUtrechtThe Netherlands
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66
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Zhou Z, Pan J, Wang F, Gu JD, Li M. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev 2018; 42:639-655. [PMID: 29790926 DOI: 10.1093/femsre/fuy023] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.
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Affiliation(s)
- Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.,Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
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67
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von Gunten K, Hamilton SM, Zhong C, Nesbø C, Li J, Muehlenbachs K, Konhauser KO, Alessi DS. Electron donor-driven bacterial and archaeal community patterns along forest ring edges in Ontario, Canada. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:663-672. [PMID: 30014579 DOI: 10.1111/1758-2229.12678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/08/2018] [Indexed: 06/08/2023]
Abstract
Forest rings are 50-1600 m diameter circular structures found in boreal forests around the globe. They are believed to be chemically reducing chimney features, having an accumulation of reduced species in the middle of the ring and oxidation processes occurring at the ring's edges. It has been suggested that microorganisms could be responsible for charge transfer from the inside to the outside of the ring. To explore this, we focused on the changes in bacterial and archaeal communities in the ring edges of two forest rings, the 'Bean' and the 'Thorn North' ring, in proximity to each other in Ontario, Canada. The drier samples from the methane-sourced Bean ring were characterized by the abundance of bacteria from the classes Deltaproteobacteria and Gemmatimonadetes. Geobacter spp. and methanotrophs, such as Candidatus Methylomirabilis and Methylobacter, were highly abundant in these samples. The Thorn North ring, centred on an H2 S accumulation in groundwater, had wetter samples and its communities were dominated by the classes Alphaproteobacteria and Anaerolineae. This ring's microbial communities showed an overall higher microbial diversity supported by higher available free energy. For both rings, the species diversity was highest near the borders of the 20-30 m broad ring edges.
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Affiliation(s)
- Konstantin von Gunten
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Stewart M Hamilton
- Ministry of Northern Development and Mines, Sudbury Office, 159 Cedar Street, Sudbury, Ontario, P3E 6A5, Canada
| | - Cheng Zhong
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Camilla Nesbø
- University of Alberta, Biological Sciences, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Jiaying Li
- University of Alberta, Biological Sciences, 11455 Saskatchewan Drive, Edmonton, Alberta, T6G 2E9, Canada
| | - Karlis Muehlenbachs
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Kurt O Konhauser
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
| | - Daniel S Alessi
- University of Alberta, Earth and Atmospheric Sciences, 1-26 Earth Sciences Building, Edmonton, Alberta, T6G 2E3, Canada
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68
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Deep-sea anthropogenic macrodebris harbours rich and diverse communities of bacteria and archaea. PLoS One 2018; 13:e0206220. [PMID: 30485275 PMCID: PMC6261660 DOI: 10.1371/journal.pone.0206220] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 10/09/2018] [Indexed: 02/01/2023] Open
Abstract
The deep sea is the largest biome on earth, and microbes dominate in biomass and abundance. Anthropogenic litter is now almost ubiquitous in this biome, and its deposition creates new habitats and environments, including for microbial assemblages. With the ever increasing accumulation of this debris, it is timely to identify and describe the bacterial and archaeal communities that are able to form biofilms on macrodebris in the deep sea. Using 16S rRNA gene high throughput sequencing, we show for the first time the composition of bacteria and archaea on macrodebris collected from the deep sea. Our data suggest differences in the microbial assemblage composition across litter of different materials including metal, rubber, glass, fabric and plastic. These results imply that anthropogenic macrodebris provide diverse habitats for bacterial and archaeal biofilms and each may harbour distinct microbial communities.
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69
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Liu Q, Kämpf H, Bussert R, Krauze P, Horn F, Nickschick T, Plessen B, Wagner D, Alawi M. Influence of CO 2 Degassing on the Microbial Community in a Dry Mofette Field in Hartoušov, Czech Republic (Western Eger Rift). Front Microbiol 2018; 9:2787. [PMID: 30524401 PMCID: PMC6258768 DOI: 10.3389/fmicb.2018.02787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/30/2018] [Indexed: 01/13/2023] Open
Abstract
The Cheb Basin (CZ) is a shallow Neogene intracontinental basin filled with fluvial and lacustrine sediments that is located in the western part of the Eger Rift. The basin is situated in a seismically active area and is characterized by diffuse degassing of mantle-derived CO2 in mofette fields. The Hartoušov mofette field shows a daily CO2 flux of 23-97 tons of CO2 released over an area of 0.35 km2 and a soil gas concentration of up to 100% CO2. The present study aims to explore the geo-bio interactions provoked by the influence of elevated CO2 concentrations on the geochemistry and microbial community of soils and sediments. To sample the strata, two 3-m cores were recovered. One core stems from the center of the degassing structure, whereas the other core was taken 8 m from the ENE and served as an undisturbed reference site. The sites were compared regarding their geochemical features, microbial abundances, and microbial community structures. The mofette site is characterized by a low pH and high TOC/sulfate contents. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and their associated side effects on microbial processes. The abundance of microbes did not show a typical decrease with depth, indicating that the uprising CO2-rich fluid provides sufficient substrate for chemolithoautotrophic anaerobic microorganisms. Illumina MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences microbial composition and explains around 38.7% of the variance at the mofette site and 22.4% of the variance between the mofette site and the undisturbed reference site. Accordingly, acidophilic microorganisms (e.g., OTUs assigned to Acidobacteriaceae and Acidithiobacillus) displayed a much higher relative abundance at the mofette site than at the reference site. The microbial community at the mofette site is characterized by a high relative abundance of methanogens and taxa involved in sulfur cycling. The present study provides intriguing insights into microbial life and geo-bio interactions in an active seismic region dominated by emanating mantle-derived CO2-rich fluids, and thereby builds the basis for further studies, e.g., focusing on the functional repertoire of the communities. However, it remains open if the observed patterns can be generalized for different time-points or sites.
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Affiliation(s)
- Qi Liu
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Horst Kämpf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Potsdam, Germany
| | - Robert Bussert
- Institute of Applied Geosciences, Technische Universität Berlin, Berlin, Germany
| | - Patryk Krauze
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
| | - Tobias Nickschick
- Institute for Geophysics and Geology, University of Leipzig, Leipzig, Germany
| | - Birgit Plessen
- GFZ German Research Centre for Geosciences, Section Climate Dynamics and Landscape Evolution, Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany.,Institute of Earth and Environmental Science, University of Potsdam, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Potsdam, Germany
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70
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Ortmann AC, Brannock PM, Wang L, Halanych KM. River Flow Impacts Bacterial and Archaeal Community Structure in Surface Sediments in the Northern Gulf of Mexico. MICROBIAL ECOLOGY 2018; 76:941-953. [PMID: 29666882 DOI: 10.1007/s00248-018-1184-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/28/2018] [Indexed: 06/08/2023]
Abstract
Meiobenthic community structure in the northern Gulf of Mexico has been shown to be driven by geographical differences due to inshore-offshore gradients and location relative to river discharge. Samples collected along three transects spanning Mobile Bay, Alabama, showed significant differences in meiobenthic communities east of the bay compared to those sampled from the west. In contrast, analysis of bacterial and archaeal communities from the same sediment samples shows that the inshore-offshore gradient has minimal impact on their community structure. Significant differences in community structure were observed for Bacteria and Archaea between the east and west samples, but there was no difference in richness or diversity. Grouped by sediment type, higher richness was observed in silty samples compared to sandy samples. Significant differences were also observed among sediment types for community structure with bacteria communities in silty samples having more anaerobic sulfate reducers compared to aerobic heterotrophs, which had higher abundances in sandy sediments. This is likely due to increased organic matter in the silty sediments from the overlying river leading to low oxygen habitats. Most archaeal sequences represented poorly characterized high-level taxa, limiting interpretation of their distributions. Overlap between groups based on transect and sediment characteristics made determining which factor is more important in structuring bacterial and archaeal communities difficult. However, both factors are driven by discharge from the Mobile River. Although inshore-offshore gradients do not affect Bacteria or Archaea to the same extent as the meiobenthic communities, all three groups are strongly affected by sediment characteristics.
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Affiliation(s)
- Alice C Ortmann
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA.
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, B2Y 4A2, Canada.
| | - Pamela M Brannock
- Department of Biological Science, Auburn University, Auburn, AL, 36849, USA
- Department of Biology, Rollins College, Winter Park, FL, 32789, USA
| | - Lei Wang
- Department of Marine Sciences, University of South Alabama, Mobile, AL, 36688, USA
- Dauphin Island Sea Lab, Dauphin Island, AL, 36528, USA
| | - Kenneth M Halanych
- Department of Biological Science, Auburn University, Auburn, AL, 36849, USA
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71
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Long-term succession in a coal seam microbiome during in situ biostimulation of coalbed-methane generation. ISME JOURNAL 2018; 13:632-650. [PMID: 30323265 PMCID: PMC6461797 DOI: 10.1038/s41396-018-0296-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/18/2018] [Accepted: 09/20/2018] [Indexed: 11/24/2022]
Abstract
Despite the significance of biogenic methane generation in coal beds, there has never been a systematic long-term evaluation of the ecological response to biostimulation for enhanced methanogenesis in situ. Biostimulation tests in a gas-free coal seam were analysed over 1.5 years encompassing methane production, cell abundance, planktonic and surface associated community composition and chemical parameters of the coal formation water. Evidence is presented that sulfate reducing bacteria are energy limited whilst methanogenic archaea are nutrient limited. Methane production was highest in a nutrient amended well after an oxic preincubation phase to enhance coal biofragmentation (calcium peroxide amendment). Compound-specific isotope analyses indicated the predominance of acetoclastic methanogenesis. Acetoclastic methanogenic archaea of the Methanosaeta and Methanosarcina genera increased with methane concentration. Acetate was the main precursor for methanogenesis, however more acetate was consumed than methane produced in an acetate amended well. DNA stable isotope probing showed incorporation of 13C-labelled acetate into methanogenic archaea, Geobacter species and sulfate reducing bacteria. Community characterisation of coal surfaces confirmed that methanogenic archaea make up a substantial proportion of coal associated biofilm communities. Ultimately, methane production from a gas-free subbituminous coal seam was stimulated despite high concentrations of sulfate and sulfate-reducing bacteria in the coal formation water. These findings provide a new conceptual framework for understanding the coal reservoir biosphere.
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72
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Rinta-Kanto J, Pehkonen K, Sinkko H, Tamminen M, Timonen S. Archaeaare prominent members of the prokaryotic communities colonizing common forest mushrooms. Can J Microbiol 2018; 64:716-726. [DOI: 10.1139/cjm-2018-0035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, the abundance and composition of prokaryotic communities associated with the inner tissue of fruiting bodies of Suillus bovinus, Boletus pinophilus, Cantharellus cibarius, Agaricus arvensis, Lycoperdon perlatum, and Piptoporus betulinus were analyzed using culture-independent methods. Our findings indicate that archaea and bacteria colonize the internal tissues of all investigated specimens and that archaea are prominent members of the prokaryotic community. The ratio of archaeal 16S rRNA gene copy numbers to those of bacteria was >1 in the fruiting bodies of four out of six fungal species included in the study. The largest proportion of archaeal 16S rRNA gene sequences belonged to thaumarchaeotal classes Terrestrial group, Miscellaneous Crenarchaeotic Group (MCG), and Thermoplasmata. Bacterial communities showed characteristic compositions in each fungal species. Bacterial classes Gammaproteobacteria, Actinobacteria, Bacilli, and Clostridia were prominent among communities in fruiting body tissues. Bacterial populations in each fungal species had different characteristics. The results of this study imply that fruiting body tissues are an important habitat for abundant and diverse populations of archaea and bacteria.
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Affiliation(s)
- J.M. Rinta-Kanto
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
| | - K. Pehkonen
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
| | - H. Sinkko
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
| | - M.V. Tamminen
- Department of Biology, University Hill, 20014 University of Turku, Finland
| | - S. Timonen
- University of Helsinki, Department of Microbiology, Viikinkaari 9, 00014 Helsinki, Finland
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73
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Liu X, Pan J, Liu Y, Li M, Gu JD. Diversity and distribution of Archaea in global estuarine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 637-638:349-358. [PMID: 29753224 DOI: 10.1016/j.scitotenv.2018.05.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/01/2018] [Accepted: 05/02/2018] [Indexed: 05/12/2023]
Abstract
Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.
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Affiliation(s)
- Xiaobo Liu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, People's Republic of China.
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, People's Republic of China; State Key Laboratory in Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, People's Republic of China.
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74
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Cheung MK, Wong CK, Chu KH, Kwan HS. Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments. Sci Rep 2018; 8:14397. [PMID: 30258074 PMCID: PMC6158284 DOI: 10.1038/s41598-018-32529-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/06/2018] [Indexed: 01/04/2023] Open
Abstract
Bacteria, archaea and fungi play crucial roles in wetland biogeochemical processes. However, little is known about their community structure, dynamics and interactions in subtropical coastal wetlands. Here, we examined communities of the three kingdoms in mangrove and mudflat sediments of a subtropical coastal wetland using Ion Torrent amplicon sequencing and co-occurrence network analysis. Bacterial, archaeal and fungal communities comprised mainly of members from the phyla Proteobacteria and Bacteroidetes, Bathyarchaeota and Euryarchaeota, and Ascomycota, respectively. Species richness and Shannon diversity were highest in bacteria, followed by archaea and were lowest in fungi. Distinct spatiotemporal patterns were observed, with bacterial and fungal communities varying, to different extent, between wet and dry seasons and between mangrove and mudflat, and archaeal community remaining relatively stable between seasons and regions. Redundancy analysis revealed temperature as the major driver of the seasonal patterns of bacterial and fungal communities but also highlighted the importance of interkingdom biotic factors in shaping the community structure of all three kingdoms. Potential ecological interactions and putative keystone taxa were identified based on co-occurrence network analysis. These findings facilitate current understanding of the microbial ecology of subtropical coastal wetlands and provide a basis for better modelling of ecological processes in this important ecosystem.
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Affiliation(s)
- Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chong Kim Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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75
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Pala C, Molari M, Nizzoli D, Bartoli M, Viaroli P, Manini E. Environmental Drivers Controlling Bacterial and Archaeal Abundance in the Sediments of a Mediterranean Lagoon Ecosystem. Curr Microbiol 2018; 75:1147-1155. [PMID: 29766233 PMCID: PMC6096605 DOI: 10.1007/s00284-018-1503-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/27/2018] [Indexed: 02/02/2023]
Abstract
The environmental factors controlling the abundance of Bacteria and Archaea in lagoon ecosystems are poorly understood. Here, an integrated physico-chemical, biogeochemical, and microbiological survey was applied in the Sacca di Goro lagoon (Po River Delta, Italy) to investigate the variation of bacterial and archaeal abundance, as assessed by Fluorescence In Situ Hybridization, along winter and summer environmental gradients. We hypothesised that bacterial and archaeal cells respond differentially to physico-chemical parameters of the sediment, which can be manifested in variations of total cells number. Our results suggest that Archaea are an important component of microbial communities (up to 20%) and they are also quite constant along the sediment depth investigated, while Bacteria tend to decrease in the subsurface sediments. The abiotic (i.e. temperature, ammonium, pH) and trophic parameters (i.e. chlorophyll a) explain differentially the variations of bacterial and archaeal distribution, and raise interesting questions about the ecological significance of the microbial composition in this area.
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Affiliation(s)
- Claudia Pala
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
- Institute for Marine Science - ISMAR, National Research Council of Italy - CNR, Ancona, Italy.
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
| | - Massimiliano Molari
- Institute for Marine Science - ISMAR, National Research Council of Italy - CNR, Ancona, Italy
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Daniele Nizzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Bartoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Pierluigi Viaroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Elena Manini
- Institute for Marine Science - ISMAR, National Research Council of Italy - CNR, Ancona, Italy
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76
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Lavergne C, Hugoni M, Dupuy C, Agogué H. First evidence of the presence and activity of archaeal C3 group members in an Atlantic intertidal mudflat. Sci Rep 2018; 8:11790. [PMID: 30087413 PMCID: PMC6081377 DOI: 10.1038/s41598-018-30222-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/18/2018] [Indexed: 11/09/2022] Open
Abstract
The phylogenetic assignment of archaeal communities is constantly evolving, and the recent discovery of new phyla that grouped into superphyla has provided novel insights into archaeal ecology and evolution in ecosystems. In intertidal sediments, archaea are known to be involved in key functional processes such as organic matter turnover, but the ecological relevance of the rarest archaeal groups is poorly investigated, due partly to the lack of cultivated members. The high resolution of microbial diversity provided by high-throughput sequencing technologies now allows the rare biosphere to be described. In this work, we focused on the archaeal C3 group, showing that this phylum is not only present (at the DNA level) independently of sediment depth but also active (at the RNA level) in specific sediment niches depending on vertical physicochemical gradients. Moreover, we highlight the ambiguous phylogenetic affiliation of this group, indicating the need of further research to get new insights into the role of the C3 group.
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Affiliation(s)
- Céline Lavergne
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France. .,Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica Valparaíso, Avenida Brasil 2085, Valparaíso, Chile.
| | - Mylène Hugoni
- Université Lyon 1 - UMR CNRS 5557/INRA 1418, Ecologie Microbienne, Villeurbanne, France
| | - Christine Dupuy
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - Hélène Agogué
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
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77
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Successive transitory distribution of Thaumarchaeota and partitioned distribution of Bathyarchaeota from the Pearl River estuary to the northern South China Sea. Appl Microbiol Biotechnol 2018; 102:8035-8048. [PMID: 29946932 DOI: 10.1007/s00253-018-9147-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 05/05/2018] [Accepted: 05/23/2018] [Indexed: 01/09/2023]
Abstract
Thaumarchaeota and Bathyarchaeota (formerly named Miscellaneous Crenarchaeotal Group, MCG) are globally occurring archaea playing potential roles in nitrogen and carbon cycling, especially in marine benthic biogeochemical cycle. Information on their distributional and compositional patterns could provide critical clues to further delineate their physiological and biochemical characteristics. Profiles of thaumarchaeotal and the total archaeal community in the northern South China Sea surface sediments revealed a successively transitional pattern of Thaumarchaeota composition using MiSeq sequencing. Shallow-sea sediment enriched phylotypes decreased gradually along the slope from estuarine and coastal marine region to the deep-sea, while deep-sea sediment enriched phylotypes showed a trend of increasing. Proportion of Thaumarchaeota within the total archaea increased with seawater depth. Phylotypes enriched in shallow- and deep-sea sediments were affiliated to OTUs originated from similar niches, suggesting that physiological adaption not geographical distance shaped the distribution of Thaumarchaeota lineages. Quantitative PCR also depicted a successive decrease of thaumarchaeotal 16S rRNA gene abundance from the highest at shallow-sea sites E708S and E709S (2.57 × 106 and 2.73 × 106 gene copies/g of dry sediment) to the lowest at deep-sea sites E525S and E407S (1.97 × 106 and 2.14 × 106 gene copies/g of dry sediment). Both of the abundance fractions of Bathyarchaeota subgroups (including subgroups 1, 6, 8, 10, 13, 15, 17, and ungrouped Bathyarchaeota) and the total Bathyarchaeota in the total archaea showed a negative distribution to seawater depth. Partitioned distribution of Bathyarchaeota fraction in the total archaea is documented for the first time in this study, and the shallow- and deep-sea Bathyarchaeota could account for 17.8 and 0.8%, respectively, on average. Subgroups 6 and 8, enriched subgroups in shallow-sea sediments, largely explained this partitioned distribution pattern according to seawater depth. Their prevalence in shallow-sea and suboxic estuarine sediments rather than deep-sea sediments hints that their metabolic properties of carbon metabolism are adapted to carbon substrates in these environments.
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78
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Liu X, Li M, Castelle CJ, Probst AJ, Zhou Z, Pan J, Liu Y, Banfield JF, Gu JD. Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages. MICROBIOME 2018; 6:102. [PMID: 29884244 PMCID: PMC5994134 DOI: 10.1186/s40168-018-0488-2] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/25/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND As a recently discovered member of the DPANN superphylum, Woesearchaeota account for a wide diversity of 16S rRNA gene sequences, but their ecology, evolution, and metabolism remain largely unknown. RESULTS Here, we assembled 133 global clone libraries/studies and 19 publicly available genomes to profile these patterns for Woesearchaeota. Phylogenetic analysis shows a high diversity with 26 proposed subgroups for this recently discovered archaeal phylum, which are widely distributed in different biotopes but primarily in inland anoxic environments. Ecological patterns analysis and ancestor state reconstruction for specific subgroups reveal that oxic status of the environments is the key factor driving the distribution and evolutionary diversity of Woesearchaeota. A selective distribution to different biotopes and an adaptive colonization from anoxic to oxic environments can be proposed and supported by evidence of the presence of ferredoxin-dependent pathways in the genomes only from anoxic biotopes but not from oxic biotopes. Metabolic reconstructions support an anaerobic heterotrophic lifestyle with conspicuous metabolic deficiencies, suggesting the requirement for metabolic complementarity with other microbes. Both lineage abundance distribution and co-occurrence network analyses across diverse biotopes confirmed metabolic complementation and revealed a potential syntrophic relationship between Woesearchaeota and methanogens, which is supported by metabolic modeling. If correct, Woesearchaeota may impact methanogenesis in inland ecosystems. CONCLUSIONS The findings provide an ecological and evolutionary framework for Woesearchaeota at a global scale and indicate their potential ecological roles, especially in methanogenesis.
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Affiliation(s)
- Xiaobo Liu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518000, China.
| | - Cindy J Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, 336 Hilgard Hall, Berkeley, CA, 94720, USA
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, 336 Hilgard Hall, Berkeley, CA, 94720, USA
- Group for Aquatic Microbial Ecology (GAME), Biofilm Center, Department of Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Zhichao Zhou
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518000, China
| | - Yang Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518000, China
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, 336 Hilgard Hall, Berkeley, CA, 94720, USA
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, 999077, China.
- State Key Laboratory in Marine Pollution, City University of Hong Kong, Hong Kong, 999077, China.
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79
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Matheus Carnevali PB, Herbold CW, Hand KP, Priscu JC, Murray AE. Distinct Microbial Assemblage Structure and Archaeal Diversity in Sediments of Arctic Thermokarst Lakes Differing in Methane Sources. Front Microbiol 2018; 9:1192. [PMID: 29930542 PMCID: PMC6000721 DOI: 10.3389/fmicb.2018.01192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/16/2018] [Indexed: 12/04/2022] Open
Abstract
Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH4) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH4-producing organisms (methanogens) would reflect the distribution of CH4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH4-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH4-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.
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Affiliation(s)
| | - Craig W Herbold
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Kevin P Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - John C Priscu
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
| | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
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80
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Abstract
Members of the archaeal phylum Bathyarchaeota are among the most abundant microorganisms on Earth. Although versatile metabolic capabilities such as acetogenesis, methanogenesis, and fermentation have been suggested for bathyarchaeotal members, no direct confirmation of these metabolic functions has been achieved through growth of Bathyarchaeota in the laboratory. Here we demonstrate, on the basis of gene-copy numbers and probing of archaeal lipids, the growth of Bathyarchaeota subgroup Bathy-8 in enrichments of estuarine sediments with the biopolymer lignin. Other organic substrates (casein, oleic acid, cellulose, and phenol) did not significantly stimulate growth of Bathyarchaeota Meanwhile, putative bathyarchaeotal tetraether lipids incorporated 13C from 13C-bicarbonate only when added in concert with lignin. Our results are consistent with organoautotrophic growth of a bathyarchaeotal group with lignin as an energy source and bicarbonate as a carbon source and shed light into the cycling of one of Earth's most abundant biopolymers in anoxic marine sediment.
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81
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Schuelke T, Pereira TJ, Hardy SM, Bik HM. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Mol Ecol 2018; 27:1930-1951. [DOI: 10.1111/mec.14539] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Taruna Schuelke
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Tiago José Pereira
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Sarah M. Hardy
- School of Fisheries and Ocean Sciences; University of Alaska; Fairbanks AK USA
| | - Holly M. Bik
- Department of Nematology; University of California, Riverside; Riverside CA USA
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82
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Frouin E, Bes M, Ollivier B, Quéméneur M, Postec A, Debroas D, Armougom F, Erauso G. Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems. Front Microbiol 2018; 9:102. [PMID: 29467733 PMCID: PMC5808123 DOI: 10.3389/fmicb.2018.00102] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/17/2018] [Indexed: 01/21/2023] Open
Abstract
The Bay of Prony, South of New Caledonia, represents a unique serpentinite-hosted hydrothermal field due to its coastal situation. It harbors both submarine and intertidal active sites, discharging hydrogen- and methane-rich alkaline fluids of low salinity and mild temperature through porous carbonate edifices. In this study, we have extensively investigated the bacterial and archaeal communities inhabiting the hydrothermal chimneys from one intertidal and three submarine sites by 16S rRNA gene amplicon sequencing. We show that the bacterial community of the intertidal site is clearly distinct from that of the submarine sites with species distribution patterns driven by only a few abundant populations, affiliated to the Chloroflexi and Proteobacteria phyla. In contrast, the distribution of archaeal taxa seems less site-dependent, as exemplified by the co-occurrence, in both submarine and intertidal sites, of two dominant phylotypes of Methanosarcinales previously thought to be restricted to serpentinizing systems, either marine (Lost City Hydrothermal Field) or terrestrial (The Cedars ultrabasic springs). Over 70% of the phylotypes were rare and included, among others, all those affiliated to candidate divisions. We finally compared the distribution of bacterial and archaeal phylotypes of Prony Hydrothermal Field with those of five previously studied serpentinizing systems of geographically distant sites. Although sensu stricto no core microbial community was identified, a few uncultivated lineages, notably within the archaeal order Methanosarcinales and the bacterial class Dehalococcoidia (the candidate division MSBL5) were exclusively found in a few serpentinizing systems while other operational taxonomic units belonging to the orders Clostridiales, Thermoanaerobacterales, or the genus Hydrogenophaga, were abundantly distributed in several sites. These lineages may represent taxonomic signatures of serpentinizing ecosystems. These findings extend our current knowledge of the microbial diversity inhabiting serpentinizing systems and their biogeography.
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Affiliation(s)
- Eléonore Frouin
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Méline Bes
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Bernard Ollivier
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Marianne Quéméneur
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Anne Postec
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Didier Debroas
- CNRS UMR 6023, Laboratoire "Microorganismes - Génome et Environnement", Université Clermont Auvergne, Clermont-Ferrand, France
| | - Fabrice Armougom
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Gaël Erauso
- Aix-Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
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83
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Lavergne C, Hugoni M, Hubas C, Debroas D, Dupuy C, Agogué H. Diel Rhythm Does Not Shape the Vertical Distribution of Bacterial and Archaeal 16S rRNA Transcript Diversity in Intertidal Sediments: a Mesocosm Study. MICROBIAL ECOLOGY 2018; 75:364-374. [PMID: 28779296 DOI: 10.1007/s00248-017-1048-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Accepted: 07/20/2017] [Indexed: 06/07/2023]
Abstract
In intertidal sediments, circadian oscillations (i.e., tidal and diel rhythms) and/or depth may affect prokaryotic activity. However, it is difficult to distinguish the effect of each single force on active community changes in these natural and complex intertidal ecosystems. Therefore, we developed a tidal mesocosm to control the tidal rhythm and test whether diel fluctuation or sediment depth influence active prokaryotes in the top 10 cm of sediment. Day- and nighttime emersions were compared as they are expected to display contrasting conditions through microphytobenthic activity in five different sediment layers. A multiple factor analysis revealed that bacterial and archaeal 16S ribosomal RNA (rRNA) transcript diversity assessed by pyrosequencing was similar between day and night emersions. Potentially active benthic Bacteria were highly diverse and influenced by chlorophyll a and phosphate concentrations. While in oxic and suboxic sediments, Thaumarchaeota Marine Group I (MGI) was the most active archaeal phylum, suggesting the importance of the nitrogen cycle in muddy sediments, in anoxic sediments, the mysterious archaeal C3 group dominated the community. This work highlighted that active prokaryotes organize themselves vertically within sediments independently of diel fluctuations suggesting adaptation to physicochemical-specific conditions associated with sediment depth.
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Affiliation(s)
- C Lavergne
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France.
- School of Biochemical Engineering, Pontificia Universidad Católica Valparaíso, Avenida Brasil, 2085, Valparaíso, Chile.
| | - M Hugoni
- CNRS, UMR5557 Ecologie Microbienne, Université Lyon 1, INRA, UMR1418, 69220, Villeurbanne Cedex, France
| | - C Hubas
- Muséum National d'Histoire Naturelle, UMR BOREA, Sorbonne Universités, UPMC Univ Paris 6, CNRS 7208, IRD 207, UCN, UA, Station de Biologie Marine, 29900, Concarneau, France
| | - D Debroas
- Clermont Université, Université Blaise Pascal, LMGE, BP 10448, 63000, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, 63171, Aubière, France
| | - C Dupuy
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
| | - H Agogué
- Université de La Rochelle - CNRS, UMR 7266, LIENSs, 2 rue Olympe de Gouges, 17000, La Rochelle, France
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84
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Maus I, Rumming M, Bergmann I, Heeg K, Pohl M, Nettmann E, Jaenicke S, Blom J, Pühler A, Schlüter A, Sczyrba A, Klocke M. Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:167. [PMID: 29951113 PMCID: PMC6010159 DOI: 10.1186/s13068-018-1162-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/01/2018] [Indexed: 05/13/2023]
Abstract
BACKGROUND Previous studies on the Miscellaneous Crenarchaeota Group, recently assigned to the novel archaeal phylum Bathyarchaeota, reported on the dominance of these Archaea within the anaerobic carbohydrate cycle performed by the deep marine biosphere. For the first time, members of this phylum were identified also in mesophilic and thermophilic biogas-forming biofilms and characterized in detail. RESULTS Metagenome shotgun libraries of biofilm microbiomes were sequenced using the Illumina MiSeq system. Taxonomic classification revealed that between 0.1 and 2% of all classified sequences were assigned to Bathyarchaeota. Individual metagenome assemblies followed by genome binning resulted in the reconstruction of five metagenome-assembled genomes (MAGs) of Bathyarchaeota. MAGs were estimated to be 65-92% complete, ranging in their genome sizes from 1.1 to 2.0 Mb. Phylogenetic classification based on core gene sets confirmed their placement within the phylum Bathyarchaeota clustering as a separate group diverging from most of the recently known Bathyarchaeota clusters. The genetic repertoire of these MAGs indicated an energy metabolism based on carbohydrate and amino acid fermentation featuring the potential for extracellular hydrolysis of cellulose, cellobiose as well as proteins. In addition, corresponding transporter systems were identified. Furthermore, genes encoding enzymes for the utilization of carbon monoxide and/or carbon dioxide via the Wood-Ljungdahl pathway were detected. CONCLUSIONS For the members of Bathyarchaeota detected in the biofilm microbiomes, a hydrolytic lifestyle is proposed. This is the first study indicating that Bathyarchaeota members contribute presumably to hydrolysis and subsequent fermentation of organic substrates within biotechnological biogas production processes.
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Affiliation(s)
- Irena Maus
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Madis Rumming
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Ingo Bergmann
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Kathrin Heeg
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Marcel Pohl
- Biochemical Conversion Department, Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany
| | - Edith Nettmann
- Urban Water Management and Environmental Engineering, Faculty of Civil and Environmental Engineering, Ruhr University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Sebastian Jaenicke
- Dept. Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Jochen Blom
- Dept. Bioinformatics and Systems Biology, Justus-Liebig University Gießen, Heinrich-Buff-Ring 58, 35392 Giessen, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Alexander Sczyrba
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany
- Computational Metagenomics, Faculty of Technology, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Michael Klocke
- Dept. Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
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85
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Mora-Ruiz MDR, Cifuentes A, Font-Verdera F, Pérez-Fernández C, Farias ME, González B, Orfila A, Rosselló-Móra R. Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments. Syst Appl Microbiol 2017; 41:139-150. [PMID: 29352612 DOI: 10.1016/j.syapm.2017.10.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 01/21/2023]
Abstract
Microorganisms are globally distributed but new evidence shows that the microbial structure of their communities can vary due to geographical location and environmental parameters. In this study, 50 samples including brines and sediments from Europe, Spanish-Atlantic and South America were analysed by applying the operational phylogenetic unit (OPU) approach in order to understand whether microbial community structures in hypersaline environments exhibited biogeographical patterns. The fine-tuned identification of approximately 1000 OPUs (almost equivalent to "species") using multivariate analysis revealed regionally distinct taxa compositions. This segregation was more diffuse at the genus level and pointed to a phylogenetic and metabolic redundancy at the higher taxa level, where their different species acquired distinct advantages related to the regional physicochemical idiosyncrasies. The presence of previously undescribed groups was also shown in these environments, such as Parcubacteria, or members of Nanohaloarchaeota in anaerobic hypersaline sediments. Finally, an important OPU overlap was observed between anoxic sediments and their overlaying brines, indicating versatile metabolism for the pelagic organisms.
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Affiliation(s)
- M Del R Mora-Ruiz
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain.
| | - A Cifuentes
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
| | - F Font-Verdera
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
| | - C Pérez-Fernández
- Environmental Microbiology Laboratory, Puerto Rico University, Rio Piedras campus, Puerto Rico
| | - M E Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - B González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez - Center of Applied Ecology and Sustainability, Santiago, Chile
| | - A Orfila
- Marine Technology and Operational Oceanography Department, IMEDEA (CSIC-UIB), Esporles, Spain
| | - R Rosselló-Móra
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
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86
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Estimating Population Turnover Rates by Relative Quantification Methods Reveals Microbial Dynamics in Marine Sediment. Appl Environ Microbiol 2017; 84:AEM.01443-17. [PMID: 29054869 DOI: 10.1128/aem.01443-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/09/2017] [Indexed: 11/20/2022] Open
Abstract
The difficulty involved in quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina, USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentrations consistent with the predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, which stands for "fraction of read abundance times cells"), to estimate the population turnover rates of uncultured clades. Most 16S rRNA reads were from deeply branching uncultured groups, and ∼98% of 16S rRNA genes did not abruptly shift in relative abundance when sulfate reduction gave way to methanogenesis. Uncultured Methanomicrobiales and Methanosarcinales increased at the onset of methanogenesis with population turnover times estimated from qPCR at 9.7 ± 3.9 and 12.6 ± 4.1 days, respectively. These were consistent with FRAxC turnover times of 9.4 ± 5.8 and 9.2 ± 3.5 days, respectively. Uncultured Syntrophaceae, which are possibly fermentative syntrophs of methanogens, and uncultured Kazan-3A-21 archaea also increased at the onset of methanogenesis, with FRAxC turnover times of 14.7 ± 6.9 and 10.6 ± 3.6 days. Kazan-3A-21 may therefore either perform methanogenesis or form a fermentative syntrophy with methanogens. Three genera of sulfate-reducing bacteria, Desulfovibrio, Desulfobacter, and Desulfobacterium, increased in the first 19 days before declining rapidly during sulfate reduction. We conclude that population turnover times on the order of days can be measured robustly in organic-rich marine sediment, and the transition from sulfate-reducing to methanogenic conditions stimulates growth only in a few clades directly involved in methanogenesis, rather than in the whole microbial community.IMPORTANCE Many microbes cannot be isolated in pure culture to determine their preferential growth conditions and predict their response to changing environmental conditions. We created a microcosm of marine sediments that allowed us to simulate a diagenetic profile using a temporal analog for depth. This allowed for the observation of the microbial community population dynamics caused by the natural shift from sulfate reduction to methanogenesis. Our research provides evidence for the population dynamics of uncultured microbes as well as the application of a novel method of turnover rate analysis for individual taxa within a mixed incubation, FRAxC, which stands for "fraction of read abundance times cells," which was verified by quantitative PCR. This allows for the calculation of population turnover times for microbes in a natural setting and the identification of uncultured clades involved in geochemical processes.
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87
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Krauze P, Kämpf H, Horn F, Liu Q, Voropaev A, Wagner D, Alawi M. Microbiological and Geochemical Survey of CO 2-Dominated Mofette and Mineral Waters of the Cheb Basin, Czech Republic. Front Microbiol 2017; 8:2446. [PMID: 29321765 PMCID: PMC5732176 DOI: 10.3389/fmicb.2017.02446] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/24/2017] [Indexed: 02/01/2023] Open
Abstract
The Cheb Basin (NW Bohemia, Czech Republic) is a shallow, neogene intracontinental basin. It is a non-volcanic region which features frequent earthquake swarms and large-scale diffuse degassing of mantle-derived CO2 at the surface that occurs in the form of CO2-rich mineral springs and wet and dry mofettes. So far, the influence of CO2 degassing onto the microbial communities has been studied for soil environments, but not for aquatic systems. We hypothesized, that deep-trenching CO2 conduits interconnect the subsurface with the surface. This admixture of deep thermal fluids should be reflected in geochemical parameters and in the microbial community compositions. In the present study four mineral water springs and two wet mofettes were investigated through an interdisciplinary survey. The waters were acidic and differed in terms of organic carbon and anion/cation concentrations. Element geochemical and isotope analyses of fluid components were used to verify the origin of the fluids. Prokaryotic communities were characterized through quantitative PCR and Illumina 16S rRNA gene sequencing. Putative chemolithotrophic, anaerobic and microaerophilic organisms connected to sulfur (e.g., Sulfuricurvum, Sulfurimonas) and iron (e.g., Gallionella, Sideroxydans) cycling shaped the core community. Additionally, CO2-influenced waters form an ecosystem containing many taxa that are usually found in marine or terrestrial subsurface ecosystems. Multivariate statistics highlighted the influence of environmental parameters such as pH, Fe2+ concentration and conductivity on species distribution. The hydrochemical and microbiological survey introduces a new perspective on mofettes. Our results support that mofettes are either analogs or rather windows into the deep biosphere and furthermore enable access to deeply buried paleo-sediments.
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Affiliation(s)
- Patryk Krauze
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Horst Kämpf
- GFZ German Research Centre for Geosciences, Section 3.2 Organic Geochemistry, Potsdam, Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
| | - Qi Liu
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
| | | | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany.,Institute for Earth and Environmental Sciences, University of Potsdam, Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Section 5.3 Geomicrobiology, Potsdam, Germany
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88
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Suter EA, Pachiadaki M, Taylor GT, Astor Y, Edgcomb VP. Free‐living chemoautotrophic and particle‐attached heterotrophic prokaryotes dominate microbial assemblages along a pelagic redox gradient. Environ Microbiol 2017; 20:693-712. [DOI: 10.1111/1462-2920.13997] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Elizabeth A. Suter
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
- Department of Biological SciencesWagner CollegeStaten Island NY 10301 USA
| | - Maria Pachiadaki
- Woods Hole Oceanographic InstitutionWoods Hole MA USA
- Bigelow Laboratory for Ocean SciencesEast Boothbay ME USA
| | - Gordon T. Taylor
- School of Marine and Atmospheric SciencesStony Brook UniversityStony Brook NY USA
| | - Yrene Astor
- Fundación La Salle de Ciencias Naturales, EDIMARPorlamar Nueva Esparta Venezuela
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89
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Farias ME, Rasuk MC, Gallagher KL, Contreras M, Kurth D, Fernandez AB, Poiré D, Novoa F, Visscher PT. Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile. PLoS One 2017; 12:e0186867. [PMID: 29140980 PMCID: PMC5687714 DOI: 10.1371/journal.pone.0186867] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 10/09/2017] [Indexed: 11/19/2022] Open
Abstract
Benthic microbial ecosystems of Laguna La Brava, Salar de Atacama, a high altitude hypersaline lake, were characterized in terms of bacterial and archaeal diversity, biogeochemistry, (including O2 and sulfide depth profiles and mineralogy), and physicochemical characteristics. La Brava is one of several lakes in the Salar de Atacama where microbial communities are growing in extreme conditions, including high salinity, high solar insolation, and high levels of metals such as lithium, arsenic, magnesium, and calcium. Evaporation creates hypersaline conditions in these lakes and mineral precipitation is a characteristic geomicrobiological feature of these benthic ecosystems. In this study, the La Brava non-lithifying microbial mats, microbialites, and rhizome-associated concretions were compared to each other and their diversity was related to their environmental conditions. All the ecosystems revealed an unusual community where Euryarchaeota, Crenarchaeota, Acetothermia, Firmicutes and Planctomycetes were the most abundant groups, and cyanobacteria, typically an important primary producer in microbial mats, were relatively insignificant or absent. This suggests that other microorganisms, and possibly novel pathways unique to this system, are responsible for carbon fixation. Depth profiles of O2 and sulfide showed active production and respiration. The mineralogy composition was calcium carbonate (as aragonite) and increased from mats to microbialites and rhizome-associated concretions. Halite was also present. Further analyses were performed on representative microbial mats and microbialites by layer. Different taxonomic compositions were observed in the upper layers, with Archaea dominating the non-lithifying mat, and Planctomycetes the microbialite. The bottom layers were similar, with Euryarchaeota, Crenarchaeota and Planctomycetes as dominant phyla. Sequences related to Cyanobacteria were very scarce. These systems may contain previously uncharacterized community metabolisms, some of which may be contributing to net mineral precipitation. Further work on these sites might reveal novel organisms and metabolisms of biotechnological interest.
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Affiliation(s)
- Maria Eugenia Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
- * E-mail:
| | - Maria Cecilia Rasuk
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Kimberley L. Gallagher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | | | - Daniel Kurth
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Ana Beatriz Fernandez
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-Tucumán, CONICET, Tucumán, Argentina
| | - Daniel Poiré
- Centro de Investigaciones Geológicas, Universidad Nacional de La Plata-Conicet, La Plata, Argentina
| | - Fernando Novoa
- Centro de Ecología Aplicada (CEA), Ñuñoa, Santiago, Chile
| | - Pieter T. Visscher
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
- Australian Centre for Astrobiology, University of New South Wales, Sydney, New South Wales, Australia
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90
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Vaksmaa A, van Alen TA, Ettwig KF, Lupotto E, Valè G, Jetten MSM, Lüke C. Stratification of Diversity and Activity of Methanogenic and Methanotrophic Microorganisms in a Nitrogen-Fertilized Italian Paddy Soil. Front Microbiol 2017; 8:2127. [PMID: 29180985 PMCID: PMC5693880 DOI: 10.3389/fmicb.2017.02127] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/18/2017] [Indexed: 11/30/2022] Open
Abstract
Paddy fields are important ecosystems, as rice is the primary food source for about half of the world's population. Paddy fields are impacted by nitrogen fertilization and are a major anthropogenic source of methane. Microbial diversity and methane metabolism were investigated in the upper 60 cm of a paddy soil by qPCR, 16S rRNA gene amplicon sequencing and anoxic 13C-CH4 turnover with a suite of electron acceptors. The bacterial community consisted mainly of Acidobacteria, Chloroflexi, Proteobacteria, Planctomycetes, and Actinobacteria. Among archaea, Euryarchaeota and Bathyarchaeota dominated over Thaumarchaeota in the upper 30 cm of the soil. Bathyarchaeota constituted up to 45% of the total archaeal reads in the top 5 cm. In the methanogenic community, Methanosaeta were generally more abundant than the versatile Methanosarcina. The measured maximum methane production rate was 444 nmol gdwh-1, and the maximum rates of nitrate-, nitrite-, and iron-dependent anaerobic oxidation of methane (AOM) were 57 nmol, 55 nmol, and 56 nmol gdwh-1, respectively, at different depths. qPCR revealed a higher abundance of 'Candidatus Methanoperedens nitroreducens' than methanotrophic NC10 phylum bacteria at all depths, except at 60 cm. These results demonstrate that there is substantial potential for AOM in fertilized paddy fields, with 'Candidatus Methanoperedens nitroreducens' archaea as a potential important contributor.
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Affiliation(s)
- Annika Vaksmaa
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Theo A. van Alen
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Katharina F. Ettwig
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Elisabetta Lupotto
- Research Centre for Food and Nutrition, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Rome, Italy
| | - Giampiero Valè
- Research Centre for Cereal and Industrial Crops, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria, Vercelli, Italy
| | - Mike S. M. Jetten
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Claudia Lüke
- Department of Microbiology – Institute of Water and Wetland Research, Radboud University, Nijmegen, Netherlands
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91
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Compte-Port S, Subirats J, Fillol M, Sànchez-Melsió A, Marcé R, Rivas-Ruiz P, Rosell-Melé A, Borrego CM. Abundance and Co-Distribution of Widespread Marine Archaeal Lineages in Surface Sediments of Freshwater Water Bodies across the Iberian Peninsula. MICROBIAL ECOLOGY 2017; 74:776-787. [PMID: 28508926 DOI: 10.1007/s00248-017-0989-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/23/2017] [Indexed: 06/07/2023]
Abstract
Archaea inhabiting marine and freshwater sediments have a relevant role in organic carbon mineralization, affecting carbon fluxes at a global scale. Despite current evidences suggesting that freshwater sediments largely contribute to this process, few large-scale surveys have been addressed to uncover archaeal diversity and abundance in freshwater sedimentary habitats. In this work, we quantified and high-throughput sequenced the archaeal 16S rRNA gene from surficial sediments collected in 21 inland waterbodies across the Iberian Peninsula differing in typology and trophic status. Whereas methanogenic groups were dominant in most of the studied systems, especially in organic-rich sediments, archaea affiliated to widespread marine lineages (the Bathyarchaeota and the Thermoplasmata) were also ubiquitous and particularly abundant in euxinic sediments. In these systems, Bathyarchaeota communities were dominated by subgroups Bathyarchaeota-6 (87.95 ± 12.71%) and Bathyarchaeota-15 (8.17 ± 9.2%) whereas communities of Thermoplasmata were mainly composed of members of the order Thermoplasmatales. Our results also indicate that Archaea accounted for a minor fraction of sedimentary prokaryotes despite remarkable exceptions in reservoirs and some stratified lakes. Copy numbers of archaeal and bathyarchaeotal 16S rRNA genes were significantly different when compared according to system type (i.e., lakes, ponds, and reservoirs), but no differences were obtained when compared according to their trophic status (from oligotrophy to eutrophy). Interestingly, we obtained significant correlations between the abundance of reads (Spearman r = 0.5, p = 0.021) and OTU richness (Spearman r = 0.677, p < 0.001) of Bathyarchaeota and Thermoplasmata across systems, reinforcing the hypothesis of a potential syntrophic interaction between members of both lineages.
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Affiliation(s)
- Sergi Compte-Port
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Jèssica Subirats
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Mireia Fillol
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Alexandre Sànchez-Melsió
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Rafael Marcé
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain
| | - Pedro Rivas-Ruiz
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Rosell-Melé
- Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010, Barcelona, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Scientific and Technological Park of the University of Girona, Girona, Spain.
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, 17003, Girona, Spain.
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92
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Xia X, Guo W, Liu H. Basin Scale Variation on the Composition and Diversity of Archaea in the Pacific Ocean. Front Microbiol 2017; 8:2057. [PMID: 29109713 PMCID: PMC5660102 DOI: 10.3389/fmicb.2017.02057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/06/2017] [Indexed: 01/09/2023] Open
Abstract
The Archaea are a widely distributed group of prokaryotes that inhabit and thrive in many different environments. In the sea, they play key roles in various global biogeochemical processes. Here, in order to investigate the vertical profiles of archaeal community across a large geographic distance, the compositions of archaeal communities in seven seawater columns in the Pacific Ocean were investigated using high throughput 454 pyrosequencing of the 16S rRNA gene. The surface archaeal communities showed lower diversity and greater variability than those in the deeper layers. Two of the major archaeal phyla that displayed different depth preferences were Thaumarchaeota and Euryarchaeota. The majority of Thaumarchaeota belonged to Marine Group I (MGI), which had high relative abundance in deep water. In contrast, Euryarchaeota, which mainly consisted of Marine Group II (MGII) and III (MGIII), were dominant in the surface layer. Compared with MGI and MGII, MGIII were less abundant in seawater and generally absent from the surface water of the subarctic Pacific. In addition, niche separation in the MGI, MGII, and MGIII subgroups was also observed. For example, MGI.C and MGII.A (the major subgroups of MGI and MGII, respectively) displayed a strong negative correlation with each other. The highest level of archaeal diversity was found in the core of an oxygen minimum zone (OMZ) located off Costa Rica, which resulted from the co-occurrence of both anaerobic and aerobic archaea. For example, methanotrophic archaea ANME-2, methanogenic archaea and several sediment origin archaea, such as Marine Benthic Group A (MBGA) and Bathyarchaeota, were all detected at relatively high abundance in the OMZ. Together, our findings indicate that vertical heterogeneities along water columns and latitudinal differentiation in the surface waters are ubiquitous features of archaeal communities in the Pacific Ocean, and the OMZ off Costa Rica is an archaeal biodiversity hot-spot.
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Affiliation(s)
| | | | - Hongbin Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
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93
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Ma KL, Li XK, Wang K, Meng LW, Liu GG, Zhang J. Establishment of thermophilic anaerobic terephthalic acid degradation system through one-step temperature increase startup strategy - Revealed by Illumina Miseq Sequencing. CHEMOSPHERE 2017; 184:951-959. [PMID: 28655114 DOI: 10.1016/j.chemosphere.2017.06.090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/16/2017] [Accepted: 06/19/2017] [Indexed: 06/07/2023]
Abstract
Over recent years, thermophilic digestion was constantly focused owing to its various advantage over mesophilic digestion. Notably, the startup approach of thermophilic digester needs to be seriously considered as unsuitable startup ways may result in system inefficiency. In this study, one-step temperature increase startup strategy from 37 °C to 55 °C was applied to establish a thermophilic anaerobic system treating terephthalic acid (TA) contained wastewater, meanwhile, the archaeal and bacterial community compositions at steady periods of 37 °C and 55 °C during the experimental process was also compared using Illumina Miseq Sequencing. The process operation demonstrated that the thermophilic TA degradation system was successfully established at 55 °C with over 95% COD reduction. For archaea community, the elevation of operational temperature from 37 °C to 55 °C accordingly increase the enrichment of hydrogenotrophic methanogens but decrease the abundance of the acetotrophic ones. While for bacterial community, the taxonomic analysis suggested that Syntrophorhabdus (27.40%) was the dominant genus promoting the efficient TA degradation under mesophilic condition, whereas OPB95 (24.99%) and TA06 (14.01%) related populations were largely observed and probably take some crucial role in TA degradation under thermophilic condition.
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Affiliation(s)
- Kai-Li Ma
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China.
| | - Xiang-Kun Li
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China.
| | - Ke Wang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China.
| | - Ling-Wei Meng
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China
| | - Gai-Ge Liu
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China
| | - Jie Zhang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, China
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94
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Wojcieszak M, Pyzik A, Poszytek K, Krawczyk PS, Sobczak A, Lipinski L, Roubinek O, Palige J, Sklodowska A, Drewniak L. Adaptation of Methanogenic Inocula to Anaerobic Digestion of Maize Silage. Front Microbiol 2017; 8:1881. [PMID: 29033919 PMCID: PMC5625012 DOI: 10.3389/fmicb.2017.01881] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/14/2017] [Indexed: 11/24/2022] Open
Abstract
A well-balanced microbial consortium is crucial for efficient biogas production. In turn, one of a major factor that influence on the structure of anaerobic digestion (AD) consortium is a source of microorganisms which are used as an inoculum. This study evaluated the influence of inoculum sources (with various origin) on adaptation of a biogas community and the efficiency of the biomethanization of maize silage. As initial inocula for AD of maize silage the samples from: (i) an agricultural biogas plant (ABP) which utilizes maize silage as a main substrate, (ii) cattle slurry (CS), which contain elevated levels of lignocelluloses materials, and (iii) raw sewage sludge (RSS) with low content of plant origin materials were used. The adaptation of methanogenic consortia was monitored during a series of passages, and the functionality of the adapted consortia was verified through start-up operation of AD in two-stage reactors. During the first stages of the adaptation phase, methanogenic consortia occurred very slowly, and only after several passages did the microbial community adapts to allow production of biogas with high methane content. The ABP consortium revealed highest biogas production in the adaptation and in the start-up process. The biodiversity dynamics monitored during adaptation and start-up process showed that community profile changed in a similar direction in three studied consortia. Native communities were very distinct to each other, while at the end of the Phase II of the start-up process microbial diversity profile was similar in all consortia. All adopted bacterial communities were dominated by representatives of Porphyromonadaceae, Rikenellaceae, Ruminococcaceae, and Synergistaceae. A shift from low acetate-preferring acetoclastic Methanosaetaceae (ABP and RSS) and/or hydrogenotrophic Archaea, e.g., Methanomicrobiaceae (CS) prevailing in the inoculum samples to larger populations of high acetate-preferring acetoclastic Methanosarcinaceae was observed by the end of the experiment. As a result, three independent, functional communities that syntrophically produced methane from acetate (primarily) and H2/CO2, methanol and methylamines were adapted. This study provides new insights into the specific process by which different inocula sampled from typical methanogenic environments that are commonly used to initiate industrial installations gradually adapted to allow biogas production from maize silage.
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Affiliation(s)
- Martyna Wojcieszak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Adam Pyzik
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Krzysztof Poszytek
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Pawel S Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Adam Sobczak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Leszek Lipinski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Otton Roubinek
- Institute of Nuclear Chemistry and Technology, Warsaw, Poland
| | - Jacek Palige
- Institute of Nuclear Chemistry and Technology, Warsaw, Poland
| | - Aleksandra Sklodowska
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Lukasz Drewniak
- Laboratory of Environmental Pollution Analysis, Faculty of Biology, University of Warsaw, Warsaw, Poland
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95
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Kip N, Jansen S, Leite MFA, de Hollander M, Afanasyev M, Kuramae EE, Veen JAV. Methanogens predominate in natural corrosion protective layers on metal sheet piles. Sci Rep 2017; 7:11899. [PMID: 28928457 PMCID: PMC5605657 DOI: 10.1038/s41598-017-11244-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 08/16/2017] [Indexed: 11/09/2022] Open
Abstract
Microorganisms are able to cause, but also to inhibit or protect against corrosion. Corrosion inhibition by microbial processes may be due to the formation of mineral deposition layers on metal objects. Such deposition layers have been found in archaeological studies on ancient metal objects, buried in soil, which were hardly corroded. Recent field investigations showed that natural mineral deposition layers can be found on sheet piles in soil. We investigated the microbial communities of these deposition layers and the adjacent soil. Our data, from five different sampling sites, all show striking differences between microbial communities of the deposition layer versus the adjacent soil over the depth profile. Bacterial species dominated in top soil while archaeal sequences increased in abundance with depth. All mineral deposition layers from the steel surface were dominated by Euryarchaeota, of which almost all sequences were phylogenetically related with the Methanobacteria genus. The mineral layer consisted of carbonate precipitates. Based on 16S rDNA gene sequencing data we hypothesize that the methanogens directly extract electrons from the metal surface, thereby, initially inducing mild corrosion, but simultaneously, inducing carbonate precipitation. This, will cause encrustation of the archaea, which drastically slow down their activity and create a natural protective layer against further corrosion.
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Affiliation(s)
- Nardy Kip
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Stefan Jansen
- Deltares, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Mattias de Hollander
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Michael Afanasyev
- Department of Geoscience & Engineering, Delft University of Technology, Stevinweg 1, 2628 CN, Delft, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Johannes A Van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
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Spang A, Caceres EF, Ettema TJG. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science 2017; 357:357/6351/eaaf3883. [DOI: 10.1126/science.aaf3883] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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97
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The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME JOURNAL 2017; 11:2407-2425. [PMID: 28777382 DOI: 10.1038/ismej.2017.122] [Citation(s) in RCA: 220] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 04/07/2017] [Accepted: 06/07/2017] [Indexed: 01/19/2023]
Abstract
The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.
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98
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Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments. Sci Rep 2017; 7:7252. [PMID: 28775334 PMCID: PMC5543129 DOI: 10.1038/s41598-017-07354-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/27/2017] [Indexed: 01/26/2023] Open
Abstract
Recent discoveries have shown that the marker gene for anaerobic methane cycling (mcrA) is more widespread in the Archaea than previously thought. However, it remains unclear whether novel mcrA genes associated with the Bathyarchaeota and Verstraetearchaeota are distributed across diverse environments. We examined two geochemically divergent but putatively methanogenic regions of Yellowstone National Park to investigate whether deeply-rooted archaea possess and express novel mcrA genes in situ. Small-subunit (SSU) rRNA gene analyses indicated that Bathyarchaeota were predominant in seven of ten sediment layers, while the Verstraetearchaeota and Euryarchaeota occurred in lower relative abundance. Targeted amplification of novel mcrA genes suggested that diverse taxa contribute to alkane cycling in geothermal environments. Two deeply-branching mcrA clades related to Bathyarchaeota were identified, while highly abundant verstraetearchaeotal mcrA sequences were also recovered. In addition, detection of SSU rRNA and mcrA transcripts from one hot spring suggested that predominant Bathyarchaeota were also active, and that methane cycling genes are expressed by the Euryarchaeota, Verstraetearchaeota, and an unknown lineage basal to the Bathyarchaeota. These findings greatly expand the diversity of the key marker gene for anaerobic alkane cycling and outline the need for greater understanding of the functional capacity and phylogenetic affiliation of novel mcrA variants.
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99
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Yu T, Liang Q, Niu M, Wang F. High occurrence of Bathyarchaeota (MCG) in the deep-sea sediments of South China Sea quantified using newly designed PCR primers. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:374-382. [PMID: 28419783 DOI: 10.1111/1758-2229.12539] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 04/06/2017] [Accepted: 04/10/2017] [Indexed: 06/07/2023]
Abstract
The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments. The abundance of Bathyarchaeota along two sediment cores from the deep-sea sediments of South China Sea (SCS, each from the Dongsha and Shenhu area) was determined. A strong correlation was found between the bathyarchaeotal abundance and the content of total organic carbon (TOC), suggesting an important role of Bathyarchaeota in organic matter remineralisation in the sediments of SCS. Furthermore, diversity analysis revealed that subgroups Bathy-2, Bathy-8 and Bathy-10 were dominant bathyarchaeotal members of the deep-sea sediments in the SCS. Bathy-8 was found predominantly within the reducing and deeper sediment layers, while Bathy-10 occurred preferentially in the oxidizing and shallower sediment layers. Our study lays a foundation for the further understanding of the ecological functions and niche differentiation of the important but not well-understood sedimentary archaeal group.
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Affiliation(s)
- Tiantian Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qianyong Liang
- Key Laboratory of Marine Mineral Resources, Guangzhou Marine Geological Survey, China Geological Survey, Guangzhou, 510070, China
| | - Mingyang Niu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, China
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100
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Effect of Sewage and Industrial Effluents on Bacterial and Archaeal Communities of Creek Sediments in the Taihu Basin. WATER 2017. [DOI: 10.3390/w9060373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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