101
|
Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019. [DOI: 10.10.3389/fmicb.2019.00849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
102
|
Jørgensen BB, Findlay AJ, Pellerin A. The Biogeochemical Sulfur Cycle of Marine Sediments. Front Microbiol 2019; 10:849. [PMID: 31105660 PMCID: PMC6492693 DOI: 10.3389/fmicb.2019.00849] [Citation(s) in RCA: 210] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/02/2019] [Indexed: 11/13/2022] Open
Abstract
Microbial dissimilatory sulfate reduction to sulfide is a predominant terminal pathway of organic matter mineralization in the anoxic seabed. Chemical or microbial oxidation of the produced sulfide establishes a complex network of pathways in the sulfur cycle, leading to intermediate sulfur species and partly back to sulfate. The intermediates include elemental sulfur, polysulfides, thiosulfate, and sulfite, which are all substrates for further microbial oxidation, reduction or disproportionation. New microbiological discoveries, such as long-distance electron transfer through sulfide oxidizing cable bacteria, add to the complexity. Isotope exchange reactions play an important role for the stable isotope geochemistry and for the experimental study of sulfur transformations using radiotracers. Microbially catalyzed processes are partly reversible whereby the back-reaction affects our interpretation of radiotracer experiments and provides a mechanism for isotope fractionation. We here review the progress and current status in our understanding of the sulfur cycle in the seabed with respect to its microbial ecology, biogeochemistry, and isotope geochemistry.
Collapse
Affiliation(s)
- Bo Barker Jørgensen
- Department of Bioscience, Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | | | | |
Collapse
|
103
|
Lee KS, Palatinszky M, Pereira FC, Nguyen J, Fernandez VI, Mueller AJ, Menolascina F, Daims H, Berry D, Wagner M, Stocker R. An automated Raman-based platform for the sorting of live cells by functional properties. Nat Microbiol 2019; 4:1035-1048. [PMID: 30886359 DOI: 10.1038/s41564-019-0394-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
Stable-isotope probing is widely used to study the function of microbial taxa in their natural environment, but sorting of isotopically labelled microbial cells from complex samples for subsequent genomic analysis or cultivation is still in its early infancy. Here, we introduce an optofluidic platform for automated sorting of stable-isotope-probing-labelled microbial cells, combining microfluidics, optical tweezing and Raman microspectroscopy, which yields live cells suitable for subsequent single-cell genomics, mini-metagenomics or cultivation. We describe the design and optimization of this Raman-activated cell-sorting approach, illustrate its operation with four model bacteria (two intestinal, one soil and one marine) and demonstrate its high sorting accuracy (98.3 ± 1.7%), throughput (200-500 cells h-1; 3.3-8.3 cells min-1) and compatibility with cultivation. Application of this sorting approach for the metagenomic characterization of bacteria involved in mucin degradation in the mouse colon revealed a diverse consortium of bacteria, including several members of the underexplored family Muribaculaceae, highlighting both the complexity of this niche and the potential of Raman-activated cell sorting for identifying key players in targeted processes.
Collapse
Affiliation(s)
- Kang Soo Lee
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Márton Palatinszky
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Fátima C Pereira
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Jen Nguyen
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Vicente I Fernandez
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Anna J Mueller
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Filippo Menolascina
- School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh, UK
| | - Holger Daims
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.,The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - David Berry
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Michael Wagner
- Center of Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria.,The Comammox Research Platform, University of Vienna, Vienna, Austria
| | - Roman Stocker
- Ralph M. Parsons Laboratory for Environmental Science and Engineering, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
| |
Collapse
|
104
|
Kessler AJ, Chen YJ, Waite DW, Hutchinson T, Koh S, Popa ME, Beardall J, Hugenholtz P, Cook PLM, Greening C. Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments. Nat Microbiol 2019; 4:1014-1023. [DOI: 10.1038/s41564-019-0391-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/28/2019] [Indexed: 11/09/2022]
|
105
|
Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients. Appl Environ Microbiol 2019; 85:AEM.02602-18. [PMID: 30635381 DOI: 10.1128/aem.02602-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/16/2018] [Indexed: 01/26/2023] Open
Abstract
Bacterial communities play essential roles in estuarine marsh ecosystems, but the interplay of ecological processes underlying their community assembly is poorly understood. Here, we studied the sediment bacterial communities along a linear gradient extending from the water-land junction toward a high marsh, using 16S rRNA gene amplicon sequencing. Bacterial community compositions differed significantly between sediment transects. Physicochemical properties, particularly sediment nutrient levels (i.e., total nitrogen [TN] and available phosphorus [AP]), as well as sediment physical structure and pH (P < 0.05), were strongly associated with the overall community variations. In addition, the topological properties of bacterial cooccurrence networks varied with distance to the water-land junction. Both node- and network-level topological features revealed that the bacterial network of sediments farthest from the junction was less intense in complexity and interactions than other sediments. Phylogenetic null modeling analysis showed a progressive transition from stochastic to deterministic community assembly for the water-land junction sites toward the emerging terrestrial system. Taken together, data from this study provide a detailed outline of the distribution pattern of the sediment bacterial community across an estuarine marsh and inform the mechanisms and processes mediating bacterial community assembly in marsh soils.IMPORTANCE Salt marshes represent highly dynamic ecosystems where the atmosphere, continents, and the ocean interact. The bacterial distribution in this ecosystem is of great ecological concern, as it provides essential functions acting on ecosystem services. However, ecological processes mediating bacterial assembly are poorly understood for salt marshes, especially the ones located in estuaries. In this study, the distribution and assembly of bacterial communities in an estuarine marsh located in south Hangzhou Bay were investigated. The results revealed an intricate interplay between stochastic and deterministic processes mediating the assembly of bacterial communities in the studied gradient system. Collectively, our findings illustrate the main drivers of community assembly, taking into consideration changes in sediment abiotic variables and potential biotic interactions. Thus, we offer new insights into estuarine bacterial communities and illustrate the interplay of ecological processes shaping the assembly of bacterial communities in estuarine marsh ecosystems.
Collapse
|
106
|
Watanabe T, Kojima H, Umezawa K, Hori C, Takasuka TE, Kato Y, Fukui M. Genomes of Neutrophilic Sulfur-Oxidizing Chemolithoautotrophs Representing 9 Proteobacterial Species From 8 Genera. Front Microbiol 2019; 10:316. [PMID: 30858836 PMCID: PMC6397845 DOI: 10.3389/fmicb.2019.00316] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/06/2019] [Indexed: 01/08/2023] Open
Abstract
Even in the current era of metagenomics, the interpretation of nucleotide sequence data is primarily dependent on knowledge obtained from a limited number of microbes isolated in pure culture. Thus, it is of fundamental importance to expand the variety of strains available in pure culture, to make reliable connections between physiological characteristics and genomic information. In this study, two sulfur oxidizers that potentially represent two novel species were isolated and characterized. They were subjected to whole-genome sequencing together with 7 neutrophilic and chemolithoautotrophic sulfur-oxidizing bacteria. The genes for sulfur oxidation in the obtained genomes were identified and compared with those of isolated sulfur oxidizers in the classes Betaproteobacteria and Gammaproteobacteria. Although the combinations of these genes in the respective genomes are diverse, typical combinations corresponding to three types of core sulfur oxidation pathways were identified. Each pathway involves one of three specific sets of proteins, SoxCD, DsrABEFHCMKJOP, and HdrCBAHypHdrCB. All three core pathways contain the SoxXYZAB proteins, and a cytoplasmic sulfite oxidase encoded by soeABC is a conserved component in the core pathways lacking SoxCD. Phylogenetically close organisms share same core sulfur oxidation pathway, but a notable exception was observed in the family ‘Sulfuricellaceae’. In this family, some strains have either core pathway involving DsrABEFHCMKJOP or HdrCBAHypHdrCB, while others have both pathways. A proteomics analysis showed that proteins constituting the core pathways were produced at high levels. While hypothesized function of HdrCBAHypHdrCB is similar to that of Dsr system, both sets of proteins were detected with high relative abundances in the proteome of a strain possessing genes for these proteins. In addition to the genes for sulfur oxidation, those for arsenic metabolism were searched for in the sequenced genomes. As a result, two strains belonging to the families Thiobacillaceae and Sterolibacteriaceae were observed to harbor genes encoding ArxAB, a type of arsenite oxidase that has been identified in a limited number of bacteria. These findings were made with the newly obtained genomes, including those from 6 genera from which no genome sequence of an isolated organism was previously available. These genomes will serve as valuable references to interpret nucleotide sequences.
Collapse
Affiliation(s)
- Tomohiro Watanabe
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Umezawa
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Chiaki Hori
- Research Faculty of Engineering, Hokkaido University, Sapporo, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yukako Kato
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
| |
Collapse
|
107
|
Bacterial community pattern along the sediment seafloor of the Arctic fjorden (Kongsfjorden, Svalbard). Antonie van Leeuwenhoek 2019; 112:1121-1136. [PMID: 30783849 DOI: 10.1007/s10482-019-01245-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
Abstract
The Arctic region has been the focus of increasing attention as an ecosystem that is highly sensitive to changes associated with global warming. Although it was assumed to be vulnerable to changes in climate, a limited number of studies have been conducted on the surface sediment bacteria of Arctic fjorden. This study assessed the diversity and distribution pattern of bacterial communities in eight marine sediments along the seafloor in a high Arctic fjorden (Kongsfjorden, Svalbard). A total of 822 operational taxonomic units (OTUs) were identified by Illumina MiSeq sequencing, targeting the V3-V4 hypervariable regions of the 16S rRNA gene. In these surface marine sediments, more than half of the sequences belonged to the phylum Proteobacteria, followed by Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi and Lentisphaerae. The bacterial genera Marinicella, Desulfobulbus, Lutimonas, Sulfurovum and clade SEEP-SRB4 were dominant in all samples. Analysis of similarity indicated that bacterial communities were significantly different among the inner, central and outer basins (r2 = 0.5, P = 0.03 < 0.05). Canonical correspondence analysis and permutation tests revealed that location depth (r2 = 0.87, P < 0.01), temperature (r2 = 0.88, P < 0.01) and salinity (r2 = 0.88, P < 0.05) were the most significant factors that correlated with the bacterial communities in the sediments. 28 differentially abundant taxonomic clades in the inner and outer basin with an LDA score higher than 2.0 were found by the LEfSe method. The Spearman correlation heat map revealed different degrees of correlation between most major OTUs and environmental factors, while some clades have an inverse correlation with environmental factors. The spatial patterns of bacterial communities along the Kongsfjorden may offer insight into the ecological responses of prokaryotes to climate change in the Arctic ecosystem, which makes it necessary to continue with monitoring.
Collapse
|
108
|
Quantifying population-specific growth in benthic bacterial communities under low oxygen using H 218O. ISME JOURNAL 2019; 13:1546-1559. [PMID: 30783213 PMCID: PMC6776007 DOI: 10.1038/s41396-019-0373-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 01/09/2023]
Abstract
The benthos in estuarine environments often experiences periods of regularly occurring hypoxic and anoxic conditions, dramatically impacting biogeochemical cycles. How oxygen depletion affects the growth of specific uncultivated microbial populations within these diverse benthic communities, however, remains poorly understood. Here, we applied H218O quantitative stable isotope probing (qSIP) in order to quantify the growth of diverse, uncultured bacterial populations in response to low oxygen concentrations in estuarine sediments. Over the course of 7- and 28-day incubations with redox conditions spanning from hypoxia to euxinia (sulfidic), 18O labeling of bacterial populations exhibited different patterns consistent with micro-aerophilic, anaerobic, facultative anaerobic, and aerotolerant anaerobic growth. 18O-labeled populations displaying anaerobic growth had a significantly non-random phylogenetic distribution, exhibited by numerous clades currently lacking cultured representatives within the Planctomycetes, Actinobacteria, Latescibacteria, Verrucomicrobia, and Acidobacteria. Genes encoding the beta-subunit of the dissimilatory sulfate reductase (dsrB) became 18O labeled only during euxinic conditions. Sequencing of these 18O-labeled dsrB genes showed that Acidobacteria were the dominant group of growing sulfate-reducing bacteria, highlighting their importance for sulfur cycling in estuarine sediments. Our findings provide the first experimental constraints on the redox conditions underlying increased growth in several groups of "microbial dark matter", validating hypotheses put forth by earlier metagenomic studies.
Collapse
|
109
|
Meier DV, Pjevac P, Bach W, Markert S, Schweder T, Jamieson J, Petersen S, Amann R, Meyerdierks A. Microbial metal-sulfide oxidation in inactive hydrothermal vent chimneys suggested by metagenomic and metaproteomic analyses. Environ Microbiol 2019; 21:682-701. [PMID: 30585382 PMCID: PMC6850669 DOI: 10.1111/1462-2920.14514] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/17/2018] [Accepted: 12/19/2018] [Indexed: 01/02/2023]
Abstract
Metal-sulfides are wide-spread in marine benthic habitats. At deep-sea hydrothermal vents, they occur as massive sulfide chimneys formed by mineral precipitation upon mixing of reduced vent fluids with cold oxygenated sea water. Although microorganisms inhabiting actively venting chimneys and utilizing compounds supplied by the venting fluids are well studied, only little is known about microorganisms inhabiting inactive chimneys. In this study, we combined 16S rRNA gene-based community profiling of sulfide chimneys from the Manus Basin (SW Pacific) with radiometric dating, metagenome (n = 4) and metaproteome (n = 1) analyses. Our results shed light on potential lifestyles of yet poorly characterized bacterial clades colonizing inactive chimneys. These include sulfate-reducing Nitrospirae and sulfide-oxidizing Gammaproteobacteria dominating most of the inactive chimney communities. Our phylogenetic analysis attributed the gammaproteobacterial clades to the recently described Woeseiaceae family and the SSr-clade found in marine sediments around the world. Metaproteomic data identified these Gammaproteobacteria as autotrophic sulfide-oxidizers potentially facilitating metal-sulfide dissolution via extracellular electron transfer. Considering the wide distribution of these gammaproteobacterial clades in marine environments such as hydrothermal vents and sediments, microbially accelerated neutrophilic mineral oxidation might be a globally relevant process in benthic element cycling and a considerable energy source for carbon fixation in marine benthic habitats.
Collapse
Affiliation(s)
- Dimitri V. Meier
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
| | - Petra Pjevac
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
| | - Wolfgang Bach
- MARUM – Center for Marine Environmental Sciences, Petrology of the Ocean Crust groupUniversity of BremenLeobener Str., 28359, BremenGermany
| | - Stephanie Markert
- Institute of PharmacyErnst‐Moritz‐Arndt‐UniversityFriedrich‐Ludwig‐Jahn‐Straße 17, 17489, GreifswaldGermany
| | - Thomas Schweder
- Institute of PharmacyErnst‐Moritz‐Arndt‐UniversityFriedrich‐Ludwig‐Jahn‐Straße 17, 17489, GreifswaldGermany
| | - John Jamieson
- Department of Earth SciencesMemorial University of Newfoundland40 Arctic Ave, Saint John'sNL, A1B 3X7Canada
| | - Sven Petersen
- GEOMAR Helmholtz Centre for Ocean ResearchWischhofstraße 1‐3, 24148, KielGermany
| | - Rudolf Amann
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
| | - Anke Meyerdierks
- Max Planck Institute for Marine MicrobiologyCelsiusstrasse 1, 28359, BremenGermany
| |
Collapse
|
110
|
Dyksma S, Lenk S, Sawicka JE, Mußmann M. Uncultured Gammaproteobacteria and Desulfobacteraceae Account for Major Acetate Assimilation in a Coastal Marine Sediment. Front Microbiol 2018; 9:3124. [PMID: 30619197 PMCID: PMC6305295 DOI: 10.3389/fmicb.2018.03124] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/03/2018] [Indexed: 11/13/2022] Open
Abstract
Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with 14C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of 14C-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31–62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover.
Collapse
Affiliation(s)
- Stefan Dyksma
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences, Emden, Germany
| | - Sabine Lenk
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Joanna E Sawicka
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Mußmann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| |
Collapse
|
111
|
King GM. Microbiomes of the Enteropneust, Saccoglossus bromophenolosus, and Associated Marine Intertidal Sediments of Cod Cove, Maine. Front Microbiol 2018; 9:3066. [PMID: 30631312 PMCID: PMC6315191 DOI: 10.3389/fmicb.2018.03066] [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: 08/10/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022] Open
Abstract
Enteropneusts are widely distributed marine invertebrates that accumulate high concentrations of halogenated aromatics. Some of these compounds affect benthic biogeochemistery (e.g., denitrification and ammonia oxidation), but little is known about interactions between enteropneusts and their associated microbial communities. Even less is known about enteropneust host-microbe relationships in the digestive tract. More generally, microbial community composition and diversity in intertidal sediments have received little attention. In this study, high throughput sequence analyses of 16S rRNA genes extracted from microbial communities associated with sediment-free whole individuals of Saccoglossus bromophenolosus and freshly excreted S. bromophenolosus gut sediments revealed a potential Spirochaete symbiont that was abundant, present in gut sediment, but absent in other sediments. Relative to surface sediments, gut communities also revealed evidence for selective losses of some groups and blooms of others, especially Colwellia, Photobacterium, Pseudoalteromonas, and Vibrio. After deposition, gut sediment communities rapidly resembled those of surface sediments. Although hierarchical cluster analysis and Linear Discriminant Analysis Effect Size (LEfSe) differentiated among burrow walls of S. bromophenolosus and a polychaete, Alitta virens, as well as between surface and sub-surface sediments, most operational taxonomic units (OTUs) were shared, with differences largely occurring in relative abundances. This suggests that sediment mixing through bioturbation might act to homogenize community composition, while species-specific impacts by infauna might alter local population abundances. Although Cod Cove is a relatively isolated intertidal system, microbial community members included groups with cosmopolitan distributions and roles in sulfur cycling, e.g., Gammaproteobacteria BD7 and Sva0071, as well as novel OTUs representing a large number of phyla.
Collapse
Affiliation(s)
- Gary M King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| |
Collapse
|
112
|
Mejia J, He S, Yang Y, Ginder-Vogel M, Roden EE. Stability of Ferrihydrite-Humic Acid Coprecipitates under Iron-Reducing Conditions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:13174-13183. [PMID: 30354092 PMCID: PMC8381759 DOI: 10.1021/acs.est.8b03615] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Recent studies have suggested the potential for release of iron (hydr)oxide-bound organic carbon (OC) during dissimilatory iron oxide reduction (DIR). However, the stability of iron (hydr)oxide-bound OC in the presence of a natural microbial consortium capable of driving both OC metabolism and DIR has not been resolved. Pure ferrihydrite (Fhy) and Fhy-humic acid coprecipitates (Fhy-HA) were inoculated with a small quantity of freshwater sediment and incubated under anoxic conditions in the presence and absence of H2 or glucose as electron donors for DIR. H2 promoted DIR led to release of ca. 1 mM dissolved organic carbon (DOC). However, comparable amounts of DOC were released from both pure Fhy and Fhy-HA, similar to DOC levels in mineral-free, inoculum-only controls. These results suggest that the observed DOC release during H2-promoted DIR originated from OC contained in the inoculum as opposed to the much larger pool (ca. 38 mM) of OC in the Fhy-HA. Thus, DIR preferentially released sorbed OC with low aromaticity (inoculum OC) versus highly aromatic OC (HA) coprecipitated with iron oxide. Our findings provide new insight into the extent and mechanisms by which DIR is likely to influence aqueous/solid-phase OC partitioning in anoxic soils and sediments.
Collapse
Affiliation(s)
- Jacqueline Mejia
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Shaomei He
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yu Yang
- Department of Civil and Environmental Engineering, University of Nevada-Reno, Reno, NV, 89557, USA
| | - Matthew Ginder-Vogel
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eric E Roden
- Department of Geoscience, University of Wisconsin-Madison, Madison, WI 53706, USA
- Corresponding Author: Eric E. Roden. , Phone: 608-890-7024. Fax: 608-262-0693
| |
Collapse
|
113
|
Marchant HK, Tegetmeyer HE, Ahmerkamp S, Holtappels M, Lavik G, Graf J, Schreiber F, Mussmann M, Strous M, Kuypers MMM. Metabolic specialization of denitrifiers in permeable sediments controls N 2 O emissions. Environ Microbiol 2018; 20:4486-4502. [PMID: 30117262 DOI: 10.1111/1462-2920.14385] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 08/10/2018] [Accepted: 08/12/2018] [Indexed: 11/28/2022]
Abstract
Coastal oceans receive large amounts of anthropogenic fixed nitrogen (N), most of which is denitrified in the sediment before reaching the open ocean. Sandy sediments, which are common in coastal regions, seem to play an important role in catalysing this N-loss. Permeable sediments are characterized by advective porewater transport, which supplies high fluxes of organic matter into the sediment, but also leads to fluctuations in oxygen and nitrate concentrations. Little is known about how the denitrifying communities in these sediments are adapted to such fluctuations. Our combined results indicate that denitrification in eutrophied sandy sediments from the world's largest tidal flat system, the Wadden Sea, is carried out by different groups of microorganisms. This segregation leads to the formation of N2 O which is advectively transported to the overlying waters and thereby emitted to the atmosphere. At the same time, the production of N2 O within the sediment supports a subset of Flavobacteriia which appear to be specialized on N2 O reduction. If the mechanisms shown here are active in other coastal zones, then denitrification in eutrophied sandy sediments may substantially contribute to current marine N2 O emissions.
Collapse
Affiliation(s)
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | | | - Gaute Lavik
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jon Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Frank Schreiber
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,ETH Zurich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, Zurich, Switzerland.,Eawag, Swiss Federal Institute of Aquatic Science and Technology, Department of Environmental Microbiology, Dübendorf, Switzerland.,Division of Biodeterioration and Reference Organisms, Department of Materials and Environment, Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Marc Mussmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Strous
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | |
Collapse
|
114
|
da Silva Câmara A, de Almeida Fernandes LD. Evaluation of the interactions between the marine bacterium Pseudomonas fluorescens and the microalga Isochrysis galbana in simulated ballast tank environment. Arch Microbiol 2018; 201:35-44. [PMID: 30187094 DOI: 10.1007/s00203-018-1569-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/11/2018] [Accepted: 08/29/2018] [Indexed: 10/28/2022]
Abstract
To evaluate the impacts of the interaction between bacteria and microalgae has been the object of study by many research groups around the world. However, little is known about the interference that pigments produced by bacteria, such as the pyoverdine siderophore, can cause to microalgae like Isochrysis galbana. Pyoverdine is a fluorochrome produced by certain Pseudomonas strains, such as P. fluorescens, which plays a role in capturing and transporting iron ions from the environment to the cell. Unlike the oceans where Fe concentrations are extremely low (< 10-15 µM), in a ballast tank it is expected that there is a great supply of iron to the cells and that the absence of light is the main limiting factor until the water is discarded. Interestingly, under certain conditions, bacteria such as P. fluorescens absorb most of the water soluble iron ions and prevent the growth of phytoplankton even if there is sufficient light. Changes in the patterns of light distribution in aquatic environments may affect the physiological characteristics of certain microalgae. This study aimed to evaluate the impacts of the presence of P. fluorescens on the survival and growth of I. galbana inside the tank. For the study, an experiment was carried out to study the interaction between P. fluorescens and I. galbana under simulated conditions of a vessel in the presence/absence of Pseudomonas and light. The results showed that the presence of the bacteria is not the main limiting factor for microalga growth. The effect of the light factor was determinant on the reproduction rate. It is believed that pyoverdine produced by P. fluorescens affected I. galbana stock either by increasing mortality or decreasing growth rate as revealed by laboratory experiments. However, it was not possible to check if the pigment concentration was affected by the growth of microalgae.
Collapse
Affiliation(s)
- Aline da Silva Câmara
- Laboratory of Microbiology and Cytometry, Biofouling and Bioinvasion Division, Marine Biotechnology Department, Instituto de Estudos do Mar Almirante Paulo Moreira - IEAPM - Brazilian Navy, Rua Kioto 253, Praia dos Anjos, Arraial do Cabo, Rio De Janeiro, 28930-000, Brazil. .,Programa de Pós-graduação em Biotecnologia Marinha - IEAPM, Rua Daniel Barreto s/n - Prédio Amazônia Azul - Praia dos Anjos, Arraial do Cabo, 28930-000, Brazil.
| | - Lohengrin Dias de Almeida Fernandes
- Laboratory of Microbiology and Cytometry, Biofouling and Bioinvasion Division, Marine Biotechnology Department, Instituto de Estudos do Mar Almirante Paulo Moreira - IEAPM - Brazilian Navy, Rua Kioto 253, Praia dos Anjos, Arraial do Cabo, Rio De Janeiro, 28930-000, Brazil.,Programa de Pós-graduação em Biotecnologia Marinha - IEAPM, Rua Daniel Barreto s/n - Prédio Amazônia Azul - Praia dos Anjos, Arraial do Cabo, 28930-000, Brazil
| |
Collapse
|
115
|
Pimenov NV, Merkel AY, Tarnovetskii IY, Malakhova TV, Samylina OS, Kanapatskii TA, Tikhonova EN, Vlasova MA. Structure of Microbial Mats in the Mramornaya Bay (Crimea) Coastal Areas. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050132] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
116
|
Hicks N, Liu X, Gregory R, Kenny J, Lucaci A, Lenzi L, Paterson DM, Duncan KR. Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments. Front Microbiol 2018; 9:1730. [PMID: 30190707 PMCID: PMC6115492 DOI: 10.3389/fmicb.2018.01730] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.
Collapse
Affiliation(s)
- Natalie Hicks
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Xuan Liu
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard Gregory
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - David M. Paterson
- Sediment Ecology Research Group, School of Biology, Scottish Oceans Institute, University of St Andrews, Fife, United Kingdom
| | - Katherine R. Duncan
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| |
Collapse
|
117
|
Issotta F, Moya-Beltrán A, Mena C, Covarrubias PC, Thyssen C, Bellenberg S, Sand W, Quatrini R, Vera M. Insights into the biology of acidophilic members of the Acidiferrobacteraceae family derived from comparative genomic analyses. Res Microbiol 2018; 169:608-617. [PMID: 30142431 DOI: 10.1016/j.resmic.2018.08.001] [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: 04/08/2018] [Revised: 08/06/2018] [Accepted: 08/08/2018] [Indexed: 10/28/2022]
Abstract
The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains Gram negative, neutrophilic sulfur oxidizers such as Sulfuricaulis and Sulfurifustis, as well as acidophilic iron and sulfur oxidizers belonging to the Acidiferrobacter genus. The diversity and taxonomy of the genus Acidiferrobacter has remained poorly explored. Although several metagenome and bioleaching studies have identified its presence worldwide, only two strains, namely Acidiferrobacter thiooxydans DSM 2932T, and Acidiferrobacter spp. SP3/III have been isolated and made publically available. Using 16S rRNA sequence data publically available for the Acidiferrobacteraceae, we herein shed light into the molecular taxonomy of this family. Results obtained support the presence of three clades Acidiferrobacter, Sulfuricaulis and Sulfurifustis. Genomic analyses of the genome sequences of A. thiooxydansT and Acidiferrobacter spp. SP3/III indicate that ANI relatedness between the SPIII/3 strain and A. thiooxydansT is below 95-96%, supporting the classification of strain SP3/III as a new species within this genus. In addition, approximately 70% of Acidiferrobacter sp. SPIII/3 predicted genes have a conserved ortholog in A. thiooxydans strains. A comparative analysis of iron, sulfur oxidation pathways, genome plasticity and cell-cell communication mechanisms of Acidiferrobacter spp. are also discussed.
Collapse
Affiliation(s)
- Francisco Issotta
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, 7780272, Santiago, Chile; Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Ana Moya-Beltrán
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, 7780272, Santiago, Chile; Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Cristóbal Mena
- Instituto de Ingeniería Biológica y Médica, Escuelas de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, 7820486, Santiago, Chile
| | - Paulo C Covarrubias
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, 7780272, Santiago, Chile; Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Christian Thyssen
- Universität Duisburg Essen, Biofilm Centre, Aquatische Biotechnologie, Universitätsstr. 5, 45141, Essen, Germany
| | - Sören Bellenberg
- Universität Duisburg Essen, Biofilm Centre, Aquatische Biotechnologie, Universitätsstr. 5, 45141, Essen, Germany
| | - Wolfgang Sand
- Universität Duisburg Essen, Biofilm Centre, Aquatische Biotechnologie, Universitätsstr. 5, 45141, Essen, Germany; College of Environmental Science and Engineering, Donghua University, 2999 North Ren Min Rd., Song Jiang District, Shanghai, 201620, PR China; Technische Universität Bergakademie Freiberg, Institut für Biowissenschaften, Leipziger Str. 29, 09599, Freiberg, Germany
| | - Raquel Quatrini
- Fundación Ciencia y Vida, Avenida Zañartu 1482, Ñuñoa, 7780272, Santiago, Chile.
| | - Mario Vera
- Instituto de Ingeniería Biológica y Médica, Escuelas de Ingeniería, Medicina y Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, 7820486, Santiago, Chile; Departamento de Ingeniería Hidráulica y Ambiental, Escuela de Ingeniería, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, 7820486, Santiago, Chile.
| |
Collapse
|
118
|
Zhang X, Hu BX, Ren H, Zhang J. Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:518-528. [PMID: 29579663 DOI: 10.1016/j.scitotenv.2018.03.158] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 05/25/2023]
Abstract
The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity.
Collapse
Affiliation(s)
- Xiaoying Zhang
- Institute of Groundwater and Earth Sciences, Jinan University, 510632 Guangzhou, China; Department of Ecology, Jinan University, 510632 Guangzhou, China.
| | - Bill X Hu
- Institute of Groundwater and Earth Sciences, Jinan University, 510632 Guangzhou, China; School of Water Resources and Environment, China University of Geosciences (Beijing), 100083 Beijing, China.
| | - Hejun Ren
- Key Laboratory of Groundwater Resources and Environment of the Ministry of Education, College of Environment and Resources, Jilin University, 130021 Changchun, China
| | - Jin Zhang
- Institute of Urban Water Management, Technische Universität Dresden, 01062 Dresden, Germany
| |
Collapse
|
119
|
Qiao Y, Liu J, Zhao M, Zhang XH. Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas. Front Microbiol 2018; 9:1128. [PMID: 29904376 PMCID: PMC5990616 DOI: 10.3389/fmicb.2018.01128] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/14/2018] [Indexed: 12/17/2022] Open
Abstract
The mud sediments of the eastern China marginal seas (ECMS) are deposited under different hydrodynamic conditions with different organic matter sources. These events have been demonstrated to exert significant influences on microbial communities and biogeochemical processes in surface sediments. However, the extent to which such effects occur in subsurface microbial communities remains unclear. In this study, both horizontal and vertical (five sites, each for eight layers) distributions of bacterial abundance and community composition in mud deposits of the South Yellow Sea (SYS) and East China Sea (ECS) were investigated by quantitative PCR and Illumina sequencing of the 16S rRNA gene. Both bacterial abundance and diversity were higher in the ECS than in the SYS, and tended to be higher in up than in deep layers. Proteobacteria (JTB255 marine benthic group), Acidobacteria and Bacteroidetes were dominant in the upper layers, whereas Lactococcus, Pseudomonas, and Dehalococcoidia were enriched in the deep layers. The bacterial communities in surface and subsurface sediments showed different inter-taxa relationships, indicating contrasting co-occurrence patterns. The bacterial communities in the upper layer samples clustered in accordance with mud zones, whereas those in the deep layer samples of all sites tended to cluster together. TOC δ13C and TON δ15N significantly affected the bacterial community composition, suggesting that the abundance and composition of organic matter played critical roles in shaping of sedimentary bacterial communities. This study provides novel insights into the distribution of subsurface bacterial communities in mud deposits of the ECMS, and provides clues for understanding the biogeochemical cycles in this area.
Collapse
Affiliation(s)
- Yanlu Qiao
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jiwen Liu
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Meixun Zhao
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, China
| | - Xiao-Hua Zhang
- Laboratory of Marine Microbiology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| |
Collapse
|
120
|
Klier J, Dellwig O, Leipe T, Jürgens K, Herlemann DPR. Benthic Bacterial Community Composition in the Oligohaline-Marine Transition of Surface Sediments in the Baltic Sea Based on rRNA Analysis. Front Microbiol 2018; 9:236. [PMID: 29520255 PMCID: PMC5827536 DOI: 10.3389/fmicb.2018.00236] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/31/2018] [Indexed: 12/16/2022] Open
Abstract
Salinity has a strong impact on bacterial community composition such that freshwater bacterial communities are very different from those in seawater. By contrast, little is known about the composition and diversity of the bacterial community in the sediments (bacteriobenthos) at the freshwater-seawater transition (mesohaline conditions). In this study, partial 16S-rRNA sequences were used to investigate the bacterial community at five stations, representing almost freshwater (oligohaline) to marine conditions, in the Baltic Sea. Samples were obtained from the silty, top-layer (0-2.5 cm) sediments with mostly oxygenated conditions. The long water residence time characteristic of the Baltic Sea, was predicted to enable the development of autochthonous bacteriobenthos at mesohaline conditions. Our results showed that, similar to the water column, salinity is a major factor in structuring the bacteriobenthos and that there is no loss of bacterial richness at intermediate salinities. The bacterial communities of marine, mesohaline, and oligohaline sediments differed in terms of the relative rRNA abundances of the major bacterial phyla/classes. At mesohaline conditions typical marine and oligohaline operational taxonomic units (OTUs) were abundant. Putative unique OTUs in mesohaline sediments were present only at low abundances, suggesting that the mesohaline environment consists mainly of marine and oligohaline bacteria with a broad salinity tolerance. Our study provides a first overview of the diversity patterns and composition of bacteria in the sediments along the Baltic Sea salinity gradient as well as new insights into the bacteriobenthos at mesohaline conditions.
Collapse
Affiliation(s)
- Julia Klier
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Olaf Dellwig
- Department of Marine Geology, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Thomas Leipe
- Department of Marine Geology, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Klaus Jürgens
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| | - Daniel P. R. Herlemann
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Rostock, Germany
| |
Collapse
|
121
|
La Cono V, Ruggeri G, Azzaro M, Crisafi F, Decembrini F, Denaro R, La Spada G, Maimone G, Monticelli LS, Smedile F, Giuliano L, Yakimov MM. Contribution of Bicarbonate Assimilation to Carbon Pool Dynamics in the Deep Mediterranean Sea and Cultivation of Actively Nitrifying and CO 2-Fixing Bathypelagic Prokaryotic Consortia. Front Microbiol 2018; 9:3. [PMID: 29403458 PMCID: PMC5780414 DOI: 10.3389/fmicb.2018.00003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/03/2018] [Indexed: 11/16/2022] Open
Abstract
Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m-3 d-1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13-14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m-2 d-1. This quantity of produced de novo organic carbon amounts to about 85-424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota "low-ammonia-concentration" deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.
Collapse
Affiliation(s)
- Violetta La Cono
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gioachino Ruggeri
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Maurizio Azzaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesca Crisafi
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Franco Decembrini
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Renata Denaro
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Gina La Spada
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Giovanna Maimone
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Luis S. Monticelli
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
| | - Francesco Smedile
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Laura Giuliano
- Mediterranean Science Commission (CIESM), Monaco, Monaco
| | - Michail M. Yakimov
- Institute for Coastal Marine Environment, National Research Council, Messina, Italy
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| |
Collapse
|
122
|
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.
Collapse
|
123
|
Danza F, Storelli N, Roman S, Lüdin S, Tonolla M. Dynamic cellular complexity of anoxygenic phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno. PLoS One 2017; 12:e0189510. [PMID: 29245157 PMCID: PMC5731995 DOI: 10.1371/journal.pone.0189510] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/28/2017] [Indexed: 11/23/2022] Open
Abstract
The meromictic Lake Cadagno is characterized by a compact chemocline with high concentrations of anoxygenic phototrophic purple sulfur bacteria (PSB) and green sulfur bacteria (GSB). The co-occurrence of phylogenetically distant bacterial groups such as PSB and GSB in the same ecological niche, makes the chemocline of Lake Cadagno an ideal system for studying the conditions and consequences of coexistence of photosynthetic bacteria populations. In this study, we applied flow cytometry (FCM) as a fast tool to identify metabolic changes due to the production and consumption of inclusion bodies such as sulfur globules (SGBs), and follow population dynamics of closely related anoxygenic photosynthetic sulfur bacteria in their natural environment. Large-celled PSB Chromatium okenii and GSB Chlorobium populations were reliably separated and identified due to differences in auto-fluorescence and cell size. Moreover, we showed that these dominant taxa share the same ecological niche over seasonal periods. Taking advantage of FCM detection of dynamic cellular complexity variation during phases of photosynthetic activity, we identified an unexpected alternation in PSB versus GSB metabolic activity, indicating dynamic interspecific interactions between these two populations.
Collapse
Affiliation(s)
- Francesco Danza
- Laboratory of Applied Microbiology (LMA), Department for Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, Bellinzona, Switzerland
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Nicola Storelli
- Laboratory of Applied Microbiology (LMA), Department for Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, Bellinzona, Switzerland
| | - Samuele Roman
- Laboratory of Applied Microbiology (LMA), Department for Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, Bellinzona, Switzerland
- Alpine Biology Center Foundation, via Mirasole 22a, Bellinzona, Switzerland
| | - Samuel Lüdin
- Laboratory of Applied Microbiology (LMA), Department for Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, Bellinzona, Switzerland
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Federal Office for Civil Protection, Spiez Laboratory, Biology Division, Spiez, Switzerland
| | - Mauro Tonolla
- Laboratory of Applied Microbiology (LMA), Department for Environmental Constructions and Design (DACD), University of Applied Sciences and Arts of Southern Switzerland (SUPSI), via Mirasole 22a, Bellinzona, Switzerland
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- Alpine Biology Center Foundation, via Mirasole 22a, Bellinzona, Switzerland
- * E-mail:
| |
Collapse
|
124
|
Probandt D, Eickhorst T, Ellrott A, Amann R, Knittel K. Microbial life on a sand grain: from bulk sediment to single grains. ISME JOURNAL 2017; 12:623-633. [PMID: 29192905 PMCID: PMC5776476 DOI: 10.1038/ismej.2017.197] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 11/09/2022]
Abstract
Globally, marine surface sediments constitute a habitat for estimated 1.7 × 1028 prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 104-105 cells were present on grains from 202 to 635 μm diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell-cell distance 4.5±5.9 μm) and protected areas more densely populated (0.5±0.7 μm). Mean cell-cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level operational taxonomic units (OTU)0.97. Only 4-8 single grains are needed to cover 50% of OTU0.97 richness found in bulk sediment. Although bacterial communities differed between sand grains, a core community accounting for >50% of all cells was present on each sand grain. The communities between sediment grains are more similar than between soil macroaggregates.
Collapse
Affiliation(s)
- David Probandt
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| | - Thilo Eickhorst
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany.,University of Bremen, Faculty 2 (Biology/Chemistry), Bremen, Germany
| | - Andreas Ellrott
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| | - Katrin Knittel
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
| |
Collapse
|
125
|
Zhang Y, Wang X, Zhen Y, Mi T, He H, Yu Z. Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea. Front Microbiol 2017; 8:2133. [PMID: 29163420 PMCID: PMC5682103 DOI: 10.3389/fmicb.2017.02133] [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: 05/07/2017] [Accepted: 10/18/2017] [Indexed: 02/03/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria (SOB) have been studied extensively in marine sediments because of their vital roles in both sulfur and carbon cycles, but the available information regarding the highly diverse SRB and SOB communities is not comprehensive. High-throughput sequencing of functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we explored the community structure, diversity, and abundance of SRB and SOB simultaneously through 16S rRNA, dsrB and soxB gene high-throughput sequencing and quantitative PCR analyses of core samples from the East China Sea. Overall, high-throughput sequencing of the dsrB and soxB genes achieved almost complete coverage (>99%) and revealed the high diversity, richness, and operational taxonomic unit (OTU) numbers of the SRB and SOB communities, which suggest the existence of an active sulfur cycle in the study area. Further analysis demonstrated that rare species make vital contributions to the high richness, diversity, and OTU numbers obtained. Depth-based distributions of the dsrB, soxB, and 16S rRNA gene abundances indicated that the SRB abundance might be more sensitive to the sedimentary dynamic environment than those of total bacteria and SOB. In addition, the results of unweighted pair group method with arithmetic mean (UPGMA) clustering analysis and redundancy analysis revealed that environmental parameters, such as depth and dissolved inorganic nitrogen concentrations, and the sedimentary dynamic environment, which differed between the two sampling stations, can significantly influence the community structures of total bacteria, SRB, and SOB. This study provided further comprehensive information regarding the characteristics of SRB and SOB communities.
Collapse
Affiliation(s)
- Yu Zhang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xungong Wang
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yu Zhen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tiezhu Mi
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hui He
- Key Laboratory of Marine Environment and Ecology, Ministry of Education, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Zhigang Yu
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Marine Chemical Theory and Technology, Ministry of Education, Qingdao, China
| |
Collapse
|
126
|
Rastelli E, Corinaldesi C, Dell'Anno A, Tangherlini M, Martorelli E, Ingrassia M, Chiocci FL, Lo Martire M, Danovaro R. High potential for temperate viruses to drive carbon cycling in chemoautotrophy-dominated shallow-water hydrothermal vents. Environ Microbiol 2017; 19:4432-4446. [DOI: 10.1111/1462-2920.13890] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/06/2017] [Accepted: 08/08/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Eugenio Rastelli
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Michael Tangherlini
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Eleonora Martorelli
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
| | - Michela Ingrassia
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Francesco L. Chiocci
- Institute of Environmental Geology and Geoengineering; Italian National Research Council; Rome Italy
- Department of Earth Science; University of Rome Sapienza; Rome Italy
| | - Marco Lo Martire
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
| | - Roberto Danovaro
- Department of Life and Environmental Sciences; Polytechnic University of Marche; Ancona 60131 Italy
- Stazione Zoologica Anton Dohrn; Villa Comunale; Naples 80121 Italy
| |
Collapse
|
127
|
Dyksma S, Pjevac P, Ovanesov K, Mussmann M. Evidence for H 2 consumption by uncultured Desulfobacterales in coastal sediments. Environ Microbiol 2017; 20:450-461. [PMID: 28772023 DOI: 10.1111/1462-2920.13880] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/30/2017] [Indexed: 12/26/2022]
Abstract
Molecular hydrogen (H2 ) is the key intermediate in the anaerobic degradation of organic matter. Its removal by H2 -oxidizing microorganisms is essential to keep anaerobic degradation energetically favourable. Sulfate-reducing microorganisms (SRM) are known as the main H2 scavengers in anoxic marine sediments. Although the community of marine SRM has been extensively studied, those consuming H2 in situ are completely unknown. We combined metagenomics, PCR-based clone libraries, single-amplified genomes (SAGs) and metatranscriptomics to identify potentially H2 -consuming SRM in anoxic coastal sediments. The vast majority of SRM-related H2 ase sequences were assigned to group 1b and 1c [NiFe]-H2 ases of the deltaproteobacterial order Desulfobacterales. Surprisingly, the same sequence types were similarly highly expressed in spring and summer, suggesting that these are stable and integral members of the H2 -consuming community. Notably, one sequence cluster from the SRM group 1 consistently accounted for around half of all [NiFe]-H2 ase transcripts. Using SAGs, we could link this cluster with the 16S rRNA genes of the uncultured Sva0081-group of the family Desulfobacteraceae. Sequencing of 16S rRNA gene amplicons and H2 ase gene libraries suggested consistently high in situ abundance of the Sva0081 group also in other marine sediments. Together with other Desulfobacterales these likely are important H2 -scavengers in marine sediments.
Collapse
Affiliation(s)
- Stefan Dyksma
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Kin Ovanesov
- Department of Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Mussmann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| |
Collapse
|
128
|
Cerqueira T, Pinho D, Froufe H, Santos RS, Bettencourt R, Egas C. Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores. MICROBIAL ECOLOGY 2017; 74:332-349. [PMID: 28144700 DOI: 10.1007/s00248-017-0943-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Menez Gwen, Lucky Strike and Rainbow are the three most visited and well-known deep-sea hydrothermal vent fields in the Azores region, located in the Mid-Atlantic Ridge. Their distinct geological and ecological features allow them to support a diversity of vent communities, which are largely dependent on Bacteria and Archaea capable of anaerobic or microaerophilic metabolism. These communities play important ecological roles through chemoautotrophy, feeding and in establishing symbiotic associations. However, the occurrence and distribution of these microbes remain poorly understood, especially in deep-sea sediments. In this study, we provide for the first time a comparative survey of the sediment-associated microbial communities from these three neighbouring vent fields. Sediment samples collected in the Menez Gwen, Lucky Strike and Rainbow vent fields showed significant differences in trace-metal concentrations and associated microbiomes. The taxonomic profiles of bacterial, archaeal and eukaryotic representatives were assessed by rRNA gene-tag pyrosequencing, identified anaerobic methanogens and microaerobic Epsilonproteobacteria, particularly at the Menez Gwen site, suggesting sediment communities potentially enriched in sub-seafloor microbes rather than from pelagic microbial taxa. Cosmopolitan OTUs were also detected mostly at Lucky Strike and Rainbow sites and affiliated with the bacterial clades JTB255, Sh765B-TzT-29, Rhodospirillaceae and OCS155 marine group and with the archaeal Marine Group I. Some variations in the community composition along the sediment depth were revealed. Elemental contents and hydrothermal influence are suggested as being reflected in the composition of the microbial assemblages in the sediments of the three vent fields. Altogether, these findings represent valuable information for the understanding of the microbial distribution and potential ecological roles in deep-sea hydrothermal fields.
Collapse
Affiliation(s)
- Teresa Cerqueira
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal.
- MARE-Marine and Environmental Sciences Centre-Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal.
| | - Diogo Pinho
- Next Generation Sequencing Unit, UCBiotech-CNC, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Hugo Froufe
- Next Generation Sequencing Unit, UCBiotech-CNC, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| | - Ricardo S Santos
- Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
- MARE-Marine and Environmental Sciences Centre-Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
- OKEANOS Centre, Department of Oceanography and Fisheries, Faculty of Sciences and Technology, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
| | - Raul Bettencourt
- MARE-Marine and Environmental Sciences Centre-Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
- OKEANOS Centre, Department of Oceanography and Fisheries, Faculty of Sciences and Technology, University of the Azores, Rua Prof. Dr. Frederico Machado, 4, 9901-862, Horta, Portugal
| | - Conceição Egas
- Next Generation Sequencing Unit, UCBiotech-CNC, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 8, 3060-197, Cantanhede, Portugal
| |
Collapse
|
129
|
Wasmund K, Mußmann M, Loy A. The life sulfuric: microbial ecology of sulfur cycling in marine sediments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:323-344. [PMID: 28419734 PMCID: PMC5573963 DOI: 10.1111/1758-2229.12538] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.
Collapse
Affiliation(s)
- Kenneth Wasmund
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
| | - Marc Mußmann
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network “Chemistry meets Microbiology”University of ViennaAlthanstrasse 14ViennaA‐1090Austria
- Austrian Polar Research InstituteViennaAustria
| |
Collapse
|
130
|
Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment. Appl Environ Microbiol 2017; 83:AEM.03517-16. [PMID: 28314724 DOI: 10.1128/aem.03517-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/09/2017] [Indexed: 11/20/2022] Open
Abstract
Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria (Thiotrichales) and Epsilonproteobacteria (Campylobacterales) were prevalent during spring, whereas Deltaproteobacteria (Desulfobacterales) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H2S, S0, and S2O32-) and electron acceptors (O2 and NO3-) regulated by seasonal hypoxia.IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments.
Collapse
|
131
|
Stagars MH, Mishra S, Treude T, Amann R, Knittel K. Microbial Community Response to Simulated Petroleum Seepage in Caspian Sea Sediments. Front Microbiol 2017; 8:764. [PMID: 28503173 PMCID: PMC5409227 DOI: 10.3389/fmicb.2017.00764] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 04/12/2017] [Indexed: 11/17/2022] Open
Abstract
Anaerobic microbial hydrocarbon degradation is a major biogeochemical process at marine seeps. Here we studied the response of the microbial community to petroleum seepage simulated for 190 days in a sediment core from the Caspian Sea using a sediment-oil-flow-through (SOFT) system. Untreated (without simulated petroleum seepage) and SOFT sediment microbial communities shared 43% bacterial genus-level 16S rRNA-based operational taxonomic units (OTU0.945) but shared only 23% archaeal OTU0.945. The community differed significantly between sediment layers. The detection of fourfold higher deltaproteobacterial cell numbers in SOFT than in untreated sediment at depths characterized by highest sulfate reduction rates and strongest decrease of gaseous and mid-chain alkane concentrations indicated a specific response of hydrocarbon-degrading Deltaproteobacteria. Based on an increase in specific CARD-FISH cell numbers, we suggest the following groups of sulfate-reducing bacteria to be likely responsible for the observed decrease in aliphatic and aromatic hydrocarbon concentration in SOFT sediments: clade SCA1 for propane and butane degradation, clade LCA2 for mid- to long-chain alkane degradation, clade Cyhx for cycloalkanes, pentane and hexane degradation, and relatives of Desulfobacula for toluene degradation. Highest numbers of archaea of the genus Methanosarcina were found in the methanogenic zone of the SOFT core where we detected preferential degradation of long-chain hydrocarbons. Sequencing of masD, a marker gene for alkane degradation encoding (1-methylalkyl)succinate synthase, revealed a low diversity in SOFT sediment with two abundant species-level MasD OTU0.96.
Collapse
Affiliation(s)
- Marion H Stagars
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Sonakshi Mishra
- Department of Marine Biogeochemistry, GEOMAR - Helmholtz Centre for Ocean Research KielKiel, Germany
| | - Tina Treude
- Department of Marine Biogeochemistry, GEOMAR - Helmholtz Centre for Ocean Research KielKiel, Germany.,Department of Earth, Planetary and Space Sciences, University of California, Los Angeles, Los AngelesCA, USA.,Department of Atmospheric and Oceanic Sciences, University of California, Los Angeles, Los AngelesCA, USA
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| |
Collapse
|
132
|
Gomez-Saez GV, Pop Ristova P, Sievert SM, Elvert M, Hinrichs KU, Bühring SI. Relative Importance of Chemoautotrophy for Primary Production in a Light Exposed Marine Shallow Hydrothermal System. Front Microbiol 2017; 8:702. [PMID: 28484442 PMCID: PMC5399606 DOI: 10.3389/fmicb.2017.00702] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/05/2017] [Indexed: 01/09/2023] Open
Abstract
The unique geochemistry of marine shallow-water hydrothermal systems promotes the establishment of diverse microbial communities with a range of metabolic pathways. In contrast to deep-sea vents, shallow-water vents not only support chemosynthesis, but also phototrophic primary production due to the availability of light. However, comprehensive studies targeting the predominant biogeochemical processes are rare, and consequently a holistic understanding of the functioning of these ecosystems is currently lacking. To this end, we combined stable isotope probing of lipid biomarkers with an analysis of the bacterial communities to investigate if chemoautotrophy, in parallel to photoautotrophy, plays an important role in autotrophic carbon fixation and to identify the key players. The study was carried out at a marine shallow-water hydrothermal system located at 5 m water depth off Dominica Island (Lesser Antilles), characterized by up to 55°C warm hydrothermal fluids that contain high amounts of dissolved Fe2+. Analysis of the bacterial diversity revealed Anaerolineae of the Chloroflexi as the most abundant bacterial class. Furthermore, the presence of key players involved in iron cycling generally known from deep-sea hydrothermal vents (e.g., Zetaproteobacteria and Geothermobacter), supported the importance of iron-driven redox processes in this hydrothermal system. Uptake of 13C-bicarbonate into bacterial fatty acids under light and dark conditions revealed active photo- and chemoautotrophic communities, with chemoautotrophy accounting for up to 65% of the observed autotrophic carbon fixation. Relatively increased 13C-incorporation in the dark allowed the classification of aiC15:0, C15:0, and iC16:0 as potential lipid biomarkers for bacterial chemoautotrophy in this ecosystem. Highest total 13C-incorporation into fatty acids took place at the sediment surface, but chemosynthesis was found to be active down to 8 cm sediment depth. In conclusion, this study highlights the relative importance of chemoautotrophy compared to photoautotrophy in a shallow-water hydrothermal system, emphasizing chemosynthesis as a prominent process for biomass production in marine coastal environments influenced by hydrothermalism.
Collapse
Affiliation(s)
- Gonzalo V Gomez-Saez
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Petra Pop Ristova
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM - Center for Marine Environmental Sciences and Department of Geosciences, University of BremenBremen, Germany
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology Group, MARUM - Center for Marine Environmental Sciences, University of BremenBremen, Germany
| |
Collapse
|
133
|
Graham EB, Crump AR, Resch CT, Fansler S, Arntzen E, Kennedy DW, Fredrickson JK, Stegen JC. Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes. Environ Microbiol 2017; 19:1552-1567. [DOI: 10.1111/1462-2920.13720] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/08/2017] [Accepted: 03/01/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Emily B. Graham
- Biological Sciences Division, Pacific Northwest National Laboratory; Richland WA USA
| | - Alex R. Crump
- Biological Sciences Division, Pacific Northwest National Laboratory; Richland WA USA
| | - Charles T. Resch
- Geochemistry Department, Pacific Northwest National Laboratory; Richland WA USA
| | - Sarah Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory; Richland WA USA
| | - Evan Arntzen
- Environmental Compliance and Emergency Preparation, Pacific Northwest National Laboratory; Richland WA USA
| | - David W. Kennedy
- Biological Sciences Division, Pacific Northwest National Laboratory; Richland WA USA
| | - Jim K. Fredrickson
- Biological Sciences Division, Pacific Northwest National Laboratory; Richland WA USA
| | - James C. Stegen
- Biological Sciences Division, Pacific Northwest National Laboratory; Richland WA USA
| |
Collapse
|
134
|
Hamann E, Tegetmeyer HE, Riedel D, Littmann S, Ahmerkamp S, Chen J, Hach PF, Strous M. Syntrophic linkage between predatory Carpediemonas and specific prokaryotic populations. ISME JOURNAL 2017; 11:1205-1217. [PMID: 28211847 PMCID: PMC5437931 DOI: 10.1038/ismej.2016.197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/28/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
Abstract
Most anoxic environments are populated by small (<10 μm) heterotrophic eukaryotes that prey on different microbial community members. How predatory eukaryotes engage in beneficial interactions with other microbes has rarely been investigated so far. Here, we studied an example of such an interaction by cultivating the anerobic marine flagellate, Carpediemonas frisia sp. nov. (supergroup Excavata), with parts of its naturally associated microbiome. This microbiome consisted of so far uncultivated members of the Deltaproteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia and Nanoarchaeota. Using genome and transcriptome informed metabolic network modeling, we showed that Carpediemonas stimulated prokaryotic growth through the release of predigested biomolecules such as proteins, sugars, organic acids and hydrogen. Transcriptional gene activities suggested niche separation between biopolymer degrading Bacteroidetes, monomer utilizing Firmicutes and Nanoarchaeota and hydrogen oxidizing Deltaproteobacteria. An efficient metabolite exchange between the different community members appeared to be promoted by the formation of multispecies aggregates. Physiological experiments showed that Carpediemonas could also benefit from an association to these aggregates, as it facilitated the removal of inhibiting metabolites and increased the availability of prey bacteria. Taken together, our results provide a framework to understand how predatory microbial eukaryotes engage, across trophic levels, in beneficial interactions with specific prokaryotic populations.
Collapse
Affiliation(s)
- Emmo Hamann
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Dietmar Riedel
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sten Littmann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jianwei Chen
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.,Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philipp F Hach
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Strous
- Department of Geoscience, University of Calgary, Calgary, AB, Canada.,Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| |
Collapse
|
135
|
Probandt D, Knittel K, Tegetmeyer HE, Ahmerkamp S, Holtappels M, Amann R. Permeability shapes bacterial communities in sublittoral surface sediments. Environ Microbiol 2017; 19:1584-1599. [PMID: 28120371 DOI: 10.1111/1462-2920.13676] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 11/29/2022]
Abstract
The first interaction of water column-derived organic matter with benthic microbial communities takes place in surface sediments which are acting as biological filters catalyzing central steps of elemental cycling. Here we analyzed the bacterial diversity and community structure of sediment top layers at seven sites in the North Sea where sediment properties ranged from coarse-grained and highly permeable to fine-grained and impermeable. Bacterial communities in surface sediments were richer, more even and significantly different from communities in bottom waters as revealed by Illumina tag sequencing of 16S rRNA genes. Sediment permeability had a clear influence on community composition which was confirmed by CARD-FISH. Sulfate-reducing Desulfobacteraceae (2-5% of total cells), Flavobacteriaceae (3-5%) were more abundant in impermeable than in highly permeable sediments where acidobacterial Sva0725 dominated (11-15%). Myxobacterial Sandaracinaceae were most abundant in medium permeable sediments (3-7%). Woeseiaceae/JTB255 and Planctomycetes were major groups in all sediments (4-6%, 8-22%). Planctomycetes were highly diverse and branched throughout the phylum. We propose Planctomycetes as key bacteria for degradation of high molecular weight compounds and recalcitrant material entering surface sediments from the water column. Benthic Flavobacteriaceae likely have restricted capabilities for macromolecule degradation and might profit with Sandaracinaceae and Acidobacteria from low molecular weight compounds.
Collapse
Affiliation(s)
- D Probandt
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - K Knittel
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - H E Tegetmeyer
- Center for Biotechnology, Bielefeld University, Bielefeld, 33615, Germany
| | - S Ahmerkamp
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - M Holtappels
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| | - R Amann
- Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany
| |
Collapse
|
136
|
Ihara H, Hori T, Aoyagi T, Takasaki M, Katayama Y. Sulfur-Oxidizing Bacteria Mediate Microbial Community Succession and Element Cycling in Launched Marine Sediment. Front Microbiol 2017; 8:152. [PMID: 28217124 PMCID: PMC5289976 DOI: 10.3389/fmicb.2017.00152] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 01/20/2017] [Indexed: 11/13/2022] Open
Abstract
A large amount of marine sediment was launched on land by the Great East Japan earthquake. Here, we employed both on-site and laboratory studies on the launched marine sediment to investigate the succession of microbial communities and its effects on geochemical properties of the sediment. Twenty-two-month on-site survey showed that microbial communities at the uppermost layer (0–2 mm depth) of the sediment changed significantly with time, whereas those at the deeper layer (20–40 mm depth) remained nearly unchanged and kept anaerobic microbial communities. Nine months after the incidence, various sulfur-oxidizing bacteria (SOB) prevailed in the uppermost layer, in which afterwards diverse chemoorganotrophic bacteria predominated. Geochemical analyses indicated that the concentration of metals other than Fe was lower in the uppermost layer than that in the deeper layer. Laboratory study was carried out by incubating the sediment for 57 days, and clearly indicated the dynamic transition of microbial communities in the uppermost layer exposed to atmosphere. SOB affiliated in the class Epsilonproteobacteria rapidly proliferated and dominated at the uppermost layer during the first 3 days, after that Fe(II)-oxidizing bacteria and chemoorganotrophic bacteria were sequentially dominant. Furthermore, the concentration of sulfate ion increased and the pH decreased. Consequently, SOB may have influenced the mobilization of heavy metals in the sediment by metal-bound sulfide oxidation and/or sediment acidification. These results demonstrate that SOB initiated the dynamic shift from the anaerobic to aerobic microbial communities, thereby playing a critical role in element cycling in the marine sediment.
Collapse
Affiliation(s)
- Hideyuki Ihara
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology Fuchu, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology Tsukuba, Japan
| | - Mitsuru Takasaki
- Department of Food and Environmental Sciences, Faculty of Science and Engineering, Ishinomaki Senshu University Ishinomaki, Japan
| | - Yoko Katayama
- Institute of Agriculture, Tokyo University of Agriculture and Technology Fuchu, Japan
| |
Collapse
|
137
|
Fabian J, Zlatanovic S, Mutz M, Premke K. Fungal-bacterial dynamics and their contribution to terrigenous carbon turnover in relation to organic matter quality. THE ISME JOURNAL 2017; 11:415-425. [PMID: 27983721 PMCID: PMC5270572 DOI: 10.1038/ismej.2016.131] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/24/2016] [Accepted: 08/05/2016] [Indexed: 01/14/2023]
Abstract
Ecological functions of fungal and bacterial decomposers vary with environmental conditions. However, the response of these decomposers to particulate organic matter (POM) quality, which varies widely in aquatic ecosystems, remains poorly understood. Here we investigated how POM pools of substrates of different qualities determine the relative contributions of aquatic fungi and bacteria to terrigenous carbon (C) turnover. To this end, surface sediments were incubated with different POM pools of algae and/or leaf litter. 13C stable-isotope measurements of C mineralization were combined with phospholipid analysis to link the metabolic activities and substrate preferences of fungal and bacterial heterotrophs to dynamics in their abundance. We found that the presence of labile POM greatly affected the dominance of bacteria over fungi within the degrader communities and stimulated the decomposition of beech litter primarily through an increase in metabolic activity. Our data indicated that fungi primarily contribute to terrigenous C turnover by providing litter C for the microbial loop, whereas bacteria determine whether the supplied C substrate is assimilated into biomass or recycled back into the atmosphere in relation to phosphate availability. Thus, this study provides a better understanding of the role of fungi and bacteria in terrestrial-aquatic C cycling in relation to environmental conditions.
Collapse
Affiliation(s)
- Jenny Fabian
- Department Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Sanja Zlatanovic
- Department of Freshwater Conservation, BTU-Cottbus Senftenberg, Bad Saarow, Germany
| | - Michael Mutz
- Department of Freshwater Conservation, BTU-Cottbus Senftenberg, Bad Saarow, Germany
| | - Katrin Premke
- Department Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| |
Collapse
|
138
|
Mußmann M, Pjevac P, Krüger K, Dyksma S. Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments. ISME JOURNAL 2017; 11:1276-1281. [PMID: 28060363 DOI: 10.1038/ismej.2016.185] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 11/09/2022]
Abstract
To date, very little is known about the bacterial core community of marine sediments. Here we study the environmental distribution, abundance and ecogenomics of the gammaproteobacterial Woeseiaceae/JTB255 marine benthic group. A meta-analysis of published work shows that the Woeseiaceae/JTB255 are ubiquitous and consistently rank among the most abundant 16S rRNA gene sequences in diverse marine sediments. They account for up to 22% of bacterial amplicons and 6% of total cell counts in European and Australian coastal sediments. The analysis of a single-cell genome, metagenomic bins and the genome of the next cultured relative Woeseia oceani indicated a broad physiological range, including heterotrophy and facultative autotrophy. All tested (meta)genomes encode a truncated denitrification pathway to nitrous oxide. The broad range of energy-yielding metabolisms possibly explains the ubiquity and high abundance of Woeseiaceae/JTB255 in marine sediments, where they carry out diverse, but yet unknown ecological functions.
Collapse
Affiliation(s)
- Marc Mußmann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Karen Krüger
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Stefan Dyksma
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| |
Collapse
|
139
|
Bourke MF, Marriott PJ, Glud RN, Hasler-Sheetal H, Kamalanathan M, Beardall J, Greening C, Cook PL. Metabolism in anoxic permeable sediments is dominated by eukaryotic dark fermentation. NATURE GEOSCIENCE 2017; 10:30-35. [PMID: 28070216 PMCID: PMC5217482 DOI: 10.1038/ngeo2843] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/21/2016] [Indexed: 05/27/2023]
Abstract
Permeable sediments are common across continental shelves and are critical contributors to marine biogeochemical cycling. Organic matter in permeable sediments is dominated by microalgae, which as eukaryotes have different anaerobic metabolic pathways to prokaryotes such as bacteria and archaea. Here we present analyses of flow-through reactor experiments showing that dissolved inorganic carbon is produced predominantly as a result of anaerobic eukaryotic metabolic activity. In our experiments, anaerobic production of dissolved inorganic carbon was consistently accompanied by large dissolved H2 production rates, suggesting the presence of fermentation. The production of both dissolved inorganic carbon and H2 persisted following administration of broad spectrum bactericidal antibiotics, but ceased following treatment with metronidazole. Metronidazole inhibits the ferredoxin/hydrogenase pathway of fermentative eukaryotic H2 production, suggesting that pathway as the source of H2 and dissolved inorganic carbon production. Metabolomic analysis showed large increases in lipid production at the onset of anoxia, consistent with documented pathways of anoxic dark fermentation in microalgae. Cell counts revealed a predominance of microalgae in the sediments. H2 production was observed in dark anoxic cultures of diatoms (Fragilariopsis sp.) and a chlorophyte (Pyramimonas) isolated from the study site, substantiating the hypothesis that microalgae undertake fermentation. We conclude that microalgal dark fermentation could be an important energy-conserving pathway in permeable sediments.
Collapse
Affiliation(s)
- Michael F Bourke
- Water Studies Centre, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Philip J. Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, VIC 3800, Australia
| | - Ronnie N. Glud
- University of Southern Denmark, Nordic Centre for Earth Evolution, Odense M-5230, Denmark
- Scottish Association for Marine Science, Oban PA37 1QA, UK
- University of Aarhus, Arctic Research Centre, Aarhus, Denmark
| | - Harald Hasler-Sheetal
- University of Southern Denmark, Nordic Centre for Earth Evolution, Odense M-5230, Denmark
- University of Southern Denmark, Villum Center for Bioanalytical Sciences, Odense M-5230, Denmark
| | - Manoj Kamalanathan
- Department of Marine Biology, Texas A&M University. Galveston, TX, 77554 USA
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Perran L.M. Cook
- Water Studies Centre, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| |
Collapse
|
140
|
Lovley DR. Happy together: microbial communities that hook up to swap electrons. ISME JOURNAL 2016; 11:327-336. [PMID: 27801905 DOI: 10.1038/ismej.2016.136] [Citation(s) in RCA: 179] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/29/2016] [Accepted: 09/04/2016] [Indexed: 12/22/2022]
Abstract
The discovery of direct interspecies electron transfer (DIET) and cable bacteria has demonstrated that microbial cells can exchange electrons over long distances (μm-cm) through electrical connections. For example, in the presence of cable bacteria electrons are rapidly transported over centimeter distances, coupling the oxidation of reduced sulfur compounds in anoxic sediments to oxygen reduction in overlying surficial sediments. Bacteria and archaea wired for DIET are found in anaerobic methane-producing and methane-consuming communities. Electrical connections between gut microbes and host cells have also been proposed. Iterative environmental and defined culture studies on methanogenic communities revealed the importance of electrically conductive pili and c-type cytochromes in natural electrical grids, and demonstrated that conductive carbon materials and magnetite can substitute for these biological connectors to facilitate DIET. This understanding has led to strategies to enhance and stabilize anaerobic digestion. Key unknowns warranting further investigation include elucidation of the archaeal electrical connections facilitating DIET-based methane production and consumption; and the mechanisms for long-range electron transfer through cable bacteria. A better understanding of mechanisms for cell-to-cell electron transfer could facilitate the hunt for additional electrically connected microbial communities with omics approaches and could advance spin-off applications such as the development of sustainable bioelectronics materials and bioelectrochemical technologies.
Collapse
Affiliation(s)
- Derek R Lovley
- Department of Microbiology, Morrill IV N Science Center, University of Massachusetts, Amherst, MA, USA
| |
Collapse
|
141
|
Lipsewers YA, Hopmans EC, Meysman FJR, Sinninghe Damsté JS, Villanueva L. Abundance and Diversity of Denitrifying and Anammox Bacteria in Seasonally Hypoxic and Sulfidic Sediments of the Saline Lake Grevelingen. Front Microbiol 2016; 7:1661. [PMID: 27812355 PMCID: PMC5071380 DOI: 10.3389/fmicb.2016.01661] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/05/2016] [Indexed: 11/13/2022] Open
Abstract
Denitrifying and anammox bacteria are involved in the nitrogen cycling in marine sediments but the environmental factors that regulate the relative importance of these processes are not well constrained. Here, we evaluated the abundance, diversity, and potential activity of denitrifying, anammox, and sulfide-dependent denitrifying bacteria in the sediments of the seasonally hypoxic saline Lake Grevelingen, known to harbor an active microbial community involved in sulfur oxidation pathways. Depth distributions of 16S rRNA gene, nirS gene of denitrifying and anammox bacteria, aprA gene of sulfur-oxidizing and sulfate-reducing bacteria, and ladderane lipids of anammox bacteria were studied in sediments impacted by seasonally hypoxic bottom waters. Samples were collected down to 5 cm depth (1 cm resolution) at three different locations before (March) and during summer hypoxia (August). The abundance of denitrifying bacteria did not vary despite of differences in oxygen and sulfide availability in the sediments, whereas anammox bacteria were more abundant in the summer hypoxia but in those sediments with lower sulfide concentrations. The potential activity of denitrifying and anammox bacteria as well as of sulfur-oxidizing, including sulfide-dependent denitrifiers and sulfate-reducing bacteria, was potentially inhibited by the competition for nitrate and nitrite with cable and/or Beggiatoa-like bacteria in March and by the accumulation of sulfide in the summer hypoxia. The simultaneous presence and activity of organoheterotrophic denitrifying bacteria, sulfide-dependent denitrifiers, and anammox bacteria suggests a tight network of bacteria coupling carbon-, nitrogen-, and sulfur cycling in Lake Grevelingen sediments.
Collapse
Affiliation(s)
- Yvonne A Lipsewers
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Ellen C Hopmans
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Filip J R Meysman
- Department of Estuarine and Delta Systems, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht UniversityDen Burg, Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht UniversityUtrecht, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Utrecht University Den Burg, Netherlands
| |
Collapse
|
142
|
Umezawa K, Watanabe T, Miura A, Kojima H, Fukui M. The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T). Stand Genomic Sci 2016; 11:71. [PMID: 27651857 PMCID: PMC5024460 DOI: 10.1186/s40793-016-0196-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/07/2016] [Indexed: 11/10/2022] Open
Abstract
Sulfurifustis variabilis and Sulfuricaulis limicola are autotrophic sulfur-oxidizing bacteria belonging to the family Acidiferrobacteraceae in the order Acidiferrobacterales. The type strains of these species, strain skN76(T) and strain HA5(T), were isolated from lakes in Japan. Here we describe the complete genome sequences of Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T). The genome of Sulfurifustis variabilis skN76(T) consists of one circular chromosome with size of 4.0 Mbp including 3864 protein-coding sequences. The genome of Sulfuricaulis limicola HA5(T) is 2.9 Mbp chromosome with 2763 protein-coding sequences. In both genomes, 46 transfer RNA-coding genes and one ribosomal RNA operon were identified. In the genomes, redundancies of the genes involved in sulfur oxidation and inorganic carbon fixation pathways were observed. This is the first report to show the complete genome sequences of bacteria belonging to the order Acidiferrobacterales in the class Gammaproteobacteria.
Collapse
Affiliation(s)
- Kazuhiro Umezawa
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Tomohiro Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Aya Miura
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819 Japan
| |
Collapse
|
143
|
Microbial ecology: Seeing growth without culture. Nat Microbiol 2016; 1:16158. [PMID: 27562270 DOI: 10.1038/nmicrobiol.2016.158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
144
|
Bienhold C, Zinger L, Boetius A, Ramette A. Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria. PLoS One 2016; 11:e0148016. [PMID: 26814838 PMCID: PMC4731391 DOI: 10.1371/journal.pone.0148016] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/12/2016] [Indexed: 11/19/2022] Open
Abstract
The deep ocean floor covers more than 60% of the Earth's surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000-5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe.
Collapse
Affiliation(s)
- Christina Bienhold
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Lucie Zinger
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Antje Boetius
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Alban Ramette
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany, and Max Planck Institute for Marine Microbiology, Bremen, Germany
| |
Collapse
|