1
|
Meyer NR, Morono Y, Dekas AE. Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant inorganic carbon fixation by heterotrophs. Appl Environ Microbiol 2024; 90:e0044624. [PMID: 38709099 DOI: 10.1128/aem.00446-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The marine subsurface is a long-term sink of atmospheric carbon dioxide with significant implications for climate on geologic timescales. Subsurface microbial cells can either enhance or reduce carbon sequestration in the subsurface, depending on their metabolic lifestyle. However, the activity of subsurface microbes is rarely measured. Here, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to quantify anabolic activity in 3,203 individual cells from the thermally altered deep subsurface in the Guaymas Basin, Mexico (3-75 m below the seafloor, 0-14°C). We observed that a large majority of cells were active (83%-100%), although the rates of biomass generation were low, suggesting cellular maintenance rather than doubling. Mean single-cell activity decreased with increasing sediment depth and temperature and was most strongly correlated with porewater sulfate concentrations. Intracommunity heterogeneity in microbial activity decreased with increasing sediment depth and age. Using a dual-isotope labeling approach, we determined that all active cells analyzed were heterotrophic, deriving the majority of their cellular carbon from organic sources. However, we also detected inorganic carbon assimilation in these heterotrophic cells, likely via processes such as anaplerosis, and determined that inorganic carbon contributes at least 5% of the total biomass carbon in heterotrophs in this community. Our results demonstrate that the deep marine biosphere at Guaymas Basin is largely active and contributes to subsurface carbon cycling primarily by not only assimilating organic carbon but also fixing inorganic carbon. Heterotrophic assimilation of inorganic carbon may be a small yet significant and widespread underappreciated source of labile carbon in the global subsurface. IMPORTANCE The global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of microbial activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay, we found that the majority of cells are active, that activity is likely driven by the availability of energy, and that although heterotrophy is the dominant metabolism, both organic and inorganic carbon are used to generate biomass. Using a new approach, we quantified inorganic carbon assimilation by heterotrophs and highlighted the importance of this often-overlooked mode of carbon assimilation in the subsurface and beyond.
Collapse
Affiliation(s)
- Nicolette R Meyer
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Yuki Morono
- Kochi Institute for Core Sample Research, Institute for Extra-cutting-edge Science and Technology Avantgarde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, Japan
| | - Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, California, USA
| |
Collapse
|
2
|
Lo HY, Wink K, Nitz H, Kästner M, Belder D, Müller JA, Kaster AK. scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling. mSystems 2023; 8:e0099823. [PMID: 37982643 PMCID: PMC10734494 DOI: 10.1128/msystems.00998-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.
Collapse
Affiliation(s)
- Hao-Yu Lo
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Konstantin Wink
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Henrike Nitz
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Detlev Belder
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Jochen A. Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
3
|
Srivastava A, De Corte D, Garcia JAL, Swan BK, Stepanauskas R, Herndl GJ, Sintes E. Interplay between autotrophic and heterotrophic prokaryotic metabolism in the bathypelagic realm revealed by metatranscriptomic analyses. MICROBIOME 2023; 11:239. [PMID: 37925458 PMCID: PMC10625248 DOI: 10.1186/s40168-023-01688-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/02/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Heterotrophic microbes inhabiting the dark ocean largely depend on the settling of organic matter from the sunlit ocean. However, this sinking of organic materials is insufficient to cover their demand for energy and alternative sources such as chemoautotrophy have been proposed. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. METHODS Seawater samples were collected from Labrador Sea Water (LSW, ~ 2000 m depth) in the North Atlantic and incubated in the dark at in situ temperature unamended, amended with 1 µM thiosulfate, or with 1 µM thiosulfate plus 10 µM glucose and 10 µM acetate (thiosulfate plus dissolved organic matter, DOM). Inorganic carbon fixation was measured in the different treatments and samples for metatranscriptomic analyses were collected after 1 h and 72 h of incubation. RESULTS Amendment of LSW with thiosulfate and thiosulfate plus DOM enhanced prokaryotic inorganic carbon fixation. The energy generated via chemoautotrophy and heterotrophy in the amended prokaryotic communities was used for the biosynthesis of glycogen and phospholipids as storage molecules. The addition of thiosulfate stimulated unclassified bacteria, sulfur-oxidizing Deltaproteobacteria (SAR324 cluster bacteria), Epsilonproteobacteria (Sulfurimonas sp.), and Gammaproteobacteria (SUP05 cluster bacteria), whereas, the amendment with thiosulfate plus DOM stimulated typically copiotrophic Gammaproteobacteria (closely related to Vibrio sp. and Pseudoalteromonas sp.). CONCLUSIONS The gene expression pattern of thiosulfate utilizing microbes specifically of genes involved in energy production via sulfur oxidation and coupled to CO2 fixation pathways coincided with the change in the transcriptional profile of the heterotrophic prokaryotic community (genes involved in promoting energy storage), suggesting a fine-tuned metabolic interplay between chemoautotrophic and heterotrophic microbes in the dark ocean. Video Abstract.
Collapse
Affiliation(s)
- Abhishek Srivastava
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Savoyenstrasse 1a, 1160, Vienna, Austria.
| | - Daniele De Corte
- Institute for Chemistry and Biology of the Marine Environment, Carl Von Ossietzky University, Oldenburg, Germany
- Currently at Ocean Technology and Engineering Department, National Oceanography Centre, Southampton, UK
| | - Juan A L Garcia
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Department of Informatics, INS La Ferreria, 08110, Montcada i Reixach, Spain
| | - Brandon K Swan
- National Biodefense Analysis and Countermeasures Center, Frederick, MD, 21702, USA
| | | | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, AB Den Burg, The Netherlands
| | - Eva Sintes
- Ecosystem Oceanography Group (GRECO), Instituto Español de Oceanografía (IEO-CSIC), Centro Oceanográfico de Baleares, Palma, Spain.
| |
Collapse
|
4
|
Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
Collapse
Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| |
Collapse
|
5
|
Burgsdorf I, Sizikov S, Squatrito V, Britstein M, Slaby BM, Cerrano C, Handley KM, Steindler L. Lineage-specific energy and carbon metabolism of sponge symbionts and contributions to the host carbon pool. THE ISME JOURNAL 2021; 16:1163-1175. [PMID: 34876682 PMCID: PMC8941161 DOI: 10.1038/s41396-021-01165-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 10/30/2021] [Accepted: 11/24/2021] [Indexed: 01/19/2023]
Abstract
Marine sponges host a wide diversity of microorganisms, which have versatile modes of carbon and energy metabolism. In this study we describe the major lithoheterotrophic and autotrophic processes in 21 microbial sponge-associated phyla using novel and existing genomic and transcriptomic datasets. We show that the main microbial carbon fixation pathways in sponges are the Calvin–Benson–Bassham cycle (energized by light in Cyanobacteria, by sulfur compounds in two orders of Gammaproteobacteria, and by a wide range of compounds in filamentous Tectomicrobia), the reductive tricarboxylic acid cycle (used by Nitrospirota), and the 3-hydroxypropionate/4-hydroxybutyrate cycle (active in Thaumarchaeota). Further, we observed that some sponge symbionts, in particular Acidobacteria, are capable of assimilating carbon through anaplerotic processes. The lithoheterotrophic lifestyle was widespread and CO oxidation is the main energy source for sponge lithoheterotrophs. We also suggest that the molybdenum-binding subunit of dehydrogenase (encoded by coxL) likely evolved to benefit also organoheterotrophs that utilize various organic substrates. Genomic potential does not necessarily inform on actual contribution of autotrophs to light and dark carbon budgets. Radioisotope assays highlight variability in the relative contributions of photo- and chemoautotrophs to the total carbon pool across different sponge species, emphasizing the importance of validating genomic potential with physiology experimentation.
Collapse
Affiliation(s)
- I Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - S Sizikov
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - V Squatrito
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - M Britstein
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - B M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RD3 Marine Ecology, RU Marine Symbioses, Kiel, Germany
| | - C Cerrano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - K M Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - L Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.
| |
Collapse
|
6
|
Nierychlo M, Singleton CM, Petriglieri F, Thomsen L, Petersen JF, Peces M, Kondrotaite Z, Dueholm MS, Nielsen PH. Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs. Front Microbiol 2021; 12:690251. [PMID: 34248915 PMCID: PMC8267870 DOI: 10.3389/fmicb.2021.690251] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Candidatus Microthrix is one of the most common bulking filamentous microorganisms found in activated sludge wastewater treatment plants (WWTPs) across the globe. One species, Ca. M. parvicella, is frequently observed, but global genus diversity, as well as important aspects of its ecology and physiology, are still unknown. Here, we use the MiDAS ecosystem-specific 16S rRNA gene database in combination with amplicon sequencing of Danish and global WWTPs to investigate Ca. Microthrix spp. diversity, distribution, and factors affecting their global presence. Only two species were abundant across the world confirming low diversity of the genus: the dominant Ca. M. parvicella and an unknown species typically present along with Ca. M. parvicella, although usually in lower abundances. Both species were mostly found in Europe at low-to-moderate temperatures and their growth was favored in municipal WWTPs with advanced process designs. As no isolate is available for the novel species, we propose the name "Candidatus Microthrix subdominans." Ten high-quality metagenome-assembled genomes recovered from Danish WWTPs, including 6 representing the novel Ca. M. subdominans, demonstrated high genetic similarity between the two species with a likely preference for lipids, a putative capability to reduce nitrate and nitrite, and the potential to store lipids and poly-P. Ca. M. subdominans had a potentially more versatile metabolism including additional sugar transporters, higher oxygen tolerance, and the potential to use carbon monoxide as energy source. Newly designed fluorescence in situ hybridization probes revealed similar filamentous morphology for both species. Raman microspectroscopy was used to quantify the in situ levels of intracellular poly-P. Despite the observed similarities in their physiology (both by genomes and in situ), the two species showed different seasonal dynamics in Danish WWTPs through a 13-years survey, possibly indicating occupation of slightly different niches. The genomic information provides the basis for future research into in situ gene expression and regulation, while the new FISH probes provide a useful tool for further characterization in situ. This study is an important step toward understanding the ecology of Ca. Microthrix in WWTPs, which may eventually lead to optimization of control strategies for its growth in this ecosystem.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Per H. Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| |
Collapse
|
7
|
Combining SIMS and mechanistic modelling to reveal nutrient kinetics in an algal-bacterial mutualism. PLoS One 2021; 16:e0251643. [PMID: 34014955 PMCID: PMC8136852 DOI: 10.1371/journal.pone.0251643] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/29/2021] [Indexed: 11/21/2022] Open
Abstract
Microbial communities are of considerable significance for biogeochemical processes, for the health of both animals and plants, and for biotechnological purposes. A key feature of microbial interactions is the exchange of nutrients between cells. Isotope labelling followed by analysis with secondary ion mass spectrometry (SIMS) can identify nutrient fluxes and heterogeneity of substrate utilisation on a single cell level. Here we present a novel approach that combines SIMS experiments with mechanistic modelling to reveal otherwise inaccessible nutrient kinetics. The method is applied to study the onset of a synthetic mutualistic partnership between a vitamin B12-dependent mutant of the alga Chlamydomonas reinhardtii and the B12-producing, heterotrophic bacterium Mesorhizobium japonicum, which is supported by algal photosynthesis. Results suggest that an initial pool of fixed carbon delays the onset of mutualistic cross-feeding; significantly, our approach allows the first quantification of this expected delay. Our method is widely applicable to other microbial systems, and will contribute to furthering a mechanistic understanding of microbial interactions.
Collapse
|
8
|
Yin X, Cai M, Liu Y, Zhou G, Richter-Heitmann T, Aromokeye DA, Kulkarni AC, Nimzyk R, Cullhed H, Zhou Z, Pan J, Yang Y, Gu JD, Elvert M, Li M, Friedrich MW. Subgroup level differences of physiological activities in marine Lokiarchaeota. THE ISME JOURNAL 2021; 15:848-861. [PMID: 33149207 PMCID: PMC8027215 DOI: 10.1038/s41396-020-00818-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 11/12/2022]
Abstract
Asgard is a recently discovered archaeal superphylum, closely linked to the emergence of eukaryotes. Among Asgard archaea, Lokiarchaeota are abundant in marine sediments, but their in situ activities are largely unknown except for Candidatus 'Prometheoarchaeum syntrophicum'. Here, we tracked the activity of Lokiarchaeota in incubations with Helgoland mud area sediments (North Sea) by stable isotope probing (SIP) with organic polymers, 13C-labelled inorganic carbon, fermentation intermediates and proteins. Within the active archaea, we detected members of the Lokiarchaeota class Loki-3, which appeared to mixotrophically participate in the degradation of lignin and humic acids while assimilating CO2, or heterotrophically used lactate. In contrast, members of the Lokiarchaeota class Loki-2 utilized protein and inorganic carbon, and degraded bacterial biomass formed in incubations. Metagenomic analysis revealed pathways for lactate degradation, and involvement in aromatic compound degradation in Loki-3, while the less globally distributed Loki-2 instead rely on protein degradation. We conclude that Lokiarchaeotal subgroups vary in their metabolic capabilities despite overlaps in their genomic equipment, and suggest that these subgroups occupy different ecologic niches in marine sediments.
Collapse
Affiliation(s)
- Xiuran Yin
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Guowei Zhou
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | | | - David A Aromokeye
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Ajinkya C Kulkarni
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Henrik Cullhed
- International Max-Planck Research School for Marine Microbiology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Zhichao Zhou
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Jie Pan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yuchun Yang
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
| | - Marcus Elvert
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Michael W Friedrich
- Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
| |
Collapse
|
9
|
Nierychlo M, McIlroy SJ, Kucheryavskiy S, Jiang C, Ziegler AS, Kondrotaite Z, Stokholm-Bjerregaard M, Nielsen PH. Candidatus Amarolinea and Candidatus Microthrix Are Mainly Responsible for Filamentous Bulking in Danish Municipal Wastewater Treatment Plants. Front Microbiol 2020; 11:1214. [PMID: 32582118 PMCID: PMC7296077 DOI: 10.3389/fmicb.2020.01214] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/12/2020] [Indexed: 01/23/2023] Open
Abstract
Filamentous bulking is a common serious operational problem leading to deteriorated sludge settling that has long been observed in activated sludge biological wastewater treatment systems. A number of bacterial genera found therein possess filamentous morphology, where some have been shown to be implicated in bulking episodes (e.g., Ca. Microthrix), the impact of many others is still not clear. In this study we performed a survey of 17 Danish municipal wastewater treatment plants (WWTPs) with nutrient removal using 16S rRNA amplicon sequencing over a period of 13 years, where all known filamentous bacteria from 30 genera were analyzed. The filamentous community constituted on average 13 ± 6%, and up to 43% of total read abundance with the same genera common to all plants. Ca. Microthrix and several genera belonging to phylum Chloroflexi were among the most abundant filamentous bacteria. The effect of filamentous bacteria on sludge settling properties was analyzed using measurements of the diluted sludge volume index (DSVI). Strong positive correlations with DSVI were observed only for Ca. Microthrix and Ca. Amarolinea, the latter being a novel, recently characterized genus belonging to the phylum Chloroflexi. The bulking potential of other filamentous bacteria was not significant despite their presence in many plants. Low phylogenetic diversity was observed for both Ca. Microthrix and Ca. Amarolinea, making physiological characterization of individual species and potential development of control strategies more feasible. In this study we show that, despite the high diversity of filamentous phylotypes in Danish WWTPs, only few of them were responsible for severe bulking episodes.
Collapse
Affiliation(s)
- Marta Nierychlo
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Simon J. McIlroy
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia
| | - Sergey Kucheryavskiy
- Section of Chemical Engineering, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Chenjing Jiang
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Anja S. Ziegler
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Zivile Kondrotaite
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Mikkel Stokholm-Bjerregaard
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
- Krüger A/S, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| |
Collapse
|
10
|
Spona-Friedl M, Braun A, Huber C, Eisenreich W, Griebler C, Kappler A, Elsner M. Substrate-dependent CO2 fixation in heterotrophic bacteria revealed by stable isotope labelling. FEMS Microbiol Ecol 2020; 96:5828077. [DOI: 10.1093/femsec/fiaa080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/30/2020] [Indexed: 11/14/2022] Open
Abstract
ABSTRACTVirtually all heterotrophs incorporate carbon dioxide by anaplerotic fixation. Little explored, however, is the interdependency of pathways and rates of CO2fixation on the concurrent usage of organic substrate(s). Potentially, this could reveal which substrates out of a pool of dissolved organic carbon are utilised by environmental microorganisms. To explore this possibility, Bacillus subtilis W23 was grown in a minimal medium with normalised amounts of either glucose, lactate or malate as only organic substrates, each together with 1 g/L NaH13CO3. Incorporation of H13CO3− was traced by elemental analysis-isotope ratio mass spectrometry of biomass and gas chromatography-mass spectrometry of protein-derived amino acids. Until the late logarithmic phase, 13C incorporation into the tricarboxylic acid cycle increased with time and occurred via [4–13C]oxaloacetate formed by carboxylation of pyruvate. The levels of 13C incorporation were highest for growth on glucose and lowest on malate. Incorporation of 13C into gluconeogenesis products was mainly detected in the lactate and malate experiment, whereas glucose down-regulated this path. A proof-of-principle study with a natural groundwater community confirmed the ability to determine incorporation from H13CO3− by natural communities leading to specific labelling patterns. This underlines the potential of the labelling approach to characterise carbon sources of heterotrophic microorganisms in their natural environments.
Collapse
Affiliation(s)
- Marina Spona-Friedl
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Alexander Braun
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Claudia Huber
- Chair of Biochemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Wolfgang Eisenreich
- Chair of Biochemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Department of Functional and Evolutionary Ecology, Universität Wien, Althanstr. 14, A-1090 Wien, Austria
| | - Andreas Kappler
- Geomicrobiology, Eberhard-Karls-University Tuebingen, Sigwartstr. 10, 72076 Tuebingen, Germany
| | - Martin Elsner
- Institute of Groundwater Ecology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
- Chair of Analytical Chemistry and Water Chemistry, Technische Universität München, Marchioninistr. 17, 81377 München, Germany
| |
Collapse
|
11
|
Fan NS, Qi R, Huang BC, Jin RC, Yang M. Factors influencing Candidatus Microthrix parvicella growth and specific filamentous bulking control: A review. CHEMOSPHERE 2020; 244:125371. [PMID: 31835053 DOI: 10.1016/j.chemosphere.2019.125371] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/19/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
Candidatus Microthrix parvicella has been frequently detected as the dominant filamentous bacteria in bulking sludge and thus seriously affects the stable operation of activated sludge processes. The extremely low growth rate of Ca. M. parvicella and its sensitivity to environmental variations greatly limit the development of effective techniques to control filamentous bulking. Based on previous investigations, a variety of restrictive substrates, operating and culture conditions, environmental factors and other potential inhibitors have varying degrees of impact on the growth of this microorganism. This review systematically summarizes the key factors affecting Ca. M. parvicella growth with a focus on the influencing mechanism. Recent filamentous bulking control strategies are also critically reviewed and discussed. Additionally, research needs for the next few years are proposed with the aim of establishing effective and specific control strategies for filamentous sludge bulking.
Collapse
Affiliation(s)
- Nian-Si Fan
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Rong Qi
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Bao-Cheng Huang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Ren-Cun Jin
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Min Yang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
12
|
Arandia-Gorostidi N, Alonso-Sáez L, Stryhanyuk H, Richnow HH, Morán XAG, Musat N. Warming the phycosphere: Differential effect of temperature on the use of diatom-derived carbon by two copiotrophic bacterial taxa. Environ Microbiol 2020; 22:1381-1396. [PMID: 32090403 DOI: 10.1111/1462-2920.14954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/25/2020] [Indexed: 11/28/2022]
Abstract
Heterotrophic bacteria associated with microphytoplankton, particularly those colonizing the phycosphere, are major players in the remineralization of algal-derived carbon. Ocean warming might impact dissolved organic carbon (DOC) uptake by microphytoplankton-associated bacteria with unknown biogeochemical implications. Here, by incubating natural seawater samples at three different temperatures, we analysed the effect of experimental warming on the abundance and C and N uptake activity of Rhodobacteraceae and Flavobacteria, two bacterial groups typically associated with microphytoplankton. Using a nano-scale secondary ion mass spectrometry (nanoSIMS) single-cell analysis, we quantified the temperature sensitivity of these two taxonomic groups to the uptake of algal-derived DOC in the microphytoplankton associated fraction with 13 C-bicarbonate and 15 N-leucine as tracers. We found that cell-specific 13 C uptake was similar for both groups (~0.42 fg C h-1 μm-3 ), but Rhodobacteraceae were more active in 15 N-leucine uptake. Due to the higher abundance of Flavobacteria associated with microphytoplankton, this group incorporated fourfold more carbon than Rhodobacteraceae. Cell-specific 13 C uptake was influenced by temperature, but no significant differences were found for 15 N-leucine uptake. Our results show that the contribution of Flavobacteria and Rhodobacteraceae to C assimilation increased up to sixfold and twofold, respectively, with an increase of 3°C above ambient temperature, suggesting that warming may differently affect the contribution of distinct copiotrophic bacterial taxa to carbon cycling.
Collapse
Affiliation(s)
- Nestor Arandia-Gorostidi
- Department of Earth System Science, Stanford University, Green Earth Sciences Building, 367 Panama St., Room 129, Stanford, CA, 94305-4216, USA.,Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Av. Príncipe de Asturias, 70 bis 33212, Gijón, Asturias, Spain
| | - Laura Alonso-Sáez
- AZTI, Marine Research Unit, Txatxarramendi Irla s/n, 48395, Sukarrieta, Bizkaia, Spain
| | - Hryhoriy Stryhanyuk
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hans H Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Xosé Anxelu G Morán
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, 23955, Thuwal, Saudi Arabia
| | - Niculina Musat
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| |
Collapse
|
13
|
Dekas AE, Parada AE, Mayali X, Fuhrman JA, Wollard J, Weber PK, Pett-Ridge J. Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP. Front Microbiol 2019; 10:2682. [PMID: 31920997 PMCID: PMC6927911 DOI: 10.3389/fmicb.2019.02682] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 11/05/2019] [Indexed: 11/28/2022] Open
Abstract
Characterizing and quantifying in situ metabolisms remains both a central goal and challenge for environmental microbiology. Here, we used a single-cell, multi-isotope approach to investigate the anabolic activity of marine microorganisms, with an emphasis on natural populations of Thaumarchaeota. After incubating coastal Pacific Ocean water with 13C-bicarbonate and 15N-amino acids, we used nanoscale secondary ion mass spectrometry (nanoSIMS) to isotopically screen 1,501 individual cells, and 16S rRNA amplicon sequencing to assess community composition. We established isotopic enrichment thresholds for activity and metabolic classification, and with these determined the percentage of anabolically active cells, the distribution of activity across the whole community, and the metabolic lifestyle—chemoautotrophic or heterotrophic—of each cell. Most cells (>90%) were anabolically active during the incubation, and 4–17% were chemoautotrophic. When we inhibited bacteria with antibiotics, the fraction of chemoautotrophic cells detected via nanoSIMS increased, suggesting archaea dominated chemoautotrophy. With fluorescence in situ hybridization coupled to nanoSIMS (FISH-nanoSIMS), we confirmed that most Thaumarchaeota were living chemoautotrophically, while bacteria were not. FISH-nanoSIMS analysis of cells incubated with dual-labeled (13C,15N-) amino acids revealed that most Thaumarchaeota cells assimilated amino-acid-derived nitrogen but not carbon, while bacteria assimilated both. This indicates that some Thaumarchaeota do not assimilate intact amino acids, suggesting intra-phylum heterogeneity in organic carbon utilization, and potentially their use of amino acids for nitrification. Together, our results demonstrate the utility of multi-isotope nanoSIMS analysis for high-throughput metabolic screening, and shed light on the activity and metabolism of uncultured marine archaea and bacteria.
Collapse
Affiliation(s)
- Anne E Dekas
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Alma E Parada
- Department of Earth System Science, Stanford University, Stanford, CA, United States.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Jessica Wollard
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States
| |
Collapse
|
14
|
Eigemann F, Vogts A, Voss M, Zoccarato L, Schulz-Vogt H. Distinctive tasks of different cyanobacteria and associated bacteria in carbon as well as nitrogen fixation and cycling in a late stage Baltic Sea bloom. PLoS One 2019; 14:e0223294. [PMID: 31830057 PMCID: PMC6907833 DOI: 10.1371/journal.pone.0223294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/19/2019] [Indexed: 01/18/2023] Open
Abstract
Cyanobacteria and associated heterotrophic bacteria hold key roles in carbon as well as nitrogen fixation and cycling in the Baltic Sea due to massive cyanobacterial blooms each summer. The species specific activities of different cyanobacterial species as well as the N- and C-exchange of associated heterotrophic bacteria in these processes, however, are widely unknown. Within one time series experiment we tested the cycling in a natural, late stage cyanobacterial bloom by adding 13C bi-carbonate and 15N2, and performed sampling after 10 min, 30 min, 1 h, 6 h and 24 h in order to determine the fixing species as well as the fate of the fixed carbon and nitrogen in the associations. Uptake of 15N and 13C isotopes by the most abundant cyanobacterial species as well as the most abundant associated heterotrophic bacterial groups was then analysed by NanoSIMS. Overall, the filamentous, heterocystous species Dolichospermum sp., Nodularia sp., and Aphanizomenon sp. revealed no or erratic uptake of carbon and nitrogen, indicating mostly inactive cells. In contrary, non-heterocystous Pseudanabaena sp. dominated the nitrogen and carbon fixation, with uptake rates up to 1.49 ± 0.47 nmol N h-1 l-1 and 2.55 ± 0.91 nmol C h-1 l-1. Associated heterotrophic bacteria dominated the subsequent nitrogen remineralization with uptake rates up to 1.2 ± 1.93 fmol N h-1 cell -1, but were also indicative for fixation of di-nitrogen.
Collapse
Affiliation(s)
- Falk Eigemann
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Angela Vogts
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Maren Voss
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Luca Zoccarato
- Department of Stratified Lakes, Leibniz-Institute for Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Heide Schulz-Vogt
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| |
Collapse
|
15
|
DNA- and RNA-SIP Reveal Nitrospira spp. as Key Drivers of Nitrification in Groundwater-Fed Biofilters. mBio 2019; 10:mBio.01870-19. [PMID: 31690672 PMCID: PMC6831773 DOI: 10.1128/mbio.01870-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nitrification, the oxidative process converting ammonia to nitrite and nitrate, is driven by microbes and plays a central role in the global nitrogen cycle. Our earlier investigations based on 16S rRNA and amoA amplicon analysis, amoA quantitative PCR and metagenomics of groundwater-fed biofilters indicated a consistently high abundance of comammox Nitrospira Here, we hypothesized that these nonclassical nitrifiers drive ammonia-N oxidation. Hence, we used DNA and RNA stable isotope probing (SIP) coupled with 16S rRNA amplicon sequencing to identify the active members in the biofilter community when subjected to a continuous supply of NH4 + or NO2 - in the presence of 13C-HCO3 - (labeled) or 12C-HCO3 - (unlabeled). Allylthiourea (ATU) and sodium chlorate were added to inhibit autotrophic ammonia- and nitrite-oxidizing bacteria, respectively. Our results confirmed that lineage II Nitrospira dominated ammonia oxidation in the biofilter community. A total of 78 (8 by RNA-SIP and 70 by DNA-SIP) and 96 (25 by RNA-SIP and 71 by DNA-SIP) Nitrospira phylotypes (at 99% 16S rRNA sequence similarity) were identified as complete ammonia- and nitrite-oxidizing, respectively. We also detected significant HCO3 - uptake by Acidobacteria subgroup10, Pedomicrobium, Rhizobacter, and Acidovorax under conditions that favored ammonia oxidation. Canonical Nitrospira alone drove nitrite oxidation in the biofilter community, and activity of archaeal ammonia-oxidizing taxa was not detected in the SIP fractions. This study provides the first in situ evidence of ammonia oxidation by comammox Nitrospira in an ecologically relevant complex microbiome.IMPORTANCE With this study we provide the first in situ evidence of ecologically relevant ammonia oxidation by comammox Nitrospira in a complex microbiome and document an unexpectedly high H13CO3 - uptake and growth of proteobacterial and acidobacterial taxa under ammonia selectivity. This finding raises the question of whether comammox Nitrospira is an equally important ammonia oxidizer in other environments.
Collapse
|
16
|
Rubio-Rincón FJ, Weissbrodt DG, Lopez-Vazquez CM, Welles L, Abbas B, Albertsen M, Nielsen PH, van Loosdrecht MCM, Brdjanovic D. "Candidatus Accumulibacter delftensis": A clade IC novel polyphosphate-accumulating organism without denitrifying activity on nitrate. WATER RESEARCH 2019; 161:136-151. [PMID: 31189123 DOI: 10.1016/j.watres.2019.03.053] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 03/18/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
Populations of "Candidatus Accumulibacter", a known polyphosphate-accumulating organism, within clade IC have been proposed to perform anoxic P-uptake activity in enhanced biological phosphorus removal (EBPR) systems using nitrate as electron acceptor. However, no consensus has been reached on the ability of "Ca. Accumulibacter" members of clade IC to reduce nitrate to nitrite. Discrepancies might relate to the diverse operational conditions which could trigger the expression of the Nap and/or Nar enzyme and/or to the accuracy in clade classification. This study aimed to assess whether and how certain operational conditions could lead to the enrichment and enhance the denitrification capacity of "Ca. Accumulibacter" within clade IC. To study the potential induction of the denitrifying enzyme, an EBPR culture was enriched under anaerobic-anoxic-oxic (A2O) conditions that, based on fluorescence in situ hybridization and ppk gene sequencing, was composed of around 97% (on a biovolume basis) of affiliates of "Ca. Accumulibacter" clade IC. The influence of the medium composition, sludge retention time (SRT), polyphosphate content of the biomass (poly-P), nitrate dosing approach, and minimal aerobic SRT on potential nitrate reduction were studied. Despite the different studied conditions applied, only a negligible anoxic P-uptake rate was observed, equivalent to maximum 13% of the aerobic P-uptake rate. An increase in the anoxic SRT at the expenses of the aerobic SRT resulted in deterioration of P-removal with limited aerobic P-uptake and insufficient acetate uptake in the anaerobic phase. A near-complete genome (completeness = 100%, contamination = 0.187%) was extracted from the metagenome of the EBPR biomass for the here-proposed "Ca. Accumulibacter delftensis" clade IC. According to full-genome-based phylogenetic analysis, this lineage was distant from the canonical "Ca. Accumulibacter phosphatis", with closest neighbor "Ca. Accumulibacter sp. UW-LDO-IC" within clade IC. This was cross-validated with taxonomic classification of the ppk1 gene sequences. The genome-centric metagenomic analysis highlighted the presence of genes for assimilatory nitrate reductase (nas) and periplasmic nitrate reductase (nap) but no gene for respiratory nitrate reductases (nar). This suggests that "Ca. Accumulibacter delftensis" clade IC was not capable to generate the required energy (ATP) from nitrate under strict anaerobic-anoxic conditions to support an anoxic EBPR metabolism. Definitely, this study stresses the incongruence in denitrification abilities of "Ca. Accumulibacter" clades and reflects the true intra-clade diversity, which requires a thorough investigation within this lineage.
Collapse
Affiliation(s)
- F J Rubio-Rincón
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - D G Weissbrodt
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands; Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - C M Lopez-Vazquez
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands.
| | - L Welles
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands.
| | - B Abbas
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - M Albertsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - P H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg, Denmark.
| | - M C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| | - D Brdjanovic
- Sanitary Engineering Chair Group. Department of Environmental Engineering and Water Technology, IHE-Delft Institute for Water Education, Westvest 7, 2611AX, Delft, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| |
Collapse
|
17
|
Ahad JME, Pakdel H, Gammon PR, Siddique T, Kuznetsova A, Savard MM. Evaluating in situ biodegradation of 13C-labelled naphthenic acids in groundwater near oil sands tailings ponds. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:392-399. [PMID: 29940450 DOI: 10.1016/j.scitotenv.2018.06.159] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
Potential seepage of naphthenic acids (NAs) from tailings ponds into surface water and groundwater is one of the main environmental concerns associated with the Canadian Athabasca oil sands mining operations. Here we report the application of 13C-labelled NA surrogate compounds to evaluate intrinsic biodegradation along groundwater flow-paths originating from oil sands tailings ponds at two different sites: a glacio-fluvial aquifer (Site 1) and a low-lying wetland (Site 2). Microcosms containing the carboxyl group labelled (99%) NA surrogates (cyclohexanecarboxylic acid, CHCA; 1,2-cyclohexanedicarboxylic acid, CHDCA; 1-adamantanecarboxylic acid, ACA) were lowered into monitoring wells for several months to allow sufficient time for substrate degradation and formation of a biofilm in conditions characteristic of the local aquifer. Phospholipid fatty acids (PLFAs), biomarkers for the active microbial population, were extracted from the biofilms for stable carbon isotope (δ13C) analysis. At Site 1, highly 13C-enriched δ13C values (up to ~+7100‰) confirmed the in situ microbial breakdown of CHCA and CHDCA. At Site 2, δ13C-PLFA values from -60.6 to -24.5‰ indicated uptake of a 13C-depleted substrate such as biogenic methane and not 13C-labelled ACA. Determination of the microbial community using 16s RNA sequencing confirmed the presence of methane-oxidizing bacteria in the subsurface at Site 2. The in situ biodegradation of NAs at Site 1 demonstrates that the indigenous microbial population in the shallow subsurface near tailings ponds can readily break down some of these compounds prior to surface water discharge. The lack of evidence for microbial uptake of 13C-labelled ACA at Site 2 demonstrates that other NAs, in particular tricyclic diamondoid acids, may persist in the environment following seepage from tailings ponds or natural sources.
Collapse
Affiliation(s)
- Jason M E Ahad
- Geological Survey of Canada, Natural Resources Canada, Québec, QC G1K 9A9, Canada.
| | - Hooshang Pakdel
- INRS, Centre Eau Terre Environnement, Québec, QC G1K 9A9, Canada
| | - Paul R Gammon
- Geological Survey of Canada, Natural Resources Canada, Ottawa, ON K1A 0E8, Canada
| | - Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Alsu Kuznetsova
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Martine M Savard
- Geological Survey of Canada, Natural Resources Canada, Québec, QC G1K 9A9, Canada
| |
Collapse
|
18
|
Gu Y, Lin D, Fei X, Wang C, Yang Q, Tang Y, Ren X. A novel fluorescent long-chain fatty acid-substituted dye: labeling and biodegrading of Microthrix parvicella. RSC Adv 2018; 8:35855-35862. [PMID: 35547900 PMCID: PMC9088196 DOI: 10.1039/c8ra06986g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/14/2018] [Indexed: 12/30/2022] Open
Abstract
Microthrix parvicella (M. parvicella) is a filamentous bacterium that induces bulking in activated sludge. Here, we used the affinity of long-chain fatty acids (LCFA) for M. parvicella to create a novel fluorescent probe of carbazole modified by LCFA. The structure was characterized by 1H NMR spectroscopy and mass spectrometry. The spectral properties, photostability, and hydrophobic properties of the probe were also characterized. Fluorescent-labeling results showed that it can label M. parvicella in situ and could be biodegraded via metabolism. The stable docking mode of carbazole probes with different fatty acid chains and lipases was also docked by the density functional tight-binding (DFTB) method. M. parvicella in situ could be biodegraded by a novel fluorescent probe of carbazole modified by LCFA(FP1).![]()
Collapse
Affiliation(s)
- Yingchun Gu
- Tianjin Engineering Technology Center of Chemical Wastewater Source Reduction and Recycling, School of Science, Tianjin Chengjian University Tianjin 300384 China
| | - Dayong Lin
- Anda Duosen New Material Technology CO., LTD Heilongjiang Province 151400 China
| | - Xuening Fei
- Tianjin Engineering Technology Center of Chemical Wastewater Source Reduction and Recycling, School of Science, Tianjin Chengjian University Tianjin 300384 China
| | - Cuihong Wang
- Tianjin Engineering Technology Center of Chemical Wastewater Source Reduction and Recycling, School of Science, Tianjin Chengjian University Tianjin 300384 China
| | - Qi Yang
- Tianjin Engineering Technology Center of Chemical Wastewater Source Reduction and Recycling, School of Science, Tianjin Chengjian University Tianjin 300384 China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences (ICCAS) Beijing 100190 China
| | - Xueling Ren
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, School of Pharmaceutical Sciences, Zhengzhou University Henan Province 450001 China
| |
Collapse
|
19
|
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
|
20
|
|
21
|
Jiao X, Fei X, Li S, Lin D, Ma H, Zhang B. Design Mechanism and Property of the Novel Fluorescent Probes for the Identification of Microthrix Parvicella In Situ. MATERIALS 2017; 10:ma10070804. [PMID: 28773166 PMCID: PMC5551847 DOI: 10.3390/ma10070804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/01/2017] [Accepted: 07/07/2017] [Indexed: 11/16/2022]
Abstract
In this study, two novel fluorescent probes, probe A and probe B were designed, synthesized and characterized, based on Microthrix parvicella (M. parvicella) preferring to utilize long-chain fatty acid (LCFA), for the labeling of M. parvicella in activated sludge. The molecular structure of probe A and probe B include long-chain alkane and LCFA, respectively. The results indicated that probe A and probe B had a large stokes shift of 118 nm and 120 nm and high quantum yield of 0.1043 and 0.1058, respectively, which were significantly helpful for the fluorescent labeling. As probe A was more stable than probe B in activated sludge, and the fluorescence intensity keep stable during 24 h, probe A was more suitable for labeling M. parvicella in situ. In addition, through the Image Pro Plus 6 (IPP 6) analysis, a quantitative relationship was established between sludge volume index (SVI) and integral optical density (IOD) of the labeled M. parvicella in activated sludge samples. The relationship between IOD and SVI conforms to Logistic curve (R2 = 0.94).
Collapse
Affiliation(s)
- Xiumei Jiao
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
- Tianjin Key Laboratory of Aquatic Science and Technology, School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China.
| | - Xuening Fei
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
- Tianjin Key Laboratory of Aquatic Science and Technology, School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China.
- School of Science, Tianjin Chengjian University, Tianjin 300384, China.
| | - Songya Li
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
| | - Dayong Lin
- School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China.
| | - Huaji Ma
- Tianjin Key Laboratory of Aquatic Science and Technology, School of Environmental and Municipal Engineering, Tianjin Chengjian University, Tianjin 300384, China.
| | - Baolian Zhang
- School of Science, Tianjin Chengjian University, Tianjin 300384, China.
| |
Collapse
|
22
|
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
|
23
|
Teira E, Hernando-Morales V, Guerrero-Feijóo E, Varela MM. Leucine, starch and bicarbonate utilization by specific bacterial groups in surface shelf waters off Galicia (NW Spain). Environ Microbiol 2017; 19:2379-2390. [PMID: 28370995 DOI: 10.1111/1462-2920.13748] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/14/2017] [Accepted: 03/21/2017] [Indexed: 11/29/2022]
Abstract
The capability of different bacterial populations to degrade abundant polymers, such as algal-derived polysaccharides, or to utilize preferentially polymers over monomers, remains largely unknown. In this study, microautoradiography was combined with fluorescence in situ hybridization (MAR-FISH) to evaluate the ability of Bacteroidetes, SAR11, Roseobacter spp., Gammaproteobacteria and SAR86 cells to use bicarbonate, leucine and starch under natural light conditions at two locations in shelf surface waters off NW Spain. The percentage of cells incorporating bicarbonate was relatively high (mean 32% ± 4%) and was positively correlated with the intensity of solar radiation. The proportion of cells using starch (mean 56% ± 4%) or leucine (mean 47% ± 4%) was significantly higher than that using bicarbonate. On average, SAR11, Roseobacter spp. and Gammaproteobacteria showed a similarly high percentage of cells using leucine (47%-65% of hybridized cells) than using starch (51%-64% of hybridized cells), while Bacteroidetes and SAR86 cells preferentially used starch (53% of hybridized cells) over leucine (34%-40% of hybridized cells). We suggest that the great percentage of bacteria using starch is related to a high ambient availability of polymers associated to algal cell lysis, which, in turn, weakens the short-term coupling between phytoplankton release and bacterial production.
Collapse
Affiliation(s)
- E Teira
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.,Estación de Ciencias Marinas de Toralla (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - V Hernando-Morales
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, 36310, Vigo, Spain.,Estación de Ciencias Marinas de Toralla (ECIMAT), Universidad de Vigo, Vigo, 36331, Spain
| | - E Guerrero-Feijóo
- Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, IEO, Apdo. 130, Coruña, 15080- A, Spain
| | - M M Varela
- Instituto Español de Oceanografía, Centro Oceanográfico de A Coruña, IEO, Apdo. 130, Coruña, 15080- A, Spain
| |
Collapse
|
24
|
Nierychlo M, Nielsen JL, Nielsen PH. Studies of the Ecophysiology of Single Cells in Microbial Communities by (Quantitative) Microautoradiography and Fluorescence In Situ Hybridization (MAR-FISH). ACTA ACUST UNITED AC 2015. [DOI: 10.1007/8623_2015_66] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
|
25
|
Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments. ISME JOURNAL 2015; 9:1966-78. [PMID: 25679534 PMCID: PMC4542026 DOI: 10.1038/ismej.2015.10] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/08/2014] [Accepted: 12/16/2014] [Indexed: 01/30/2023]
Abstract
Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following 13C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas 13C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.
Collapse
|
26
|
Roslev P, Lentz T, Hesselsoe M. Microbial toxicity of methyl tert-butyl ether (MTBE) determined with fluorescent and luminescent bioassays. CHEMOSPHERE 2015; 120:284-291. [PMID: 25128634 DOI: 10.1016/j.chemosphere.2014.07.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/30/2014] [Accepted: 07/05/2014] [Indexed: 06/03/2023]
Abstract
The inhibitory effects of the fuel additive methyl tert-butyl ether (MTBE) and potential degradation products tert-butanol (TBA) and formaldehyde was examined using mixed microbial biomass, and six strains of bioluminescent bacteria and yeast. The purpose was to assess microbial toxicity with quantitative bioluminescent and fluorescent endpoints, and to identify sensitive proxies suitable for monitoring MTBE contamination. Bioluminescent Aliivibrio fischeri DSM 7151 (formerly Vibrio fischeri) appeared highly sensitive to MTBE exposure, and was a superior test organisms compared to lux-tagged Escherichia coli DH5α, Pseudomonas fluorescens DF57-40E7 and Saccharomyces cerevisiae BLYR. EC10 and EC50 for acute MTBE toxicity in A. fischeri were 1.1 and 10.9 mg L(-1), respectively. Long term (24h) MTBE exposure resulted in EC10 values of 0.01 mg L(-1). TBA was significantly less toxic with EC10 and EC50 for acute and chronic toxicity >1000 mg L(-1). Inhibition of bioluminescence was generally a more sensitive endpoint for MTBE toxicity than measuring intracellular ATP levels and heterotrophic CO2 assimilation. A weak estrogenic response was detected for MTBE at concentrations ⩾ 3.7 g L(-1) using an estrogen inducible bioluminescent yeast strain (S. cerevisiae BLYES). Microbial hydrolytic enzyme activity in groundwater was affected by MTBE with EC10 values of 0.5-787 mg L(-1), and EC50 values of 59-3073 for alkaline phosphatase, arylsulfatase, beta-1,4-glucanase, N-acetyl-beta-d-glucosaminidase, and leucine-aminopeptidase. Microbial alkaline phosphatase and beta-1,4-glucanase activity were most sensitive to MTBE exposure with EC50 ⩽ 64.8 mg L(-1). The study suggests that bioassays with luminescent A. fischeri, and fluorescent assays targeting hydrolytic enzyme activity are good candidates for monitoring microbial MTBE toxicity in contaminated water.
Collapse
Affiliation(s)
- Peter Roslev
- Section of Biology and Environmental Science, Aalborg University, DK-9000 Aalborg, Denmark.
| | - Trine Lentz
- Section of Biology and Environmental Science, Aalborg University, DK-9000 Aalborg, Denmark
| | - Martin Hesselsoe
- Amphi Consult ApS, Niels Jernes Vej 10, DK-9220 Aalborg, Denmark.
| |
Collapse
|
27
|
Tracking heavy water (D2O) incorporation for identifying and sorting active microbial cells. Proc Natl Acad Sci U S A 2014; 112:E194-203. [PMID: 25550518 DOI: 10.1073/pnas.1420406112] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort active microbes on the single-cell level in complex samples using stable isotope probing with heavy water (D2O) combined with Raman microspectroscopy. Incorporation of D2O-derived D into the biomass of autotrophic and heterotrophic bacteria and archaea could be unambiguously detected via C-D signature peaks in single-cell Raman spectra, and the obtained labeling pattern was confirmed by nanoscale-resolution secondary ion MS. In fast-growing Escherichia coli cells, label detection was already possible after 20 min. For functional analyses of microbial communities, the detection of D incorporation from D2O in individual microbial cells via Raman microspectroscopy can be directly combined with FISH for the identification of active microbes. Applying this approach to mouse cecal microbiota revealed that the host-compound foragers Akkermansia muciniphila and Bacteroides acidifaciens exhibited distinctive response patterns to amendments of mucin and sugars. By Raman-based cell sorting of active (deuterated) cells with optical tweezers and subsequent multiple displacement amplification and DNA sequencing, novel cecal microbes stimulated by mucin and/or glucosamine were identified, demonstrating the potential of the nondestructive D2O-Raman approach for targeted sorting of microbial cells with defined functional properties for single-cell genomics.
Collapse
|
28
|
Yakimov MM, La Cono V, Smedile F, Crisafi F, Arcadi E, Leonardi M, Decembrini F, Catalfamo M, Bargiela R, Ferrer M, Golyshin PN, Giuliano L. Heterotrophic bicarbonate assimilation is the main process of de novo organic carbon synthesis in hadal zone of the Hellenic Trench, the deepest part of Mediterranean Sea. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:709-722. [PMID: 25756124 DOI: 10.1111/1758-2229.12192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Ammonium-oxidizing chemoautotrophic members of Thaumarchaea are proposed to be the key players in the assimilation of bicarbonate in the dark (ABD). However, this process may also involve heterotrophic metabolic pathways, such as fixation of carbon dioxide (CO2) via various anaplerotic reactions. We collected samples from the depth of 4900 m at the Matapan-Vavilov Deep (MVD) station (Hellenic Trench, Eastern Mediterranean) and used the multiphasic approach to study the ABD mediators in this deep-sea ecosystem. At this depth, our analysis indicated the occurrence of actively CO2-fixing heterotrophic microbial assemblages dominated by Gammaproteobacteria with virtually no Thaumarchaea present. [14C]-bicarbonate incorporation experiments combined with shotgun [14C]-proteomic analysis identified a series of proteins of gammaproteobacterial origin. More than quarter of them were closely related with Alteromonas macleodii ‘deep ecotype’ AltDE, the predominant organism in the microbial community of MVD. The present study demonstrated that in the aphotic/hadal zone of the Mediterranean Sea, the assimilation of bicarbonate is associated with both chemolithoauto- and heterotrophic ABD. In some deep-sea areas, the latter may predominantly contribute to the de novo synthesis of organic carbon which points at the important and yet underestimated role heterotrophic bacterial populations can play the in global carbon cycle/sink in the ocean interior.
Collapse
|
29
|
Lesutienė J, Gorokhova E, Stankevičienė D, Bergman E, Greenberg L. Light increases energy transfer efficiency in a boreal stream. PLoS One 2014; 9:e113675. [PMID: 25412343 PMCID: PMC4239105 DOI: 10.1371/journal.pone.0113675] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 10/30/2014] [Indexed: 11/19/2022] Open
Abstract
Periphyton communities of a boreal stream were exposed to different light and nutrient levels to estimate energy transfer efficiency from primary to secondary producers using labeling with inorganic (13)C. In a one-day field experiment, periphyton grown in fast-flow conditions and dominated by opportunistic green algae were exposed to light levels corresponding to sub-saturating (forest shade) and saturating (open stream section) irradiances, and to N and P nutrient additions. In a two-week laboratory experiment, periphyton grown in low-flow conditions and dominated by slowly growing diatoms were incubated under two sub-saturating light and nutrient enrichment levels as well as grazed and non-grazed conditions. Light had significant positive effect on (13)C uptake by periphyton. In the field experiment, P addition had a positive effect on (13)C uptake but only at sub-saturating light levels, whereas in the laboratory experiment nutrient additions had no effect on the periphyton biomass, (13)C uptake, biovolume and community composition. In the laboratory experiment, the grazer (caddisfly) effect on periphyton biomass specific (13)C uptake and nutrient content was much stronger than the effects of light and nutrients. In particular, grazers significantly reduced periphyton biomass and increased biomass specific (13)C uptake and C:nutrient ratios. The energy transfer efficiency, estimated as a ratio between (13)C uptake by caddisfly and periphyton, was positively affected by light conditions, whereas the nutrient effect was not significant. We suggest that the observed effects on energy transfer were related to the increased diet contribution of highly palatable green algae, stimulated by higher light levels. Also, high heterotrophic microbial activity under low light levels would facilitate energy loss through respiration and decrease overall trophic transfer efficiency. These findings suggest that even a small increase in light intensity could result in community-wide effects on periphyton in boreal streams, with a subsequent increase in energy transfer and system productivity.
Collapse
Affiliation(s)
- Jūratė Lesutienė
- Marine Science and Technology Center, Klaipėda University, Klaipėda, Lithuania
- Department of Biology, Karlstad University, Karlstad, Sweden
- * E-mail:
| | - Elena Gorokhova
- Department of Applied Environmental Sciences, Stockholm University, Stockholm, Sweden
| | | | - Eva Bergman
- Department of Biology, Karlstad University, Karlstad, Sweden
| | - Larry Greenberg
- Department of Biology, Karlstad University, Karlstad, Sweden
| |
Collapse
|
30
|
Muthusamy S, Baltar F, González JM, Pinhassi J. Dynamics of metabolic activities and gene expression in the Roseobacter clade bacterium Phaeobacter sp. strain MED193 during growth with thiosulfate. Appl Environ Microbiol 2014; 80:6933-42. [PMID: 25172867 PMCID: PMC4249017 DOI: 10.1128/aem.02038-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/27/2014] [Indexed: 11/20/2022] Open
Abstract
Metagenomic analyses of surface seawater reveal that genes for sulfur oxidation are widespread in bacterioplankton communities. However, little is known about the metabolic processes used to exploit the energy potentially gained from inorganic sulfur oxidation in oxic seawater. We therefore studied the sox gene system containing Roseobacter clade isolate Phaeobacter sp. strain MED193 in acetate minimal medium with and without thiosulfate. The addition of thiosulfate enhanced the bacterial growth yields up to 40% in this strain. Concomitantly, soxB and soxY gene expression increased about 8-fold with thiosulfate and remained 11-fold higher than that in controls through stationary phase. At stationary phase, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation rates up to 5- and 35-fold, respectively. Several genes involved in anaplerotic CO2 fixation (i.e., pyruvate carboxylase, propionyl coenzyme A [CoA], and crotonyl-CoA carboxylase) were highly expressed during active growth, coinciding with high CO2 fixation rates. The high expression of key genes in the ethylmalonyl-CoA pathway suggests that this is an important pathway for the utilization of two-carbon compounds in Phaeobacter sp. MED193. Overall, our findings imply that Roseobacter clade bacteria carrying sox genes can use their lithotrophic potential to gain additional energy from sulfur oxidation for both increasing their growth capacity and improving their long-term survival.
Collapse
Affiliation(s)
- Saraladevi Muthusamy
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Federico Baltar
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Tenerife, Spain
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| |
Collapse
|
31
|
McIlroy SJ, Starnawska A, Starnawski P, Saunders AM, Nierychlo M, Nielsen PH, Nielsen JL. Identification of active denitrifiers in full-scale nutrient removal wastewater treatment systems. Environ Microbiol 2014; 18:50-64. [DOI: 10.1111/1462-2920.12614] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/22/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Jon McIlroy
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Anna Starnawska
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Piotr Starnawski
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Aaron Marc Saunders
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Marta Nierychlo
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Per Halkjaer Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| | - Jeppe Lund Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering; Center for Microbial Communities; Aalborg University; Aalborg Denmark
| |
Collapse
|
32
|
Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol 2014; 16:2568-90. [PMID: 24571640 PMCID: PMC4122687 DOI: 10.1111/1462-2920.12436] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/14/2014] [Accepted: 02/18/2014] [Indexed: 12/01/2022]
Abstract
Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for l-methionine, followed by fluorescent labelling of AHA-containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)-targeted fluorescence in situ hybridization (FISH), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano-scale secondary ion mass spectrometry ((15)NH(3) assimilation) for individual cells within a sediment-sourced enrichment culture showed concordance between AHA-positive cells and (15)N enrichment. BONCAT-FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single-cell level.
Collapse
Affiliation(s)
- Roland Hatzenpichler
- Divisions of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | | | | | | | | |
Collapse
|
33
|
Sheik AR, Muller EEL, Wilmes P. A hundred years of activated sludge: time for a rethink. Front Microbiol 2014; 5:47. [PMID: 24624120 PMCID: PMC3939435 DOI: 10.3389/fmicb.2014.00047] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/22/2014] [Indexed: 11/28/2022] Open
Abstract
Biological wastewater treatment plants (BWWTPs) based on the activated sludge (AS) process have dramatically improved worldwide water sanitation despite increased urbanization and industrialization. However, current AS-based operations are considered economically and environmentally unsustainable. In this Perspective, we discuss our current understanding of microbial populations and their metabolic transformations in AS-based BWWTPs in view of developing more sustainable processes in the future. In particular, much has been learned over the course of the past 25 years about specialized microorganisms, which could be more comprehensively leveraged to recover energy and/or nutrients from wastewater streams. To achieve this, we propose a bottom-up design approach, focused around the concept of a "wastewater biorefinery column", which would rely on the engineering of distinct ecological niches into a BWWTP in order to guarantee the targeted enrichment of specific organismal groups which in turn will allow the harvest of high-value resources from wastewater. This concept could be seen as a possible grand challenge to microbial ecologists and engineers alike at the centenary of the discovery of the AS process.
Collapse
Affiliation(s)
- Abdul R. Sheik
- Eco-Systems Biology Group, Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| | | | - Paul Wilmes
- Eco-Systems Biology Group, Luxembourg Centre for Systems Biomedicine, University of LuxembourgEsch-sur-Alzette, Luxembourg
| |
Collapse
|
34
|
Hatzenpichler R, Scheller S, Tavormina PL, Babin BM, Tirrell DA, Orphan VJ. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environ Microbiol 2014. [PMID: 24571640 DOI: 10.1111/1462‐2920.12436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Here we describe the application of a new click chemistry method for fluorescent tracking of protein synthesis in individual microorganisms within environmental samples. This technique, termed bioorthogonal non-canonical amino acid tagging (BONCAT), is based on the in vivo incorporation of the non-canonical amino acid L-azidohomoalanine (AHA), a surrogate for l-methionine, followed by fluorescent labelling of AHA-containing cellular proteins by azide-alkyne click chemistry. BONCAT was evaluated with a range of phylogenetically and physiologically diverse archaeal and bacterial pure cultures and enrichments, and used to visualize translationally active cells within complex environmental samples including an oral biofilm, freshwater and anoxic sediment. We also developed combined assays that couple BONCAT with ribosomal RNA (rRNA)-targeted fluorescence in situ hybridization (FISH), enabling a direct link between taxonomic identity and translational activity. Using a methanotrophic enrichment culture incubated under different conditions, we demonstrate the potential of BONCAT-FISH to study microbial physiology in situ. A direct comparison of anabolic activity using BONCAT and stable isotope labelling by nano-scale secondary ion mass spectrometry ((15)NH(3) assimilation) for individual cells within a sediment-sourced enrichment culture showed concordance between AHA-positive cells and (15)N enrichment. BONCAT-FISH offers a fast, inexpensive and straightforward fluorescence microscopy method for studying the in situ activity of environmental microbes on a single-cell level.
Collapse
Affiliation(s)
- Roland Hatzenpichler
- Divisions of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | | | | | | | | | | |
Collapse
|
35
|
Maurice CF, Turnbaugh PJ. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales. FEMS Microbiol Rev 2013; 37:830-48. [PMID: 23550823 DOI: 10.1111/1574-6976.12022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 12/15/2022] Open
Abstract
Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small-to-moderate-sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single-cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities.
Collapse
Affiliation(s)
- Corinne F Maurice
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, 02138, USA
| | | |
Collapse
|
36
|
McIlroy SJ, Kristiansen R, Albertsen M, Karst SM, Rossetti S, Nielsen JL, Tandoi V, Seviour RJ, Nielsen PH. Metabolic model for the filamentous 'Candidatus Microthrix parvicella' based on genomic and metagenomic analyses. ISME JOURNAL 2013; 7:1161-72. [PMID: 23446830 DOI: 10.1038/ismej.2013.6] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
'Candidatus Microthrix parvicella' is a lipid-accumulating, filamentous bacterium so far found only in activated sludge wastewater treatment plants, where it is a common causative agent of sludge separation problems. Despite attracting considerable interest, its detailed physiology is still unclear. In this study, the genome of the RN1 strain was sequenced and annotated, which facilitated the construction of a theoretical metabolic model based on available in situ and axenic experimental data. This model proposes that under anaerobic conditions, this organism accumulates preferentially long-chain fatty acids as triacylglycerols. Utilisation of trehalose and/or polyphosphate stores or partial oxidation of long-chain fatty acids may supply the energy required for anaerobic lipid uptake and storage. Comparing the genome sequence of this isolate with metagenomes from two full-scale wastewater treatment plants with enhanced biological phosphorus removal reveals high similarity, with few metabolic differences between the axenic and the dominant community 'Ca. M. parvicella' strains. Hence, the metabolic model presented in this paper could be considered generally applicable to strains in full-scale treatment systems. The genomic information obtained here will provide the basis for future research into in situ gene expression and regulation. Such information will give substantial insight into the ecophysiology of this unusual and biotechnologically important filamentous bacterium.
Collapse
Affiliation(s)
- Simon Jon McIlroy
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers. Proc Natl Acad Sci U S A 2011; 108:16771-6. [PMID: 21930919 DOI: 10.1073/pnas.1106427108] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Nitrification is a core process in the global nitrogen cycle that is essential for the functioning of many ecosystems. The discovery of autotrophic ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota has changed our perception of the microbiology of nitrification, in particular since their numerical dominance over ammonia-oxidizing bacteria (AOB) in many environments has been revealed. These and other data have led to a widely held assumption that all amoA-encoding members of the Thaumarchaeota (AEA) are autotrophic nitrifiers. In this study, 52 municipal and industrial wastewater treatment plants were screened for the presence of AEA and AOB. Thaumarchaeota carrying amoA were detected in high abundance only in four industrial plants. In one plant, thaumarchaeotes closely related to soil group I.1b outnumbered AOB up to 10,000-fold, and their numbers, which can only be explained by active growth in this continuous culture system, were two to three orders of magnitude higher than could be sustained by autotrophic ammonia oxidation. Consistently, (14)CO(2) fixation could only be detected in AOB but not in AEA in actively nitrifying sludge from this plant via FISH combined with microautoradiography. Furthermore, in situ transcription of archaeal amoA, and very weak in situ labeling of crenarchaeol after addition of (13)CO(2), was independent of the addition of ammonium. These data demonstrate that some amoA-carrying group I.1b Thaumarchaeota are not obligate chemolithoautotrophs.
Collapse
|
38
|
Cultivation-independent detection of autotrophic hydrogen-oxidizing bacteria by DNA stable-isotope probing. Appl Environ Microbiol 2011; 77:4931-8. [PMID: 21622787 DOI: 10.1128/aem.00285-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knallgas bacteria are a physiologically defined group that is primarily studied using cultivation-dependent techniques. Given that current cultivation techniques fail to grow most bacteria, cultivation-independent techniques that selectively detect and identify knallgas bacteria will improve our ability to study their diversity and distribution. We used stable-isotope probing (SIP) to identify knallgas bacteria in rhizosphere soil of legumes and in a microbial mat from Obsidian Pool in Yellowstone National Park. When samples were incubated in the dark, incorporation of (13)CO(2) was H(2) dependent. SIP enabled the detection of knallgas bacteria that were not detected by cultivation, and the majority of bacteria identified in the rhizosphere soils were betaproteobacteria predominantly related to genera previously known to oxidize hydrogen. Bacteria in soil grew on hydrogen at concentrations as low as 100 ppm. A hydB homolog encoding a putative high-affinity NiFe hydrogenase was amplified from (13)C-labeled DNA from both vetch and clover rhizosphere soil. The results indicate that knallgas bacteria can be detected by SIP and populations that respond to different H(2) concentrations can be distinguished. The methods described here should be applicable to a variety of ecosystems and will enable the discovery of additional knallgas bacteria that are resistant to cultivation.
Collapse
|
39
|
Kragelund C, Thomsen TR, Mielczarek AT, Nielsen PH. Eikelboom's morphotype 0803 in activated sludge belongs to the genus Caldilinea in the phylum Chloroflexi. FEMS Microbiol Ecol 2011; 76:451-62. [PMID: 21299573 DOI: 10.1111/j.1574-6941.2011.01065.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Micromanipulated filamentous bacteria from bulking and foaming activated sludge morphologically identified as Eikelboom type 0803 were shown to be affiliated to the genus Caldilinea within the phylum Chloroflexi. Specific FISH probes were designed for their in situ detection and quantification in seven Danish wastewater treatment plants with biological nutrient removal. The survey applied all species-specific probes for Chloroflexi of relevance in activated sludge treatment plants as well as the phylum-specific probes. Type 0803 filaments constituted around 20% of the total Chloroflexi population. In four of the treatment plants, type 0803 and type 0092 co-occurred and were the dominating fraction of the Chloroflexi population. In the other plants, most Chloroflexi could not be identified beyond the phylum level, suggesting a yet far larger diversity. On average, for all plants, the total Chloroflexi population constituted 12% of the entire microbial population and seems to play an important structural role in the sludge floc formation. Ecophysiological characterization of type 0803 showed their potential role in macromolecule conversion as evident by high levels of exoenzyme expression. Acetate was not consumed. Glucose was consumed with oxygen, nitrite and nitrite as electron acceptors, suggesting that type 0803 may be a denitrifier. Their surfaces were hydrophobic, explaining their occasional occurrence in foaming incidents.
Collapse
Affiliation(s)
- Caroline Kragelund
- Department of Biotechnology, Chemistry and Environmental Engineering, Section of Biotechnology, Aalborg University, Aalborg, Denmark
| | | | | | | |
Collapse
|
40
|
Nielsen PH, Mielczarek AT, Kragelund C, Nielsen JL, Saunders AM, Kong Y, Hansen AA, Vollertsen J. A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants. WATER RESEARCH 2010; 44:5070-5088. [PMID: 20723961 DOI: 10.1016/j.watres.2010.07.036] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 07/09/2010] [Accepted: 07/13/2010] [Indexed: 05/29/2023]
Abstract
The microbial populations in 25 full-scale activated sludge wastewater treatment plants with enhanced biological phosphorus removal (EBPR plants) have been intensively studied over several years. Most of the important bacterial groups involved in nitrification, denitrification, biological P removal, fermentation, and hydrolysis have been identified and quantified using quantitative culture-independent molecular methods. Surprisingly, a limited number of core species was present in all plants, constituting on average approx. 80% of the entire communities in the plants, showing that the microbial populations in EBPR plants are rather similar and not very diverse, as sometimes suggested. By focusing on these organisms it is possible to make a comprehensive ecosystem model, where many important aspects in relation to microbial ecosystems and wastewater treatment can be investigated. We have reviewed the current knowledge about these microorganisms with focus on key ecophysiological factors and combined this into a conceptual ecosystem model for EBPR plants. It includes the major pathways of carbon flow with specific organic substances, the dominant populations involved in the transformations, interspecies interactions, and the key factors controlling their presence and activity. We believe that the EBPR process is a perfect model system for studies of microbial ecology in water engineering systems and that this conceptual model can be used for proposing and testing theories based on microbial ecosystem theories, for the development of new and improved quantitative ecosystem models and is beneficial for future design and management of wastewater treatment systems.
Collapse
Affiliation(s)
- Per Halkjaer Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
| | | | | | | | | | | | | | | |
Collapse
|
41
|
|
42
|
Nielsen JL, Kragelund C, Nielsen PH. Combination of fluorescence in situ hybridization with staining techniques for cell viability and accumulation of PHA and polyP in microorganisms in complex microbial systems. Methods Mol Biol 2010; 599:103-116. [PMID: 19882282 DOI: 10.1007/978-1-60761-439-5_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Fluorescence in situ hybridization (FISH) can be combined with a number of staining techniques to reveal the relationships between the microorganisms and their function in complex microbial systems with a single-cell resolution. In this chapter, we have focused on staining methods for intracellular storage compounds (polyhydroxyalkanoates, polyphosphate) and a measure for cell viability, reduction of the tetrazolium-based redox stain CTC. These protocols are optimized for the study of microorganisms in waste-water treatment (activated sludge and biofilms), but they may also be used with minor modifications in many other ecosystems.
Collapse
Affiliation(s)
- Jeppe Lund Nielsen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
| | | | | |
Collapse
|
43
|
Nielsen PH, Kragelund C, Seviour RJ, Nielsen JL. Identity and ecophysiology of filamentous bacteria in activated sludge. FEMS Microbiol Rev 2009; 33:969-98. [DOI: 10.1111/j.1574-6976.2009.00186.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
44
|
Hesselsoe M, Füreder S, Schloter M, Bodrossy L, Iversen N, Roslev P, Nielsen PH, Wagner M, Loy A. Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge. ISME JOURNAL 2009; 3:1349-64. [DOI: 10.1038/ismej.2009.78] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
45
|
Abstract
Among prokaryotes, the large vacuolated marine sulphur bacteria are unique in their ability to store, transport and metabolize significant quantities of sulphur, nitrogen, phosphorus and carbon compounds. In this study, unresolved questions of metabolism, storage management and behaviour were addressed in laboratory experiments with Thioploca species collected on the continental shelf off Chile. The Thioploca cells had an aerobic metabolism with a potential oxygen uptake rate of 1760 micromol O2 per dm(3) biovolume per h, equivalent to 4.4 nmol O2 per min per mg protein. When high ambient sulphide concentrations (approximately 200 microM) were present, a sulphide uptake of 6220+/-2230 micromol H2S per dm(3) per h, (mean+/-s.e.m., n=4) was measured. This sulphide uptake rate was six times higher than the oxidation rate of elemental sulphur by oxygen or nitrate, thus indicating a rapid sulphur accumulation by Thioploca. Thioploca reduce nitrate to ammonium and we found that dinitrogen was not produced, neither through denitrification nor through anammox activity. Unexpectedly, polyphosphate storage was not detectable by microautoradiography in physiological assays or by staining and microscopy. Carbon dioxide fixation increased when nitrate and nitrite were externally available and when organic carbon was added to incubations. Sulphide addition did not increase carbon dioxide fixation, indicating that Thioploca use excess of sulphide to rapidly accumulate sulphur rather than to accelerate growth. This is interpreted as an adaptation to infrequent high sulphate reduction rates in the seabed. The physiology and behaviour of Thioploca are summarized and the adaptations to an environment, dominated by infrequent oxygen availability and periods of high sulphide abundance, are discussed.
Collapse
|
46
|
Morgan-Sagastume F, Nielsen JL, Nielsen PH. Substrate-dependent denitrification of abundant probe-defined denitrifying bacteria in activated sludge. FEMS Microbiol Ecol 2008; 66:447-61. [DOI: 10.1111/j.1574-6941.2008.00571.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
47
|
Kong Y, Xia Y, Nielsen PH. Activity and identity of fermenting microorganisms in full-scale biological nutrient removing wastewater treatment plants. Environ Microbiol 2008; 10:2008-19. [DOI: 10.1111/j.1462-2920.2008.01617.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
48
|
Feisthauer S, Wick LY, Kästner M, Kaschabek SR, Schlömann M, Richnow HH. Differences of heterotrophic 13CO2 assimilation by Pseudomonas knackmussii strain B13 and Rhodococcus opacus 1CP and potential impact on biomarker stable isotope probing. Environ Microbiol 2008; 10:1641-51. [PMID: 18341583 DOI: 10.1111/j.1462-2920.2008.01573.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Motivated by the finding that Pseudomonas knackmussii B13 but not Rhodococcus opacus 1CP grows in the absence of externally provided CO(2), we investigated the assimilation of (13)CO(2) into active cells cultivated with non-labelled glucose as sole energy substrate. (13)C found in the bulk biomass indicated a substantial but different CO(2) assimilation by Pseudomonas and Rhodococcus, respectively (3500 per thousand and 2600 per thousand). Cellular fatty acids were labelled from -15 per thousand to 470 per thousand and amino acids from 500 per thousand to 24,000 per thousand demonstrating clear differences between various compound classes. 'You are what you eat plus 1 per thousand' is therefore only valid for the average bulk C without specific isotope signature deviation of the external CO(2) or carbonates. Odd-numbered and 10-methyl fatty acids, which are much more abundant in Rhodococcus or other Gram-positive bacteria, were up to fivefold higher enriched in (13)C relative to the Pseudomonas fatty acids. A high-level growth-phase-independent, labelling of the oxaloacetate-derived amino acids indicated heterotrophic CO(2) fixation by anaplerotic reactions known to replenish the tricarboxylic acid cycle. Although both strains assimilate CO(2) via similar general pathways, Rhodococcus depends to a much higher extent on carboxylations reactions with external CO(2) owing to the formation of odd-numbered fatty acids. As a general consequence, heterotrophic fixation of CO(2) should be taken into account in investigations of degradation experiments using isotope tracer compounds.
Collapse
Affiliation(s)
- Stefan Feisthauer
- Department of Isotope Biogeochemistry, UFZ - Helmholtz Centre for Environmental Research Leipzig, Permoserstrasse 15, D-04318 Leipzig, Germany
| | | | | | | | | | | |
Collapse
|
49
|
Ecophysiology of the Actinobacteria in activated sludge systems. Antonie van Leeuwenhoek 2008; 94:21-33. [DOI: 10.1007/s10482-008-9226-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Accepted: 02/01/2008] [Indexed: 10/22/2022]
|
50
|
Hesselsoe M, Bjerring ML, Henriksen K, Loll P, Nielsen JL. Method for measuring substrate preferences by individual members of microbial consortia proposed for bioaugmentation. Biodegradation 2007; 19:621-33. [PMID: 18080209 DOI: 10.1007/s10532-007-9167-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Accepted: 11/22/2007] [Indexed: 11/28/2022]
Abstract
In this study we used the assimilation of isotope labeled CO(2) to measure the substrate preferences by two different bioaugmentation mixtures proposed for bioremediation of diesel oil contamination. All active microorganisms assimilate CO(2) in various carboxylation processes involved in growth. The CO(2) assimilation by the two mixtures was measured upon addition of glucose, diesel oil or specific compounds present in diesel oil (naphthalene, toluene, hexadecane, and octane). It was shown that within short term incubations with diesel oil (<5 h), one bioaugmentation mixture was superior to the other regarding the assimilation of CO(2). This observation was confirmed in a labor-intensive long term microcosm study (60 days). The applied method open various possibilities for fast pre-testing of substrate-preferences by microbial-bioaugmentation mixtures without microcosm experiments, on-site tests, and complicated chemical analysis. This study also demonstrates the possibility to obtain further information on the substrate preferences at a single cell level of phylogenetically defined microbial subgroups in bioaugmentation mixtures, based on combined analyses of microautoradiography and fluorescence in situ hybridization.
Collapse
Affiliation(s)
- Martin Hesselsoe
- Department of biotechnology, chemistry and environmental engineering, Aalborg University Denmark, Aalborg, Denmark.
| | | | | | | | | |
Collapse
|