1
|
Hiralal A, Geelhoed JS, Neukirchen S, Meysman FJR. Comparative genomic analysis of nickel homeostasis in cable bacteria. BMC Genomics 2024; 25:692. [PMID: 39009997 PMCID: PMC11247825 DOI: 10.1186/s12864-024-10594-7] [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: 03/27/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetre‑scale electron transport in marine and freshwater sediments. This long‑distance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetre‑long filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickel‑containing cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickel‑dependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genome‑encoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order. RESULTS Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria: Candidatus Electrothrix gigas strain HY10‑6 and Candidatus Electrothrix antwerpensis strain GW3‑4, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genome‑encoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickel‑binding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidine‑rich loop that has been largely expanded compared to RcnA homologs in other organisms. CONCLUSION Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickel‑dependent conduction mechanism that is uniquely found in cable bacteria.
Collapse
Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Sinje Neukirchen
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | - Filip J R Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium.
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| |
Collapse
|
2
|
Hiralal A, Geelhoed JS, Hidalgo-Martinez S, Smets B, van Dijk JR, Meysman FJR. Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads. Microb Genom 2024; 10:001197. [PMID: 38376381 PMCID: PMC10926707 DOI: 10.1099/mgen.0.001197] [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: 11/13/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.
Collapse
Affiliation(s)
- Anwar Hiralal
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | | | - Bent Smets
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
| | | | - Filip J. R. Meysman
- Geobiology Research Group, University of Antwerp, Antwerp, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| |
Collapse
|
3
|
Geelhoed JS, Thorup CA, Bjerg JJ, Schreiber L, Nielsen LP, Schramm A, Meysman FJR, Marshall IPG. Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov. Microbiol Spectr 2023; 11:e0053823. [PMID: 37732806 PMCID: PMC10580974 DOI: 10.1128/spectrum.00538-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.
Collapse
Affiliation(s)
- Jeanine S. Geelhoed
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
| | - Casper A. Thorup
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Jesper J. Bjerg
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Schreiber
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Lars Peter Nielsen
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Filip J. R. Meysman
- Department of Biology, Research Group Geobiology, University of Antwerp, Wilrijk, Belgium
- Department of Biotechnology, Delft University of Technology, Delft, the Netherlands
| | - Ian P. G. Marshall
- Department of Biology, Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| |
Collapse
|
4
|
Xu X, Weng N, Zhang H, van de Velde SJ, Hermans M, Wu F, Huo S. Cable bacteria regulate sedimentary phosphorus release in freshwater sediments. WATER RESEARCH 2023; 242:120218. [PMID: 37390661 DOI: 10.1016/j.watres.2023.120218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 05/14/2023] [Accepted: 06/11/2023] [Indexed: 07/02/2023]
Abstract
Previous studies have demonstrated that e-SOx can regulate the sedimentary release of phosphorus (P) in brackish and marine sediments. When e-SOx is active, an iron (Fe) and manganese (Mn) oxide rich layer is formed near the sediment surface, which prevents P release. When e-SOx becomes inactive, the metal oxide layer is reduced via sulfide-mediated dissolution, and P is subsequently released to the water column. Cable bacteria have been shown to also occur in freshwater sediments. In these sediments, sulfide production is limited, and the metal oxide layer would thus dissolve less efficiently, leaving the P trapped at the sediment surface. This lack of an efficient dissolution mechanism implies that e-SOx could play an important role in the regulation of P availability in eutrophied freshwater streams. To test this hypothesis, we incubated sediments from a eutrophic freshwater river to investigate the impact of cable bacteria on sedimentary cycling of Fe, Mn and P. High-resolution depth profiling of pH, O2 and ΣH2S complemented with FISH analysis and high-throughput gene sequencing showed that the development of e-SOx activity was closely linked to the enrichment of cable bacteria in incubated sediments. Cable bacteria activity caused a strong acidification in the suboxic zone, leading to the dissolution of Fe and Mn minerals and consequently a strong release of dissolved Fe2+ and Mn2+ to the porewater. Oxidation of these mobilized ions at the sediment surface led to the formation of a metal oxide layer that trapped dissolved P, as shown by the enrichment of P-bearing metal oxides in the top layer of the sediment and low phosphate in the pore and overlying water. After e-SOx activity declined, the metal oxide layer did not dissolve and P remained trapped at the surface. Overall, our results suggested cable bacteria can play an important role to counteract eutrophication in freshwater systems.
Collapse
Affiliation(s)
- Xiaoling Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Sebastiaan J van de Velde
- Department of Biology, University of Antwerp, Wilrijk, Belgium; Operationale Directorate Natural Environment, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Martijn Hermans
- Baltic Sea Centre, Stockholm University, Stockholm 106 91, Sweden; Environmental Geochemistry Group, Faculty of Science, University of Helsinki, Helsinki 00560, Finland
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| |
Collapse
|
5
|
Jiang Q, Jing H, Liu H, Du M. Biogeographic distributions of microbial communities associated with anaerobic methane oxidation in the surface sediments of deep-sea cold seeps in the South China Sea. Front Microbiol 2022; 13:1060206. [PMID: 36620029 PMCID: PMC9822730 DOI: 10.3389/fmicb.2022.1060206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Cold seeps are oasis for the microbes in the deep-sea ecosystems, and various cold seeps are located along the northern slope of the South China Sea (SCS). However, by far most microbial ecological studies were limited to specific cold seep in the SCS, and lack of comparison between different regions. Here, the surface sediments (0-4 cm) from the Site F/Haima cold seeps and the Xisha trough in the SCS were used to elucidate the biogeography of microbial communities, with particular interest in the typical functional groups involved in the anaerobic oxidation of methane (AOM) process. Distinct microbial clusters corresponding to the three sampling regions were formed, and significantly higher gene abundance of functional groups were present in the cold seeps than the trough. This biogeographical distribution could be explained by the geochemical characteristics of sediments, such as total nitrogen (TN), total phosphorus (TP), nitrate (NO3 -), total sulfur (TS) and carbon to nitrogen ratios (C/N). Phylogenetic analysis demonstrated that mcrA and pmoA genotypes were closely affiliated with those from wetland and mangroves, where denitrifying anaerobic methane oxidation (DAMO) process frequently occurred; and highly diversified dsrB genotypes were revealed as well. In addition, significantly higher relative abundance of NC10 group was found in the Xisha trough, suggesting that nitrite-dependent DAMO (N-DAMO) process was more important in the hydrate-bearing trough, although its potential ecological contribution to AOM deserves further investigation. Our study also further demonstrated the necessity of combining functional genes and 16S rRNA gene to obtain a comprehensive picture of the population shifts of natural microbial communities among different oceanic regions.
Collapse
Affiliation(s)
- Qiuyun Jiang
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,University of Chinese Academy of Sciences, Beijing, China
| | - Hongmei Jing
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China,HKUST-CAS Sanya Joint Laboratory of Marine Science Research, Chinese Academy of Sciences, Sanya, China,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China,*Correspondence: Hongmei Jing,
| | - Hao Liu
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Mengran Du
- CAS Key Laboratory for Experimental Study Under Deep-sea Extreme Conditions, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| |
Collapse
|
6
|
Vasquez-Cardenas D, Hidalgo-Martinez S, Hulst L, Thorleifsdottir T, Helgason GV, Eiriksson T, Geelhoed JS, Agustsson T, Moodley L, Meysman FJR. Biogeochemical impacts of fish farming on coastal sediments: Insights into the functional role of cable bacteria. Front Microbiol 2022; 13:1034401. [PMID: 36620049 PMCID: PMC9814725 DOI: 10.3389/fmicb.2022.1034401] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Fish farming in sea cages is a growing component of the global food industry. A prominent ecosystem impact of this industry is the increase in the downward flux of organic matter, which stimulates anaerobic mineralization and sulfide production in underlying sediments. When free sulfide is released to the overlying water, this can have a toxic effect on local marine ecosystems. The microbially-mediated process of sulfide oxidation has the potential to be an important natural mitigation and prevention strategy that has not been studied in fish farm sediments. We examined the microbial community composition (DNA-based 16S rRNA gene) underneath two active fish farms on the Southwestern coast of Iceland and performed laboratory incubations of resident sediment. Field observations confirmed the strong geochemical impact of fish farming on the sediment (up to 150 m away from cages). Sulfide accumulation was evidenced under the cages congruent with a higher supply of degradable organic matter from the cages. Phylogenetically diverse microbes capable of sulfide detoxification were present in the field sediment as well as in lab incubations, including cable bacteria (Candidatus Electrothrix), which display a unique metabolism based on long-distance electron transport. Microsensor profiling revealed that the activity of cable bacteria did not exert a dominant impact on the geochemistry of fish farm sediment at the time of sampling. However, laboratory incubations that mimic the recovery process during fallowing, revealed successful enrichment of cable bacteria within weeks, with concomitant high sulfur-oxidizing activity. Overall our results give insight into the role of microbially-mediated sulfide detoxification in aquaculture impacted sediments.
Collapse
Affiliation(s)
- Diana Vasquez-Cardenas
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium,*Correspondence: Diana Vasquez-Cardenas,
| | | | - Lucas Hulst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | | | | | | | | | | | - Leon Moodley
- NORCE Norwegian Research Centre, Randaberg, Norway
| | - Filip J. R. Meysman
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands,Geobiology, Department of Biology, University of Antwerp, Antwerp, Belgium
| |
Collapse
|
7
|
Reductive Cr(VI) Removal under Different Reducing and Electron Donor Conditions—A Soil Microcosm Study. WATER 2022. [DOI: 10.3390/w14142179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Increased groundwater and soil contamination by hexavalent chromium have led to the employment of a variety of detoxification methods. Biological remediation of Cr(VI) polluted aquifers is an eco-friendly method that can be performed in situ by stimulating the indigenous microbial population with organic and inorganic electron donors. In order to study the effect of different redox conditions on microbial remediated Cr(VI) reduction to Cr(III), microcosm experiments were conducted under anaerobic, anoxic, and sulfate-reducing conditions and at hexavalent chromium groundwater concentrations in the 0–3000 μg/L range, with groundwater and soil collected from an industrial area (Inofyta region). As electron donors, molasses, emulsified vegetable oil (EVO), and FeSO4 were employed. To quantitatively describe the degradation kinetics of Cr(VI), pseudo-first-order kinetics were adopted. The results indicate that an anaerobic system dosed with simple or complex external organic carbon sources can lead to practically complete Cr(VI) reduction to Cr(III), while the addition of Fe2+ can further increase Cr(VI) removal rate significantly. Furthermore, Cr(VI) microbial reduction is possible in the presence of NO3− at rates comparable to anaerobic Cr(VI) microbial reduction, while high sulfate concentrations have a negative effect on Cr(VI) bioreduction rates in comparison to lower sulfate concentrations.
Collapse
|
8
|
Xu X, Huo S, Weng N, Zhang H, Ma C, Zhang J, Wu F. Effects of sulfide availability on the metabolic activity and population dynamics of cable bacteria in freshwater sediment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151817. [PMID: 34848270 DOI: 10.1016/j.scitotenv.2021.151817] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Cable bacteria occur in many natural environments, and their electrogenic sulfide oxidation (e-SOx) may influence sediment biogeochemistry. The environmental factors determining the growth and diversity of cable bacteria are poorly known, especially in freshwater sediments. We conducted a laboratory incubation experiment, using freshwater sediments with different sulfide supply levels, to study how sulfide availability in sediment affects the metabolic activity and population dynamics of cable bacteria. A moderate increase in the sulfide availability in sediment significantly promoted metabolic activity and the proliferation of the cable bacteria population, as revealed by enhanced e-SOx intensity and increased bacteria abundance. In high-sulfide treatments there was a more significant increase in the population of cable bacteria in the deeper sediment layers, indicating that increased sulfide availability may expand the vertical scale impact of cable bacteria activities on sediment biogeochemistry. The relative proportions of co-existing species in the cable bacteria population also changed with sulfide supply levels, indicating that sulfide availability can be involved in determining the interspecies relationships of cable bacteria. Our findings provide new insight into the relationship between sediment sulfide availability and the growth, depth distribution, and species composition of cable bacteria, implying the consideration of regulating environmental sulfide availability as a potential management practice for the development of cable bacteria-based environmental biotechnologies.
Collapse
Affiliation(s)
- Xiaoling Xu
- College of Water Sciences, Beijing Normal University, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Shouliang Huo
- College of Water Sciences, Beijing Normal University, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Nanyan Weng
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Hanxiao Zhang
- College of Water Sciences, Beijing Normal University, Beijing 100012, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Chunzi Ma
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Jingtian Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| |
Collapse
|
9
|
Biotic and Abiotic Biostimulation for the Reduction of Hexavalent Chromium in Contaminated Aquifers. WATER 2022. [DOI: 10.3390/w14010089] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Hexavalent chromium is a carcinogenic heavy metal that needs to be removed effectively from polluted aquifers in order to protect public health and the environment. This work aims to evaluate the reduction of Cr(VI) to Cr(III) in a contaminated aquifer through the stimulation of indigenous microbial communities with the addition of reductive agents. Soil-column experiments were conducted in the absence of oxygen and at hexavalent chromium (Cr(VI)) groundwater concentrations in the 1000–2000 μg/L range. Two carbon sources (molasses and EVO) and one iron electron donor (FeSO4·7H2O) were used as ways to stimulate the metabolism and proliferation of Cr(VI) reducing bacteria in-situ. The obtained results indicate that microbial anaerobic respiration and electron transfer can be fundamental to alleviate polluted groundwater from hazardous Cr(VI). The addition of organic electron donors increased significantly Cr(VI) reduction rates in comparison to natural soil attenuation rates. Furthermore, a combination of organic carbon and iron electron donors led to a longer life span of the remediation process and thus increased total Cr(VI) removal. This is the first study to investigate biotic and abiotic Cr(VI) removal by conducting experiments with natural soil and by applying biostimulation to modify the natural existing microbial communities.
Collapse
|
10
|
Using Oxidative Electrodes to Enrich Novel Members in the Desulfobulbaceae Family from Intertidal Sediments. Microorganisms 2021; 9:microorganisms9112329. [PMID: 34835454 PMCID: PMC8618199 DOI: 10.3390/microorganisms9112329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023] Open
Abstract
Members in the family of Desulfobulbaceae may be influential in various anaerobic microbial communities, including those in anoxic aquatic sediments and water columns, and within wastewater treatment facilities and bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs). However, the diversity and roles of the Desulfobulbaceae in these communities have received little attention, and large portions of this family remain uncultured. Here we expand on findings from an earlier study (Li, Reimers, and Alleau, 2020) to more fully characterize Desulfobulbaceae that became prevalent in biofilms on oxidative electrodes of bioelectrochemical reactors. After incubations, DNA extraction, microbial community analyses, and microscopic examination, we found that a group of uncultured Desulfobulbaceae were greatly enriched on electrode surfaces. These Desulfobulbaceae appeared to form filaments with morphological features ascribed to cable bacteria, but the majority were taxonomically distinct from recognized cable bacteria genera. Thus, the present study provides new information about a group of Desulfobulbaceae that can exhibit filamentous morphologies and respire on the oxidative electrodes. While the phylogeny of cable bacteria is still being defined and updated, further enriching these members can contribute to the overall understanding of cable bacteria and may also lead to identification of successful isolation strategies.
Collapse
|
11
|
Frolov EN, Gololobova AV, Klyukina AA, Bonch-Osmolovskaya EA, Pimenov NV, Chernyh NA, Merkel AY. Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs. Microorganisms 2021; 9:2072. [PMID: 34683394 PMCID: PMC8539903 DOI: 10.3390/microorganisms9102072] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Microbial communities of the Kamchatka Peninsula terrestrial hot springs were studied using radioisotopic and cultural approaches, as well as by the amplification and sequencing of dsrB and 16S rRNA genes fragments. Radioisotopic experiments with 35S-labeled sulfate showed that microbial communities of the Kamchatka hot springs are actively reducing sulfate. Both the cultivation experiments and the results of dsrB and 16S rRNA genes fragments analyses indicated the presence of microorganisms participating in the reductive part of the sulfur cycle. It was found that sulfate-reducing prokaryotes (SRP) belonging to Desulfobacterota, Nitrospirota and Firmicutes phyla inhabited neutral and slightly acidic hot springs, while bacteria of phylum Thermodesulofobiota preferred moderately acidic hot springs. In high-temperature acidic springs sulfate reduction was mediated by archaea of the phylum Crenarchaeota, chemoorganoheterotrophic representatives of genus Vulcanisaeta being the most probable candidates. The 16S rRNA taxonomic profiling showed that in most of the studied communities SRP was present only as a minor component. Only in one microbial community, the representatives of genus Vulcanisaeta comprised a significant group. Thus, in spite of comparatively low sulfate concentrations in terrestrial hot springs of the Kamchatka, phylogenetically and metabolically diverse groups of sulfate-reducing prokaryotes are operating there coupling carbon and sulfur cycles in these habitats.
Collapse
Affiliation(s)
- Evgenii N. Frolov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Alexandra V. Gololobova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Elizaveta A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Nikolay A. Chernyh
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| |
Collapse
|
12
|
Asif M, Aziz A, Ashraf G, Iftikhar T, Sun Y, Liu H. Turning the Page: Advancing Detection Platforms for Sulfate Reducing Bacteria and their Perks. CHEM REC 2021; 22:e202100166. [PMID: 34415677 DOI: 10.1002/tcr.202100166] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/05/2021] [Indexed: 12/27/2022]
Abstract
Sulfate reducing bacteria (SRB) are blamed as main culprits in triggering huge corrosion damages by microbiologically influenced corrosion. They obtained their energy through enzymatic conversion of sulfates to sulfides which are highly corrosive. However, conventional SRB detection methods are complex, time-consuming and are not enough sensitive for reliable detection. The advanced biosensing technologies capable of overcoming the aforementioned drawbacks are in demand. So, nanomaterials being economical, environmental friendly and showing good electrocatalytic properties are promising candidates for electrochemical detection of SRB as compared with antibody based assays. Here, we summarize the recent advances in the detection of SRB using different techniques such as PCR, UV visible method, fluorometric method, immunosensors, electrochemical sensors and photoelectrochemical sensors. We also discuss the SRB detection based on determination of sulfide, typical metabolic product of SRB.
Collapse
Affiliation(s)
- Muhammad Asif
- Hubei key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, 430205, China.,Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ayesha Aziz
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, PR China
| | - Ghazala Ashraf
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, PR China
| | - Tayyaba Iftikhar
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Yimin Sun
- Hubei key Laboratory of Plasma Chemistry and Advanced Materials, School of Materials Science and Engineering, Wuhan Institute of Technology, Wuhan, 430205, China
| | - Hongfang Liu
- Key Laboratory of Material Chemistry for Energy Conversion and Storage, Ministry of Education, Hubei Key Laboratory of Material Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| |
Collapse
|
13
|
Thorup C, Petro C, Bøggild A, Ebsen TS, Brokjær S, Nielsen LP, Schramm A, Bjerg JJ. How to grow your cable bacteria: Establishment of a stable single-strain culture in sediment and proposal of Candidatus Electronema aureum GS. Syst Appl Microbiol 2021; 44:126236. [PMID: 34332367 DOI: 10.1016/j.syapm.2021.126236] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023]
Abstract
Cable bacteria are multicellular filamentous bacteria within the Desulfobulbaceae that couple the oxidation of sulfide to the reduction of oxygen over centimeter distances via long distance electron transport (LDET). So far, none of the freshwater or marine cable bacteria species have been isolated into pure culture. Here we describe a method for establishing a stable single-strain cable bacterium culture in partially sterilized sediment. By repeated transfers of a single cable bacterium filament from freshwater pond sediment into autoclaved sediment, we obtained strain GS, identified by its 16S rRNA gene as a member of Ca. Electronema. This strain was further propagated by transferring sediment clumps, and has now been stable within its semi-natural microbial community for several years. Its metagenome-assembled genome was 93% complete, had a size of 2.76 Mbp, and a DNA G + C content of 52%. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) suggest the affiliation of strain GS to Ca. Electronema as a novel species. Cell size, number of outer ridges, and detection of LDET in the GS culture are likewise consistent with Ca. Electronema. Based on these combined features, we therefore describe strain GS as a new cable bacterium species of the candidate genus Electronema, for which we propose the name Candidatus Electronema aureum sp.nov. Although not a pure culture, this stable single-strain culture will be useful for physiological and omics-based studies; similar approaches with single-cell or single-filament transfers into natural medium may also aid the characterization of other difficult-to-culture microbes.
Collapse
Affiliation(s)
- Casper Thorup
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Caitlin Petro
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Andreas Bøggild
- Department for Molecular Biology and Genetics, Aarhus University, Denmark
| | | | - Signe Brokjær
- Section for Microbiology, Department of Biology, Aarhus University, Denmark
| | - Lars Peter Nielsen
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark.
| | - Jesper Jensen Bjerg
- Section for Microbiology, Department of Biology, Aarhus University, Denmark; Center for Electromicrobiology, Aarhus University, Denmark; Center for Geomicrobiology, Aarhus University, Denmark; ECOBE, Department of Biology, University of Antwerp, Belgium
| |
Collapse
|
14
|
Xu X, Huo S, Zhang H, Li X, Wu F. Identification of cable bacteria and its biogeochemical impact on sulfur in freshwater sediments from the Wenyu River. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 769:144541. [PMID: 33482557 DOI: 10.1016/j.scitotenv.2020.144541] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Cable bacteria are filamentous sulfur-oxidizing microorganisms that couple the reduction of oxygen or nitrate in surface sediments with the oxidation of free sulfide in deeper sediments by transferring electrons across centimeter scale distances. The distribution and activities of cable bacteria in freshwater sediments are still poorly understood, especially the impact of cable bacteria on sulfur cycling. The goal of this study was to investigate electrogenic sulfide oxidation associated with cable bacteria in laboratory microcosm incubations of freshwater sediments using microsensor technology, 16S full-length rRNA sequencing, and fluorescence in situ hybridization (FISH) microscopy. Their activity was characterized by a pH maximum of 8.56 in the oxic zone and the formation of a 13.7 ± 0.6 mm wide suboxic zone after 25 days of incubation. Full-length 16S rRNA gene sequences related to cable bacteria were recovered from the sediments and exhibited 93.3%-99.4% nucleotide (nt) similarities with those from other reported freshwater cable bacteria, indicating that new species of cable bacteria were present in the sediments. FISH analysis indicated that cable bacteria density increased with time, reaching a maximum of 95.48 m cm-2 on day 50. The cells grew downwards to 40 mm but were mainly concentrated on the top 0-20 mm of sediment. The cable bacteria continuously consumed H2S in deeper layers and oxidized sulfide into sulfate in the 0-20 mm surface layers, thereby affecting the sulfur cycling within sediments. These findings provide new evidence for the existence of higher diversity of cable bacteria in freshwater sediments than previously known.
Collapse
Affiliation(s)
- Xiaoling Xu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100012, China
| | - Shouliang Huo
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China.
| | - Hanxiao Zhang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China; College of Water Sciences, Beijing Normal University, Beijing 100012, China
| | - Xiaochuang Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| | - Fengchang Wu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Science, Beijing 100012, China
| |
Collapse
|
15
|
Sayavedra L, Li T, Bueno Batista M, Seah BKB, Booth C, Zhai Q, Chen W, Narbad A. Desulfovibrio diazotrophicus sp. nov., a sulfate-reducing bacterium from the human gut capable of nitrogen fixation. Environ Microbiol 2021; 23:3164-3181. [PMID: 33876566 DOI: 10.1111/1462-2920.15538] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/24/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
Sulfate-reducing bacteria (SRB) are widespread in human guts, yet their expansion has been linked to colonic diseases. We report the isolation, sequencing and physiological characterization of strain QI0027T , a novel SRB species belonging to the class Desulfovibrionia. Metagenomic sequencing of stool samples from 45 Chinese individuals, and comparison with 1690 Desulfovibrionaceae metagenome-assembled genomes recovered from humans of diverse geographic locations, revealed the presence of QI0027T in 22 further individuals. QI0027T encoded nitrogen fixation genes and based on the acetylene reduction assay, actively fixed nitrogen. Transcriptomics revealed that QI0027T overexpressed 42 genes in nitrogen-limiting conditions compared to cultures supplemented with ammonia, including genes encoding nitrogenases, a urea uptake system and the urease complex. Reanalyses of 835 public stool metatranscriptomes showed that nitrogenase genes from Desulfovibrio bacteria were expressed in six samples suggesting that nitrogen fixation might be active in the gut environment. Although frequently thought of as a nutrient-rich environment, nitrogen fixation can occur in the human gut. Animals are often nitrogen limited and have evolved diverse strategies to capture biologically active nitrogen, ranging from amino acid transporters to stable associations with beneficial microbes that provide fixed nitrogen. QI0027T is the first Desulfovibrio human isolate for which nitrogen fixation has been demonstrated, suggesting that some sulfate-reducing bacteria could also play a role in the availability of nitrogen in the gut.
Collapse
Affiliation(s)
- Lizbeth Sayavedra
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Tianqi Li
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Marcelo Bueno Batista
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Brandon K B Seah
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Catherine Booth
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Arjan Narbad
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| |
Collapse
|
16
|
Sánchez-Soto MF, Cerqueda-García D, Alcántara-Hernández RJ, Falcón LI, Pech D, Árcega-Cabrera F, Aguirre-Macedo ML, García-Maldonado JQ. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. MICROBIAL ECOLOGY 2021; 81:908-921. [PMID: 33196853 DOI: 10.1007/s00248-020-01631-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
Collapse
Affiliation(s)
- Ma Fernanda Sánchez-Soto
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | | | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Ma Leopoldina Aguirre-Macedo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico.
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México.
| |
Collapse
|
17
|
Sandfeld T, Marzocchi U, Petro C, Schramm A, Risgaard-Petersen N. Electrogenic sulfide oxidation mediated by cable bacteria stimulates sulfate reduction in freshwater sediments. THE ISME JOURNAL 2020; 14:1233-1246. [PMID: 32042102 PMCID: PMC7174387 DOI: 10.1038/s41396-020-0607-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/27/2020] [Accepted: 01/30/2020] [Indexed: 11/08/2022]
Abstract
Cable bacteria are filamentous members of the Desulfobulbaceae family that oxidize sulfide with oxygen or nitrate by transferring electrons over centimeter distances in sediments. Recent studies show that freshwater sediments can support populations of cable bacteria at densities comparable to those found in marine environments. This is surprising since sulfide availability is presumably low in freshwater sediments due to sulfate limitation of sulfate reduction. Here we show that cable bacteria stimulate sulfate reduction in freshwater sediment through promotion of sulfate availability. Comparing experimental freshwater sediments with and without active cable bacteria, we observed a three- to tenfold increase in sulfate concentrations and a 4.5-fold increase in sulfate reduction rates when cable bacteria were present, while abundance and community composition of sulfate-reducing microorganisms (SRM) were unaffected. Correlation and ANCOVA analysis supported the hypothesis that the stimulation of sulfate reduction activity was due to relieve of the kinetic limitations of the SRM community through the elevated sulfate concentrations in sediments with cable bacteria activity. The elevated sulfate concentration was caused by cable bacteria-driven sulfide oxidation, by sulfate production from an indigenous sulfide pool, likely through cable bacteria-mediated dissolution and oxidation of iron sulfides, and by enhanced retention of sulfate, triggered by an electric field generated by the cable bacteria. Cable bacteria in freshwater sediments may thus be an integral component of a cryptic sulfur cycle and provide a mechanism for recycling of the scarce resource sulfate, stimulating sulfate reduction. It is possible that this stimulation has implication for methanogenesis and greenhouse gas emissions.
Collapse
Affiliation(s)
- Tobias Sandfeld
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
| | - Ugo Marzocchi
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
- Department of Chemistry, Vrije Universiteit Brussel, Brussel, Belgium
| | - Caitlin Petro
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark
| | - Nils Risgaard-Petersen
- Department of Bioscience, Section for Microbiology, Aarhus University, Aarhus, Denmark.
- Center for Geomicrobiology, Aarhus University, Aarhus, Denmark.
- Center for Electromicrobiology, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
18
|
Rotterová J, Salomaki E, Pánek T, Bourland W, Žihala D, Táborský P, Edgcomb VP, Beinart RA, Kolísko M, Čepička I. Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis. Curr Biol 2020; 30:2037-2050.e6. [PMID: 32330419 DOI: 10.1016/j.cub.2020.03.064] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/10/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
Oxygen plays a crucial role in energetic metabolism of most eukaryotes. Yet adaptations to low-oxygen concentrations leading to anaerobiosis have independently arisen in many eukaryotic lineages, resulting in a broad spectrum of reduced and modified mitochondrion-related organelles (MROs). In this study, we present the discovery of two new class-level lineages of free-living marine anaerobic ciliates, Muranotrichea, cl. nov. and Parablepharismea, cl. nov., that, together with the class Armophorea, form a major clade of obligate anaerobes (APM ciliates) within the Spirotrichea, Armophorea, and Litostomatea (SAL) group. To deepen our understanding of the evolution of anaerobiosis in ciliates, we predicted the mitochondrial metabolism of cultured representatives from all three classes in the APM clade by using transcriptomic and metagenomic data and performed phylogenomic analyses to assess their evolutionary relationships. The predicted mitochondrial metabolism of representatives from the APM ciliates reveals functional adaptations of metabolic pathways that were present in their last common ancestor and likely led to the successful colonization and diversification of the group in various anoxic environments. Furthermore, we discuss the possible relationship of Parablepharismea to the uncultured deep-sea class Cariacotrichea on the basis of single-gene analyses. Like most anaerobic ciliates, all studied species of the APM clade host symbionts, which we propose to be a significant accelerating factor in the transitions to an obligately anaerobic lifestyle. Our results provide an insight into the evolutionary mechanisms of early transitions to anaerobiosis and shed light on fine-scale adaptations in MROs over a relatively short evolutionary time frame.
Collapse
Affiliation(s)
- Johana Rotterová
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic.
| | - Eric Salomaki
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| | - William Bourland
- Department of Biological Sciences, Boise State University, Boise, ID 83725-1515, USA
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Petr Táborský
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Roxanne A Beinart
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice 370 05, Czech Republic; Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague 128 43, Czech Republic
| |
Collapse
|
19
|
An efficient, cost-effective method for determining the growth rate of sulfate-reducing bacteria using spectrophotometry. MethodsX 2019; 6:2248-2257. [PMID: 31667126 PMCID: PMC6812320 DOI: 10.1016/j.mex.2019.09.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 09/26/2019] [Indexed: 11/21/2022] Open
Abstract
The use of sulfate reducing bacteria (SRBs) in laboratory studies is a common approach for investigating microbially influenced corrosion (MIC). The characteristic formation of black iron sulfide precipitates during SRB growth, however, preclude the use of traditional spectrophotometric approaches for capturing growth data instead necessitating labour-intensive or technically specialized approaches. As such, an understanding of SRB growth responses to experimental conditions is often missing from MIC studies. Bernardez and de Andrade Lima (2015) have outlined a spectrophotometric approach for estimating SRB cell mass via the addition of HCl. This method has potential for the study SRB growth however its applicability is currently limited by the use of large aliquot volumes (45 mL), which restrict the number of timepoints that can sampled from one culture, and the extensive time devoted to cell preparation prior to OD readings. We demonstrate an improved method for capturing SRB growth data via spectrophotometry following acidification. We incorporate lower sample volumes and adapt the method described in Bernardez and de Andrade Lima (2015) to a high throughput microtiter plate approach that increases the efficiency of this method and its applicability to growth rate studies. Our results allay theoretical concerns that acidification may distort growth rate analysis by impacting cells differently depending on their metabolic state. We further demonstrate that this method (acid-amended OD measurements) is more accurate and far more cost efficient than traditional methods (dilution spread-plate counting) and popular molecular methods (quantitative PCR) currently in use in SRB growth research.
Collapse
|
20
|
Martin BC, Bougoure J, Ryan MH, Bennett WW, Colmer TD, Joyce NK, Olsen YS, Kendrick GA. Oxygen loss from seagrass roots coincides with colonisation of sulphide-oxidising cable bacteria and reduces sulphide stress. THE ISME JOURNAL 2019; 13:707-719. [PMID: 30353038 PMCID: PMC6461758 DOI: 10.1038/s41396-018-0308-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 10/02/2018] [Accepted: 10/09/2018] [Indexed: 02/04/2023]
Abstract
Seagrasses thrive in anoxic sediments where sulphide can accumulate to phytotoxic levels. So how do seagrasses persist in this environment? Here, we propose that radial oxygen loss (ROL) from actively growing root tips protects seagrasses from sulphide intrusion not only by abiotically oxidising sulphides in the rhizosphere of young roots, but also by influencing the abundance and spatial distribution of sulphate-reducing and sulphide-oxidising bacteria. We used a novel multifaceted approach combining imaging techniques (confocal fluorescence in situ hybridisation, oxygen planar optodes, and sulphide diffusive gradients in thin films) with microbial community profiling to build a complete picture of the microenvironment of growing roots of the seagrasses Halophila ovalis and Zostera muelleri. ROL was restricted to young root tips, indicating that seagrasses will have limited ability to influence sulphide oxidation in bulk sediments. On the microscale, however, ROL corresponded with decreased abundance of potential sulphate-reducing bacteria and decreased sulphide concentrations in the rhizosphere surrounding young roots. Furthermore, roots leaking oxygen had a higher abundance of sulphide-oxidising cable bacteria; which is the first direct observation of these bacteria on seagrass roots. Thus, ROL may enhance both abiotic and bacterial sulphide oxidation and restrict bacterial sulphide production around vulnerable roots, thereby helping seagrasses to colonise sulphide-rich anoxic sediments.
Collapse
Affiliation(s)
- Belinda C Martin
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- The UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
- Ooid Scientific Graphics and Editing, White Gum Valley, WA, 6163, Australia.
| | - Jeremy Bougoure
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Megan H Ryan
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - William W Bennett
- Environmental Futures Research Institute, Griffith University, Parklands Drive, Southport, QLD, 4215, Australia
| | - Timothy D Colmer
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Natalie K Joyce
- Ooid Scientific Graphics and Editing, White Gum Valley, WA, 6163, Australia
| | - Ylva S Olsen
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| | - Gary A Kendrick
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- The UWA Oceans Institute, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
| |
Collapse
|
21
|
Carvalho V, Freitas E, Fradinho J, Reis M, Oehmen A. The effect of seed sludge on the selection of a photo-EBPR system. N Biotechnol 2019; 49:112-119. [DOI: 10.1016/j.nbt.2018.10.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 10/10/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
|
22
|
Falås P, Jewell KS, Hermes N, Wick A, Ternes TA, Joss A, Nielsen JL. Transformation, CO 2 formation and uptake of four organic micropollutants by carrier-attached microorganisms. WATER RESEARCH 2018; 141:405-416. [PMID: 29859473 DOI: 10.1016/j.watres.2018.03.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/11/2018] [Accepted: 03/15/2018] [Indexed: 05/27/2023]
Abstract
A tiered process was developed to assess the transformation, CO2 formation and uptake of four organic micropollutants by carrier-attached microorganisms from two municipal wastewater treatment plants. At the first tier, primary transformation of ibuprofen, naproxen, diclofenac, and mecoprop by carrier-attached microorganisms was shown by the dissipation of the target compounds and the formation of five transformation products using LC-tandem MS. At the second tier, the microbial cleavage of the four organic micropollutants was confirmed with 14C-labeled micropollutants through liquid scintillation counting of the 14CO2 formed. At the third tier, microautoradiography coupled with fluorescence in situ hybridization (MAR-FISH) was used to screen carrier-attached microorganisms for uptake of the four radiolabeled micropollutants. Results from the MAR-FISH screening indicated that only a small fraction of the microbial community (≤1‰) was involved in the uptake of the radiolabeled micropollutants and that the responsible microorganisms differed between the compounds. At the fourth tier, the microbial community structure of the carrier-attached biofilms was analyzed by 16S rRNA gene amplicon sequencing. The sequencing results showed that the MAR-FISH screening targeted ∼80% of the microbial community and that several taxonomic families within the FISH-probed populations with MAR-positive signals (i.e. Firmicutes, Gammaproteobacteria, and Deltaproteobacteria) were present in both biofilms. From the broader perspective of organic micropollutant removal in biological wastewater treatment, the MAR-FISH results of this study indicate a high degree of microbial substrate specialization that could explain differences in transformation rates and patterns between micropollutants and microbial communities.
Collapse
Affiliation(s)
- Per Falås
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland; Water and Environmental Engineering, Department of Chemical Engineering, Lund University, 221 00 Lund, Sweden.
| | - Kevin S Jewell
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Nina Hermes
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Arne Wick
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Thomas A Ternes
- Federal Institute of Hydrology, Am Mainzer Tor 1, 56068 Koblenz, Germany
| | - Adriano Joss
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Jeppe Lund Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| |
Collapse
|
23
|
Otte JM, Harter J, Laufer K, Blackwell N, Straub D, Kappler A, Kleindienst S. The distribution of active iron‐cycling bacteria in marine and freshwater sediments is decoupled from geochemical gradients. Environ Microbiol 2018; 20:2483-2499. [DOI: 10.1111/1462-2920.14260] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Julia M. Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
| | - Johannes Harter
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
| | - Katja Laufer
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
- Center for Geomicrobiology, Department of BioscienceAarhus University Denmark
| | - Nia Blackwell
- Microbial Ecology, Center for Applied GeosciencesUniversity of Tübingen Germany
| | - Daniel Straub
- Microbial Ecology, Center for Applied GeosciencesUniversity of Tübingen Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen Germany
- Center for Geomicrobiology, Department of BioscienceAarhus University Denmark
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied GeosciencesUniversity of Tübingen Germany
| |
Collapse
|
24
|
Sun J, Ni BJ, Sharma KR, Wang Q, Hu S, Yuan Z. Modelling the long-term effect of wastewater compositions on maximum sulfide and methane production rates of sewer biofilm. WATER RESEARCH 2018; 129:58-65. [PMID: 29132122 DOI: 10.1016/j.watres.2017.11.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/10/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Abstract
Reliable modelling of sulfide and methane production in sewer systems is required for efficient sewer emission management. Wastewater compositions affect sulfide and methane production kinetics through both its short-term variation influencing the substrate availability to sewer biofilms, and its long-term variation affecting the sewer biofilm structure. While the short-term effect is well considered in existing sewer models with the use of Monod or half-order equations, the long-term effect has not been explicitly considered in current sewer models suitable for network modelling. In this study, the long-term effect of wastewater compositions on sulfide and methane production activities in rising main sewers was investigated. A detailed biofilm model was firstly developed, and then calibrated and validated using experimental data measured during the entire biofilm development period of a laboratory sewer reactor. Based on scenario simulations using the detailed biofilm model, empirical equations describing the long-term effect of sulfate and sCOD (soluble chemical oxygen demand) concentrations on kH2S (the maximum sulfide production rate of sewer biofilm) and kCH4 (the maximum methane production rate of sewer biofilm) were proposed. These equations require further verification in future studies before their potential integration into network-wide sewer models.
Collapse
Affiliation(s)
- Jing Sun
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, QLD, 4072, Australia; Cooperative Research Centre for Water Sensitive Cities, Melbourne, Australia; State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, PR China
| | - Bing-Jie Ni
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Keshab Raj Sharma
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, QLD, 4072, Australia; Cooperative Research Centre for Water Sensitive Cities, Melbourne, Australia
| | - Qilin Wang
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Shihu Hu
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Zhiguo Yuan
- Advanced Water Management Centre (AWMC), The University of Queensland, St. Lucia, QLD, 4072, Australia; Cooperative Research Centre for Water Sensitive Cities, Melbourne, Australia.
| |
Collapse
|
25
|
Reimers CE, Li C, Graw MF, Schrader PS, Wolf M. The Identification of Cable Bacteria Attached to the Anode of a Benthic Microbial Fuel Cell: Evidence of Long Distance Extracellular Electron Transport to Electrodes. Front Microbiol 2017; 8:2055. [PMID: 29114243 PMCID: PMC5660804 DOI: 10.3389/fmicb.2017.02055] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/06/2017] [Indexed: 12/14/2022] Open
Abstract
Multicellular, filamentous, sulfur-oxidizing bacteria, known as cable bacteria, were discovered attached to fibers of a carbon brush electrode serving as an anode of a benthic microbial fuel cell (BMFC). The BMFC had been operated in a temperate estuarine environment for over a year before collecting anode samples for scanning electron microscopy and phylogenetic analyses. Individual filaments were attached by single terminus cells with networks of pilus-like nano-filaments radiating out from these cells, across the anode fiber surface, and between adjacent attachment locations. Current harvesting by the BMFC poised the anode at potentials of ~170-250 mV vs. SHE, and these surface potentials appear to have allowed the cable bacteria to use the anode as an electron acceptor in a completely anaerobic environment. A combination of catalyzed reporter deposition fluorescent in situ hybridization (CARD-FISH) and 16S rRNA gene sequence analysis confirmed the phylogeny of the cable bacteria and showed that filaments often occurred in bundles and in close association with members of the genera Desulfuromonas. However, the Desulfobulbaceae Operational Taxonomic Units (OTUs) from the 16S sequencing did not cluster closely with other putative cable bacteria sequences suggesting that the taxonomic delineation of cable bacteria is far from complete.
Collapse
Affiliation(s)
- Clare E Reimers
- College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Cheng Li
- College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Michael F Graw
- College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Paul S Schrader
- College of Earth, Ocean and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
| | - Michael Wolf
- Teledyne Benthos, North Falmouth, MA, United States
| |
Collapse
|
26
|
Mager LF, Koelzer VH, Stuber R, Thoo L, Keller I, Koeck I, Langenegger M, Simillion C, Pfister SP, Faderl M, Genitsch V, Tcymbarevich I, Juillerat P, Li X, Xia Y, Karamitopoulou E, Lyck R, Zlobec I, Hapfelmeier S, Bruggmann R, McCoy KD, Macpherson AJ, Müller C, Beutler B, Krebs P. The ESRP1-GPR137 axis contributes to intestinal pathogenesis. eLife 2017; 6:28366. [PMID: 28975893 PMCID: PMC5665647 DOI: 10.7554/elife.28366] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Aberrant alternative pre-mRNA splicing (AS) events have been associated with several disorders. However, it is unclear whether deregulated AS directly contributes to disease. Here, we reveal a critical role of the AS regulator epithelial splicing regulator protein 1 (ESRP1) for intestinal homeostasis and pathogenesis. In mice, reduced ESRP1 function leads to impaired intestinal barrier integrity, increased susceptibility to colitis and altered colorectal cancer (CRC) development. Mechanistically, these defects are produced in part by modified expression of ESRP1-specific Gpr137 isoforms differently activating the Wnt pathway. In humans, ESRP1 is downregulated in inflamed biopsies from inflammatory bowel disease patients. ESRP1 loss is an adverse prognostic factor in CRC. Furthermore, generation of ESRP1-dependent GPR137 isoforms is altered in CRC and expression of a specific GPR137 isoform predicts CRC patient survival. These findings indicate a central role of ESRP1-regulated AS for intestinal barrier integrity. Alterations in ESRP1 function or expression contribute to intestinal pathology.
Collapse
Affiliation(s)
- Lukas Franz Mager
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | | | - Regula Stuber
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Lester Thoo
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Irene Keller
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Ivonne Koeck
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Cedric Simillion
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Simona P Pfister
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Martin Faderl
- Institute of Pathology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Irina Tcymbarevich
- Division of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Pascal Juillerat
- Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Xiaohong Li
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yu Xia
- Department of Genetics, The Scripps Research Institute, La Jolla, United States
| | | | - Ruth Lyck
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Bern, Switzerland
| | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Kathy D McCoy
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Andrew J Macpherson
- Department of BioMedical Research, University of Bern, Bern, Switzerland.,Department of Gastroenterology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Bruce Beutler
- Center for Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, United States
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
| |
Collapse
|
27
|
Nobu MK, Narihiro T, Liu M, Kuroda K, Mei R, Liu WT. Thermodynamically diverse syntrophic aromatic compound catabolism. Environ Microbiol 2017; 19:4576-4586. [PMID: 28892300 DOI: 10.1111/1462-2920.13922] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/19/2017] [Indexed: 11/28/2022]
Abstract
Specialized organotrophic Bacteria 'syntrophs' and methanogenic Archaea 'methanogens' form a unique metabolic interaction to accomplish cooperative mineralization of organic compounds to CH4 and CO2 . Due to challenges in cultivation of syntrophs, mechanisms for how their organotrophic catabolism circumvents thermodynamic restrictions remain unclear. In this study, we investigate two communities hosting diverse syntrophic aromatic compound metabolizers (Syntrophus, Syntrophorhabdus, Pelotomaculum and an uncultivated Syntrophorhabdacaeae member) to uncover their catabolic diversity and flexibility. Although syntrophs have been generally presumed to metabolize aromatic compounds to acetate, CO2 , H2 and formate, combined metagenomics and metatranscriptomics show that uncultured syntrophs utilize unconventional alternative metabolic pathways in situ producing butyrate, cyclohexanecarboxylate and benzoate as catabolic byproducts. In addition, we also find parallel utilization of diverse H2 and formate generating pathways to facilitate interactions with partner methanogens. Based on thermodynamic calculations, these pathways may enable syntrophs to combat thermodynamic restrictions. In addition, when fed with specific substrates (i.e., benzoate, terephthalate or trimellitate), each syntroph population expresses different pathways, suggesting ecological diversification among syntrophs. These findings suggest we may be drastically underestimating the biochemical capabilities, strategies and diversity of syntrophic bacteria thriving at the thermodynamic limit.
Collapse
Affiliation(s)
- Masaru Konishi Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Miaomiao Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Kyohei Kuroda
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Ave, Urbana, IL 61801, USA
| |
Collapse
|
28
|
Irie K, Fujitani H, Tsuneda S. Physical enrichment of uncultured Accumulibacter and Nitrospira from activated sludge by unlabeled cell sorting technique. J Biosci Bioeng 2016; 122:475-81. [DOI: 10.1016/j.jbiosc.2016.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/07/2016] [Accepted: 03/24/2016] [Indexed: 02/04/2023]
|
29
|
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal-bacterial consortia. Proc Natl Acad Sci U S A 2016; 113:E4069-78. [PMID: 27357680 DOI: 10.1073/pnas.1603757113] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To understand the biogeochemical roles of microorganisms in the environment, it is important to determine when and under which conditions they are metabolically active. Bioorthogonal noncanonical amino acid tagging (BONCAT) can reveal active cells by tracking the incorporation of synthetic amino acids into newly synthesized proteins. The phylogenetic identity of translationally active cells can be determined by combining BONCAT with rRNA-targeted fluorescence in situ hybridization (BONCAT-FISH). In theory, BONCAT-labeled cells could be isolated with fluorescence-activated cell sorting (BONCAT-FACS) for subsequent genetic analyses. Here, in the first application, to our knowledge, of BONCAT-FISH and BONCAT-FACS within an environmental context, we probe the translational activity of microbial consortia catalyzing the anaerobic oxidation of methane (AOM), a dominant sink of methane in the ocean. These consortia, which typically are composed of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria, have been difficult to study due to their slow in situ growth rates, and fundamental questions remain about their ecology and diversity of interactions occurring between ANME and associated partners. Our activity-correlated analyses of >16,400 microbial aggregates provide the first evidence, to our knowledge, that AOM consortia affiliated with all five major ANME clades are concurrently active under controlled conditions. Surprisingly, sorting of individual BONCAT-labeled consortia followed by whole-genome amplification and 16S rRNA gene sequencing revealed previously unrecognized interactions of ANME with members of the poorly understood phylum Verrucomicrobia This finding, together with our observation that ANME-associated Verrucomicrobia are found in a variety of geographically distinct methane seep environments, suggests a broader range of symbiotic relationships within AOM consortia than previously thought.
Collapse
|
30
|
Brasseit J, Althaus-Steiner E, Faderl M, Dickgreber N, Saurer L, Genitsch V, Dolowschiak T, Li H, Finke D, Hardt WD, McCoy KD, Macpherson AJ, Corazza N, Noti M, Mueller C. CD4 T cells are required for both development and maintenance of disease in a new mouse model of reversible colitis. Mucosal Immunol 2016; 9:689-701. [PMID: 26376366 DOI: 10.1038/mi.2015.93] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 08/06/2015] [Indexed: 02/04/2023]
Abstract
Current therapies to treat inflammatory bowel diseases have limited efficacy, significant side effects, and often wane over time. Little is known about the cellular and molecular mechanisms operative in the process of mucosal healing from colitis. To study such events, we developed a new model of reversible colitis in which adoptive transfer of CD4(+)CD45RB(hi) T cells into Helicobacter typhlonius-colonized lymphopenic mice resulted in a rapid onset of colonic inflammation that was reversible through depletion of colitogenic T cells. Remission was associated with an improved clinical and histopathological score, reduced immune cell infiltration to the intestinal mucosa, altered intestinal gene expression profiles, regeneration of the colonic mucus layer, and the restoration of epithelial barrier integrity. Notably, colitogenic T cells were not only critical for induction of colitis but also for maintenance of disease. Depletion of colitogenic T cells resulted in a rapid drop in tumor necrosis factor α (TNFα) levels associated with reduced infiltration of inflammatory immune cells to sites of inflammation. Although neutralization of TNFα prevented the onset of colitis, anti-TNFα treatment of mice with established disease failed to resolve colonic inflammation. Collectively, this new model of reversible colitis provides an important research tool to study the dynamics of mucosal healing in chronic intestinal remitting-relapsing disorders.
Collapse
Affiliation(s)
- J Brasseit
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - E Althaus-Steiner
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - M Faderl
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - N Dickgreber
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - L Saurer
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - V Genitsch
- Division of Clinical Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - T Dolowschiak
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - H Li
- Maurice E. Müller Laboratories, University Clinic for Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - D Finke
- Division of Developmental Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - W-D Hardt
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - K D McCoy
- Maurice E. Müller Laboratories, University Clinic for Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - A J Macpherson
- Maurice E. Müller Laboratories, University Clinic for Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - N Corazza
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - M Noti
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - C Mueller
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| |
Collapse
|
31
|
Qi P, Zhang D, Zeng Y, Wan Y. Biosynthesis of CdS nanoparticles: A fluorescent sensor for sulfate-reducing bacteria detection. Talanta 2016; 147:142-6. [DOI: 10.1016/j.talanta.2015.09.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/12/2015] [Accepted: 09/19/2015] [Indexed: 02/08/2023]
|
32
|
Costabile A, Walton GE, Tzortzis G, Vulevic J, Charalampopoulos D, Gibson GR. Effects of orange juice formulation on prebiotic functionality using an in vitro colonic model system. PLoS One 2015; 10:e0121955. [PMID: 25807417 PMCID: PMC4373861 DOI: 10.1371/journal.pone.0121955] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 02/06/2015] [Indexed: 01/03/2023] Open
Abstract
A three-stage continuous fermentative colonic model system was used to monitor in vitro the effect of different orange juice formulations on prebiotic activity. Three different juices with and without Bimuno, a GOS mixture containing galactooligosaccharides (B-GOS) were assessed in terms of their ability to induce a bifidogenic microbiota. The recipe development was based on incorporating 2.75g B-GOS into a 250 ml serving of juice (65°Brix of concentrate juice). Alongside the production of B-GOS juice, a control juice--orange juice without any additional Bimuno and a positive control juice, containing all the components of Bimuno (glucose, galactose and lactose) in the same relative proportions with the exception of B-GOS were developed. Ion Exchange Chromotography analysis was used to test the maintenance of bimuno components after the production process. Data showed that sterilisation had no significant effect on concentration of B-GOS and simple sugars. The three juice formulations were digested under conditions resembling the gastric and small intestinal environments. Main bacterial groups of the faecal microbiota were evaluated throughout the colonic model study using 16S rRNA-based fluorescence in situ hybridization (FISH). Potential effects of supplementation of the juices on microbial metabolism were studied measuring short chain fatty acids (SCFAs) using gas chromatography. Furthermore, B-GOS juices showed positive modulations of the microbiota composition and metabolic activity. In particular, numbers of faecal bifidobacteria and lactobacilli were significantly higher when B-GOS juice was fermented compared to controls. Furthermore, fermentation of B-GOS juice resulted in an increase in Roseburia subcluster and concomitantly increased butyrate production, which is of potential benefit to the host. In conclusion, this study has shown B-GOS within orange juice can have a beneficial effect on the fecal microbiota.
Collapse
Affiliation(s)
- Adele Costabile
- Department of Food and Nutritional Sciences, The University of Reading, Reading, United Kingdom
| | - Gemma E. Walton
- Department of Food and Nutritional Sciences, The University of Reading, Reading, United Kingdom
| | - George Tzortzis
- Clasado Research Services Ltd, Science and Technology Centre, Whiteknights, Reading, United Kingdom
| | - Jelena Vulevic
- Clasado Research Services Ltd, Science and Technology Centre, Whiteknights, Reading, United Kingdom
| | | | - Glenn R. Gibson
- Department of Food and Nutritional Sciences, The University of Reading, Reading, United Kingdom
| |
Collapse
|
33
|
Woebken D, Burow LC, Behnam F, Mayali X, Schintlmeister A, Fleming ED, Prufert-Bebout L, Singer SW, Cortés AL, Hoehler TM, Pett-Ridge J, Spormann AM, Wagner M, Weber PK, Bebout BM. Revisiting N₂ fixation in Guerrero Negro intertidal microbial mats with a functional single-cell approach. THE ISME JOURNAL 2015; 9:485-96. [PMID: 25303712 PMCID: PMC4303640 DOI: 10.1038/ismej.2014.144] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 06/15/2014] [Accepted: 06/29/2014] [Indexed: 11/09/2022]
Abstract
Photosynthetic microbial mats are complex, stratified ecosystems in which high rates of primary production create a demand for nitrogen, met partially by N₂ fixation. Dinitrogenase reductase (nifH) genes and transcripts from Cyanobacteria and heterotrophic bacteria (for example, Deltaproteobacteria) were detected in these mats, yet their contribution to N2 fixation is poorly understood. We used a combined approach of manipulation experiments with inhibitors, nifH sequencing and single-cell isotope analysis to investigate the active diazotrophic community in intertidal microbial mats at Laguna Ojo de Liebre near Guerrero Negro, Mexico. Acetylene reduction assays with specific metabolic inhibitors suggested that both sulfate reducers and members of the Cyanobacteria contributed to N₂ fixation, whereas (15)N₂ tracer experiments at the bulk level only supported a contribution of Cyanobacteria. Cyanobacterial and nifH Cluster III (including deltaproteobacterial sulfate reducers) sequences dominated the nifH gene pool, whereas the nifH transcript pool was dominated by sequences related to Lyngbya spp. Single-cell isotope analysis of (15)N₂-incubated mat samples via high-resolution secondary ion mass spectrometry (NanoSIMS) revealed that Cyanobacteria were enriched in (15)N, with the highest enrichment being detected in Lyngbya spp. filaments (on average 4.4 at% (15)N), whereas the Deltaproteobacteria (identified by CARD-FISH) were not significantly enriched. We investigated the potential dilution effect from CARD-FISH on the isotopic composition and concluded that the dilution bias was not substantial enough to influence our conclusions. Our combined data provide evidence that members of the Cyanobacteria, especially Lyngbya spp., actively contributed to N₂ fixation in the intertidal mats, whereas support for significant N₂ fixation activity of the targeted deltaproteobacterial sulfate reducers could not be found.
Collapse
Affiliation(s)
- Dagmar Woebken
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Luke C Burow
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | - Faris Behnam
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Arno Schintlmeister
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Erich D Fleming
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | | | - Steven W Singer
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alejandro López Cortés
- Laboratory of Geomicrobiology and Biotechnology, Northwestern Center for Biological Research (CIBNOR), La Paz, Mexico
| | - Tori M Hoehler
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Alfred M Spormann
- Departments of Chemical Engineering, and of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Michael Wagner
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Advanced Isotope Research, University of Vienna, Vienna, Austria
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Brad M Bebout
- Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
| |
Collapse
|
34
|
Wilbanks EG, Jaekel U, Salman V, Humphrey PT, Eisen JA, Facciotti MT, Buckley DH, Zinder SH, Druschel GK, Fike DA, Orphan VJ. Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh. Environ Microbiol 2014; 16:3398-415. [PMID: 24428801 PMCID: PMC4262008 DOI: 10.1111/1462-2920.12388] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/30/2013] [Accepted: 01/05/2014] [Indexed: 11/27/2022]
Abstract
Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over short spatiotemporal scales that elude detection by traditional analytical approaches. We investigate syntrophic sulfur cycling in the 'pink berry' consortia of the Sippewissett Salt Marsh through an integrative study at the microbial scale. The pink berries are macroscopic, photosynthetic microbial aggregates composed primarily of two closely associated species: sulfide-oxidizing purple sulfur bacteria (PB-PSB1) and sulfate-reducing bacteria (PB-SRB1). Using metagenomic sequencing and (34) S-enriched sulfate stable isotope probing coupled with nanoSIMS, we demonstrate interspecies transfer of reduced sulfur metabolites from PB-SRB1 to PB-PSB1. The pink berries catalyse net sulfide oxidation and maintain internal sulfide concentrations of 0-500 μm. Sulfide within the berries, captured on silver wires and analysed using secondary ion mass spectrometer, increased in abundance towards the berry interior, while δ(34) S-sulfide decreased from 6‰ to -31‰ from the exterior to interior of the berry. These values correspond to sulfate-sulfide isotopic fractionations (15-53‰) consistent with either sulfate reduction or a mixture of reductive and oxidative metabolisms. Together this combined metagenomic and high-resolution isotopic analysis demonstrates active sulfur cycling at the microscale within well-structured macroscopic consortia consisting of sulfide-oxidizing anoxygenic phototrophs and sulfate-reducing bacteria.
Collapse
Affiliation(s)
- Elizabeth G Wilbanks
- Department of Department of Microbiology Graduate Group, University of CaliforniaDavis, CA, 95616, USA
| | - Ulrike Jaekel
- Department of Evolution and Ecology, University of CaliforniaDavis, CA, 95616, USA
- Department of Microbiology and Immunology, University of CaliforniaDavis, CA, 95616, USA
| | - Verena Salman
- Department of Biomedical Engineering, University of CaliforniaDavis, CA, 95616, USA
| | - Parris T Humphrey
- UC Davis Genome Center, University of CaliforniaDavis, CA, 95616, USA
| | - Jonathan A Eisen
- Arctic Technology, Shell Technology NorwayOslo, N-0277, Norway
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, 02138, USA
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, 27599, USA
| | - Marc T Facciotti
- Department of Marine Sciences, University of North Carolina at Chapel HillChapel Hill, NC, 27599, USA
- Ecology and Evolutionary Biology, University of ArizonaTucson, AZ, 85721, USA
| | - Daniel H Buckley
- Crop and Soil Sciences, Cornell UniversityIthaca, NY, 14853, USA
| | - Stephen H Zinder
- Department of Microbiology, Cornell UniversityIthaca, NY, 14853, USA
| | - Gregory K Druschel
- Department of Earth Sciences, Indiana University-Purdue UniversityIndianapolis, IN, 46202, USA
| | - David A Fike
- Department of Earth and Planetary Sciences, Washington UniversitySt. Louis, MO, 63130, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of TechnologyPasadena, CA, 91125, USA
| |
Collapse
|
35
|
Costabile A, Santarelli S, Claus SP, Sanderson J, Hudspith BN, Brostoff J, Ward JL, Lovegrove A, Shewry PR, Jones HE, Whitley AM, Gibson GR. Effect of breadmaking process on in vitro gut microbiota parameters in irritable bowel syndrome. PLoS One 2014; 9:e111225. [PMID: 25356771 PMCID: PMC4214745 DOI: 10.1371/journal.pone.0111225] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/31/2014] [Indexed: 12/13/2022] Open
Abstract
A variety of foods have been implicated in symptoms of patients with Irritable Bowel Syndrome (IBS) but wheat products are most frequently cited by patients as a trigger. Our aim was to investigate the effects of breads, which were fermented for different lengths of time, on the colonic microbiota using in vitro batch culture experiments. A set of in vitro anaerobic culture systems were run over a period of 24 h using faeces from 3 different IBS donors (Rome Criteria-mainly constipated) and 3 healthy donors. Changes in gut microbiota during a time course were identified by fluorescence in situ hybridisation (FISH), whilst the small-molecular weight metabolomic profile was determined by NMR analysis. Gas production was separately investigated in non pH-controlled, 36 h batch culture experiments. Numbers of bifidobacteria were higher in healthy subjects compared to IBS donors. In addition, the healthy donors showed a significant increase in bifidobacteria (P<0.005) after 8 h of fermentation of a bread produced using a sourdough process (type C) compared to breads produced with commercial yeasted dough (type B) and no time fermentation (Chorleywood Breadmaking process) (type A). A significant decrease of δ-Proteobacteria and most Gemmatimonadetes species was observed after 24 h fermentation of type C bread in both IBS and healthy donors. In general, IBS donors showed higher rates of gas production compared to healthy donors. Rates of gas production for type A and conventional long fermentation (type B) breads were almost identical in IBS and healthy donors. Sourdough bread produced significantly lower cumulative gas after 15 h fermentation as compared to type A and B breads in IBS donors but not in the healthy controls. In conclusion, breads fermented by the traditional long fermentation and sourdough are less likely to lead to IBS symptoms compared to bread made using the Chorleywood Breadmaking Process.
Collapse
Affiliation(s)
- Adele Costabile
- Department of Food and Nutritional Sciences, The University of Reading, Reading, United Kingdom
| | - Sara Santarelli
- Department of Food and Nutritional Sciences, The University of Reading, Reading, United Kingdom
| | - Sandrine P. Claus
- Department of Food and Nutritional Sciences, The University of Reading, Reading, United Kingdom
| | - Jeremy Sanderson
- King’s College London, Biomedical & Health Sciences, Dept. of Nutrition and Dietetics, London, United Kingdom
| | - Barry N. Hudspith
- King’s College London, Biomedical & Health Sciences, Dept. of Nutrition and Dietetics, London, United Kingdom
| | - Jonathan Brostoff
- King’s College London, Biomedical & Health Sciences, Dept. of Nutrition and Dietetics, London, United Kingdom
| | - Jane L. Ward
- Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | | | - Peter R. Shewry
- Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
- School of Agriculture, Policy and Development, Earley Gate, Reading, United Kingdom
| | - Hannah E. Jones
- School of Agriculture, Policy and Development, Earley Gate, Reading, United Kingdom
| | - Andrew M. Whitley
- Bread Matters Limited, Macbiehill Farmhouse, Lamancha, West Linton, Peeblesshire, Scotland
| | - Glenn R. Gibson
- Department of Food and Nutritional Sciences, The University of Reading, Reading, United Kingdom
| |
Collapse
|
36
|
Stratified microbial structure and activity in sulfide- and methane-producing anaerobic sewer biofilms. Appl Environ Microbiol 2014; 80:7042-52. [PMID: 25192994 DOI: 10.1128/aem.02146-14] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simultaneous production of sulfide and methane by anaerobic sewer biofilms has recently been observed, suggesting that sulfate-reducing bacteria (SRB) and methanogenic archaea (MA), microorganisms known to compete for the same substrates, can coexist in this environment. This study investigated the community structures and activities of SRB and MA in anaerobic sewer biofilms (average thickness of 800 μm) using a combination of microelectrode measurements, molecular techniques, and mathematical modeling. It was seen that sulfide was mainly produced in the outer layer of the biofilm, between the depths of 0 and 300 μm, which is in good agreement with the distribution of SRB population as revealed by cryosection-fluorescence in situ hybridization (FISH). SRB had a higher relative abundance of 20% on the surface layer, which decreased gradually to below 3% at a depth of 400 μm. In contrast, MA mainly inhabited the inner layer of the biofilm. Their relative abundances increased from 10% to 75% at depths of 200 μm and 700 μm, respectively, from the biofilm surface layer. High-throughput pyrosequencing of 16S rRNA amplicons showed that SRB in the biofilm were mainly affiliated with five genera, Desulfobulbus, Desulfomicrobium, Desulfovibrio, Desulfatiferula, and Desulforegula, while about 90% of the MA population belonged to the genus Methanosaeta. The spatial organizations of SRB and MA revealed by pyrosequencing were consistent with the FISH results. A biofilm model was constructed to simulate the SRB and MA distributions in the anaerobic sewer biofilm. The good fit between model predictions and the experimental data indicate that the coexistence and spatial structure of SRB and MA in the biofilm resulted from the microbial types and their metabolic transformations and interactions with substrates.
Collapse
|
37
|
Qi P, Zhang D, Wan Y. A novel sulfate-reducing bacteria detection method based on inhibition of cysteine protease activity. Talanta 2014; 129:270-5. [PMID: 25127594 DOI: 10.1016/j.talanta.2014.04.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 04/15/2014] [Accepted: 04/21/2014] [Indexed: 12/29/2022]
Abstract
Sulfate-reducing bacteria (SRB) have been extensively studied in corrosion and environmental science. However, fast enumeration of SRB population is still a difficult task. This work presents a novel specific SRB detection method based on inhibition of cysteine protease activity. The hydrolytic activity of cysteine protease was inhibited by taking advantage of sulfide, the characteristic metabolic product of SRB, to attack active cysteine thiol group in cysteine protease catalytic sites. The active thiol S-sulfhydration process could be used for SRB detection, since the amount of sulfide accumulated in culture medium was highly related with initial bacterial concentration. The working conditions of cysteine protease have been optimized to obtain better detection capability, and the SRB detection performances have been evaluated in this work. The proposed SRB detection method based on inhibition of cysteine protease activity avoided the use of biological recognition elements. In addition, compared with the widely used most probable number (MPN) method which would take up to at least 15days to accomplish whole detection process, the method based on inhibition of papain activity could detect SRB in 2 days, with a detection limit of 5.21×10(2) cfu mL(-1). The detection time for SRB population quantitative analysis was greatly shortened.
Collapse
Affiliation(s)
- Peng Qi
- Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; University of the Chinese Academy of Sciences, 19 (Jia) Yuquan Road, Beijing 100039, China
| | - Dun Zhang
- Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China.
| | - Yi Wan
- Key Laboratory of Marine Environmental Corrosion and Bio-fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| |
Collapse
|
38
|
Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor. ISME JOURNAL 2014; 8:1843-54. [PMID: 24671086 PMCID: PMC4139731 DOI: 10.1038/ismej.2014.41] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/04/2014] [Accepted: 02/16/2014] [Indexed: 11/26/2022]
Abstract
Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution.
Collapse
|
39
|
Qi P, Zhang D, Wan Y. Sulfate-reducing bacteria detection based on the photocatalytic property of microbial synthesized ZnS nanoparticles. Anal Chim Acta 2013; 800:65-70. [PMID: 24120169 DOI: 10.1016/j.aca.2013.09.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/21/2013] [Accepted: 09/07/2013] [Indexed: 12/01/2022]
Abstract
This work presented a novel method for specific detection of sulfate-reducing bacteria (SRB) based on the photocatalytic property of ZnS nanoparticles. ZnS semiconductor nanoparticles were synthesized by taking advantage of the characteristic bacterial metabolite, sulfide, and then ZnS nanomaterials were used as photocatalyst for methylene blue (MB) photodegradation. As the amount of ZnS photocatalyst synthesized from microbe metabolized sulfide was affected by initial bacterial concentration before cultivation, the photodegradation ratio of MB was highly related with initial SRB concentration. Under the optimized conditions, a linear relationship between the MB photodegradation ratio and the logarithm of SRB concentration was observed in the range of 1.0×10(3)-1.0×10(8) cfu mL(-1). Besides, this proposed method showed excellent specificity for SRB detection. To the best of our knowledge, this is the first example of using the photocatalytic property of microbial synthesized ZnS for bacterial detection.
Collapse
Affiliation(s)
- Peng Qi
- National Engineering Research Center for Marine Corrosion Protection, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China; University of the Chinese Academy of Sciences, 19 (Jia) Yuquan Road, Beijing 100039, China
| | | | | |
Collapse
|
40
|
Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge. Syst Appl Microbiol 2013; 36:281-90. [DOI: 10.1016/j.syapm.2013.03.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 11/22/2022]
|
41
|
Campbell AG, Campbell JH, Schwientek P, Woyke T, Sczyrba A, Allman S, Beall CJ, Griffen A, Leys E, Podar M. Multiple single-cell genomes provide insight into functions of uncultured Deltaproteobacteria in the human oral cavity. PLoS One 2013; 8:e59361. [PMID: 23555659 PMCID: PMC3608642 DOI: 10.1371/journal.pone.0059361] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/13/2013] [Indexed: 01/10/2023] Open
Abstract
Despite a long history of investigation, many bacteria associated with the human oral cavity have yet to be cultured. Studies that correlate the presence or abundance of uncultured species with oral health or disease highlight the importance of these community members. Thus, we sequenced several single-cell genomic amplicons from Desulfobulbus and Desulfovibrio (class Deltaproteobacteria) to better understand their function within the human oral community and their association with periodontitis, as well as other systemic diseases. Genomic data from oral Desulfobulbus and Desulfovibrio species were compared to other available deltaproteobacterial genomes, including from a subset of host-associated species. While both groups share a large number of genes with other environmental Deltaproteobacteria genomes, they encode a wide array of unique genes that appear to function in survival in a host environment. Many of these genes are similar to virulence and host adaptation factors of known human pathogens, suggesting that the oral Deltaproteobacteria have the potential to play a role in the etiology of periodontal disease.
Collapse
Affiliation(s)
- Alisha G. Campbell
- Genome Science and Technology Program, University of Tennessee, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratories, Oak Ridge, Tennessee, United States of America
| | - James H. Campbell
- Biosciences Division, Oak Ridge National Laboratories, Oak Ridge, Tennessee, United States of America
| | - Patrick Schwientek
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alexander Sczyrba
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Steve Allman
- Biosciences Division, Oak Ridge National Laboratories, Oak Ridge, Tennessee, United States of America
| | - Clifford J. Beall
- College of Dentistry, Ohio State University, Columbus, Ohio, United States of America
| | - Ann Griffen
- College of Dentistry, Ohio State University, Columbus, Ohio, United States of America
| | - Eugene Leys
- College of Dentistry, Ohio State University, Columbus, Ohio, United States of America
| | - Mircea Podar
- Genome Science and Technology Program, University of Tennessee, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratories, Oak Ridge, Tennessee, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| |
Collapse
|
42
|
From macro to lab-scale: Changes in bacterial community led to deterioration of EBPR in lab reactor. Open Life Sci 2013. [DOI: 10.2478/s11535-013-0116-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AbstractA laboratory scale sequencing batch reactor (SBR), fed with synthetic wastewater containing a mixture of organic compounds, was operated for nearly six months. Despite maintaining the same operational conditions, a deterioration of enhanced biological phosphorus removal (EBPR) occurred after 40 days of SBR operation. The Prel/Cupt ratio decreased from 0.28 to 0.06 P-mol C-mol−1, and C requirements increased from 11 to 32 mg C h−1 g−1 of mixed liquor suspended solids. A FISH analysis showed that the percentage of Accumulibacter in an overall community of polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs) dropped from 93% to 13%. An increase in abundance of Gammaproteobacteria (from 2.6% to 22%) and Alphaproteobacteria (from 1.8% to 10%) was observed. The number of Competibacter increased from 0.5% to nearly 9%. Clusters 1 and 2 of Defluviicoccus-related GAOs, not detected before deterioration, constituted 35% and 27% of Alphaproteobacteria, respectively. We concluded that lab-scale experiments should not be extended implicitly to full-scale EBPR systems because some bacterial groups are detected mainlyin lab-scale reactors. Well-defined, lab-scale operational conditions reduce the number of ecological niches available to bacteria.
Collapse
|
43
|
Qi P, Wan Y, Zhang D. Impedimetric biosensor based on cell-mediated bioimprinted films for bacterial detection. Biosens Bioelectron 2013; 39:282-8. [DOI: 10.1016/j.bios.2012.07.078] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 07/30/2012] [Accepted: 07/31/2012] [Indexed: 10/28/2022]
|
44
|
Orsi W, Charvet S, Vd'ačný P, Bernhard JM, Edgcomb VP. Prevalence of partnerships between bacteria and ciliates in oxygen-depleted marine water columns. Front Microbiol 2012; 3:341. [PMID: 23049527 PMCID: PMC3446810 DOI: 10.3389/fmicb.2012.00341] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/04/2012] [Indexed: 11/30/2022] Open
Abstract
Symbioses between Bacteria, Archaea, and Eukarya in deep-sea marine environments represent a means for eukaryotes to exploit otherwise inhospitable habitats. Such symbioses are abundant in many low-oxygen benthic marine environments, where the majority of microbial eukaryotes contain prokaryotic symbionts. Here, we present evidence suggesting that in certain oxygen-depleted marine water-column habitats, the majority of microbial eukaryotes are also associated with prokaryotic cells. Ciliates (protists) associated with bacteria were found to be the dominant eukaryotic morphotype in the haloclines of two different deep-sea hypersaline anoxic basins (DHABs) in the Eastern Mediterranean Sea. These findings are compared to associations between ciliates and bacteria documented from the permanently anoxic waters of the Cariaco Basin (Caribbean Sea). The dominance of ciliates exhibiting epibiotic bacteria across three different oxygen-depleted marine water column habitats suggests that such partnerships confer a fitness advantage for ciliates in these environments.
Collapse
Affiliation(s)
- William Orsi
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution Woods Hole, MA, USA
| | | | | | | | | |
Collapse
|
45
|
Quillet L, Besaury L, Popova M, Paissé S, Deloffre J, Ouddane B. Abundance, diversity and activity of sulfate-reducing prokaryotes in heavy metal-contaminated sediment from a salt marsh in the Medway Estuary (UK). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:363-381. [PMID: 22124626 DOI: 10.1007/s10126-011-9420-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 11/17/2011] [Indexed: 05/31/2023]
Abstract
We investigated the diversity and activity of sulfate-reducing prokaryotes (SRP) in a 3.5-m sediment core taken from a heavy metal-contaminated site in the Medway Estuary, UK. The abundance of SRPs was quantified by qPCR of the dissimilatory sulfite reductase gene β-subunit (dsrB) and taking into account DNA extraction efficiency. This showed that SRPs were abundant throughout the core with maximum values in the top 50 cm of the sediment core making up 22.4% of the total bacterial community and were 13.6% at 250 cm deep. Gene libraries for dsrA (dissimilatory sulfite reductase α-subunit) were constructed from the heavily contaminated (heavy metals) surface sediment (top 20 cm) and from the less contaminated and sulfate-depleted, deeper zone (250 cm). Certain cloned sequences were similar to dsrA found in members of the Syntrophobacteraceae, Desulfobacteraceae and Desulfovibrionaceae as well as a large fraction (60%) of novel sequences that formed a deep branching dsrA lineage. Phylogenetic analysis of metabolically active SRPs was performed by reverse transcription PCR and single strand conformational polymorphism analysis (RT-PCR-SSCP) of dsrA genes derived from extracted sediment RNA. Subsequent comparative sequence analysis of excised SSCP bands revealed a high transcriptional activity of dsrA belonging to Desulfovibrio species in the surface sediment. These results may suggest that members of the Desulfovibrionaceae are more active than other SRP groups in heavy metal-contaminated surface sediments.
Collapse
Affiliation(s)
- Laurent Quillet
- Faculté des Sciences, Université de Rouen-CNRS 6143-M2C, Groupe de Microbiologie, Place Emile Blondel, Mont Saint Aignan Cedex 76821, France.
| | | | | | | | | | | |
Collapse
|
46
|
Quantification of Tinto River sediment microbial communities: importance of sulfate-reducing bacteria and their role in attenuating acid mine drainage. Appl Environ Microbiol 2012; 78:4638-45. [PMID: 22544246 DOI: 10.1128/aem.00848-12] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tinto River (Huelva, Spain) is a natural acidic rock drainage (ARD) environment produced by the bio-oxidation of metallic sulfides from the Iberian Pyritic Belt. This study quantified the abundance of diverse microbial populations inhabiting ARD-related sediments from two physicochemically contrasting sampling sites (SN and JL dams). Depth profiles of total cell numbers differed greatly between the two sites yet were consistent in decreasing sharply at greater depths. Although catalyzed reporter deposition fluorescence in situ hybridization with domain-specific probes showed that Bacteria (>98%) dominated over Archaea (<2%) at both sites, important differences were detected at the class and genus levels, reflecting differences in pH, redox potential, and heavy metal concentrations. At SN, where the pH and redox potential are similar to that of the water column (pH 2.5 and +400 mV), the most abundant organisms were identified as iron-reducing bacteria: Acidithiobacillus spp. and Acidiphilium spp., probably related to the higher iron solubility at low pH. At the JL dam, characterized by a banded sediment with higher pH (4.2 to 6.2), more reducing redox potential (-210 mV to 50 mV), and a lower solubility of iron, members of sulfate-reducing genera Syntrophobacter, Desulfosporosinus, and Desulfurella were dominant. The latter was quantified with a newly designed CARD-FISH probe. In layers where sulfate-reducing bacteria were abundant, pH was higher and redox potential and levels of dissolved metals and iron were lower. These results suggest that the attenuation of ARD characteristics is biologically driven by sulfate reducers and the consequent precipitation of metals and iron as sulfides.
Collapse
|
47
|
Belila A, Abbas B, Fazaa I, Saidi N, Snoussi M, Hassen A, Muyzer G. Sulfur bacteria in wastewater stabilization ponds periodically affected by the 'red-water' phenomenon. Appl Microbiol Biotechnol 2012; 97:379-94. [PMID: 22354366 PMCID: PMC3536956 DOI: 10.1007/s00253-012-3931-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/27/2012] [Accepted: 01/28/2012] [Indexed: 11/26/2022]
Abstract
Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the ‘red-water’ phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menzeh WSP and focused in particular on the different functional groups of sulfur bacteria. For this purpose, we used denaturing gradient gel electrophoresis of PCR-amplified fragments of the 16S rRNA gene and of different functional genes involved in microbial sulfur metabolism (dsrB, aprA, and pufM). Analyses of the 16S rRNA revealed a relatively high microbial diversity where Proteobacteria, Chlorobi, Bacteroidetes, and Cyanobacteria constitute the major bacterial groups. The dsrB and aprA gene analysis revealed the presence of deltaproteobacterial sulfate-reducing bacteria (i.e., Desulfobacter and Desulfobulbus), while the analysis of 16S rRNA, aprA, and pufM genes assigned the sulfur-oxidizing bacteria community to the photosynthetic representatives belonging to the Chlorobi (green sulfur bacteria) and the Proteobacteria (purple sulfur and non sulfur bacteria) phyla. These results point on the diversity of the metabolic processes within this wastewater plant and/or the availability of sulfate and diverse electron donors.
Collapse
Affiliation(s)
- Abdelaziz Belila
- Water Treatment and Reuse Laboratory, Water Researches and Technologies Centre of Bordj-Cedria, BP. 273, 8020 Soliman, Tunisia
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, NL-2628 BC Delft, The Netherlands
| | - Imed Fazaa
- Water Treatment and Reuse Laboratory, Water Researches and Technologies Centre of Bordj-Cedria, BP. 273, 8020 Soliman, Tunisia
| | - Neila Saidi
- Water Treatment and Reuse Laboratory, Water Researches and Technologies Centre of Bordj-Cedria, BP. 273, 8020 Soliman, Tunisia
| | - Mejdi Snoussi
- Water Treatment and Reuse Laboratory, Water Researches and Technologies Centre of Bordj-Cedria, BP. 273, 8020 Soliman, Tunisia
| | - Abdennaceur Hassen
- Water Treatment and Reuse Laboratory, Water Researches and Technologies Centre of Bordj-Cedria, BP. 273, 8020 Soliman, Tunisia
| | - Gerard Muyzer
- Department of Biotechnology, Delft University of Technology, NL-2628 BC Delft, The Netherlands
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystems Dynamics, University of Amsterdam, NL-1098 XH Amsterdam, The Netherlands
| |
Collapse
|
48
|
Denitrification likely catalyzed by endobionts in an allogromiid foraminifer. ISME JOURNAL 2011; 6:951-60. [PMID: 22134648 DOI: 10.1038/ismej.2011.171] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Nitrogen can be a limiting macronutrient for carbon uptake by the marine biosphere. The process of denitrification (conversion of nitrate to gaseous compounds, including N(2) (nitrogen gas)) removes bioavailable nitrogen, particularly in marine sediments, making it a key factor in the marine nitrogen budget. Benthic foraminifera reportedly perform complete denitrification, a process previously considered nearly exclusively performed by bacteria and archaea. If the ability to denitrify is widespread among these diverse and abundant protists, a paradigm shift is required for biogeochemistry and marine microbial ecology. However, to date, the mechanisms of foraminiferal denitrification are unclear, and it is possible that the ability to perform complete denitrification is because of the symbiont metabolism in some foraminiferal species. Using sequence analysis and GeneFISH, we show that for a symbiont-bearing foraminifer, the potential for denitrification resides in the endobionts. Results also identify the endobionts as denitrifying pseudomonads and show that the allogromiid accumulates nitrate intracellularly, presumably for use in denitrification. Endobionts have been observed within many foraminiferal species, and in the case of associations with denitrifying bacteria, may provide fitness for survival in anoxic conditions. These associations may have been a driving force for early foraminiferal diversification, which is thought to have occurred in the Neoproterozoic era when anoxia was widespread.
Collapse
|
49
|
Beaudoin DJ, Bernhard JM, Edgcomb VP. A Novel Ciliate (Ciliophora: Hypotrichida) Isolated from Bathyal Anoxic Sediments. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/978-94-007-1896-8_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
50
|
Bader KC, Grothoff C, Meier H. Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets. Bioinformatics 2011; 27:1546-54. [PMID: 21471017 DOI: 10.1093/bioinformatics/btr161] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION PCR, hybridization, DNA sequencing and other important methods in molecular diagnostics rely on both sequence-specific and sequence group-specific oligonucleotide primers and probes. Their design depends on the identification of oligonucleotide signatures in whole genome or marker gene sequences. Although genome and gene databases are generally available and regularly updated, collections of valuable signatures are rare. Even for single requests, the search for signatures becomes computationally expensive when working with large collections of target (and non-target) sequences. Moreover, with growing dataset sizes, the chance of finding exact group-matching signatures decreases, necessitating the application of relaxed search methods. The resultant substantial increase in complexity is exacerbated by the dearth of algorithms able to solve these problems efficiently. RESULTS We have developed CaSSiS, a fast and scalable method for computing comprehensive collections of sequence- and sequence group-specific oligonucleotide signatures from large sets of hierarchically clustered nucleic acid sequence data. Based on the ARB Positional Tree (PT-)Server and a newly developed BGRT data structure, CaSSiS not only determines sequence-specific signatures and perfect group-covering signatures for every node within the cluster (i.e. target groups), but also signatures with maximal group coverage (sensitivity) within a user-defined range of non-target hits (specificity) for groups lacking a perfect common signature. An upper limit of tolerated mismatches within the target group, as well as the minimum number of mismatches with non-target sequences, can be predefined. Test runs with one of the largest phylogenetic gene sequence datasets available indicate good runtime and memory performance, and in silico spot tests have shown the usefulness of the resulting signature sequences as blueprints for group-specific oligonucleotide probes. AVAILABILITY Software and Supplementary Material are available at http://cassis.in.tum.de/.
Collapse
Affiliation(s)
- Kai Christian Bader
- Services Department of Informatics, Technische Universität München, Boltzmannstrasse 3, 85748 Garching, Germany
| | | | | |
Collapse
|