1
|
Tezuka T, Mitsuyama K, Date R, Ohnishi Y. A unique sigma/anti-sigma system in the actinomycete Actinoplanes missouriensis. Nat Commun 2023; 14:8483. [PMID: 38123564 PMCID: PMC10733313 DOI: 10.1038/s41467-023-44291-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/07/2023] [Indexed: 12/23/2023] Open
Abstract
Bacteria of the genus Actinoplanes form sporangia that contain dormant sporangiospores which, upon contact with water, release motile spores (zoospores) through a process called sporangium dehiscence. Here, we set out to study the molecular mechanisms behind sporangium dehiscence in Actinoplanes missouriensis and discover a sigma/anti-sigma system with unique features. Protein σSsdA contains a functional sigma factor domain and an anti-sigma factor antagonist domain, while protein SipA contains an anti-sigma factor domain and an anti-sigma factor antagonist domain. Remarkably, the two proteins interact with each other via the anti-sigma factor antagonist domain of σSsdA and the anti-sigma factor domain of SipA. Although it remains unclear whether the SipA/σSsdA system plays direct roles in sporangium dehiscence, the system seems to modulate oxidative stress responses in zoospores. In addition, we identify a two-component regulatory system (RsdK-RsdR) that represses initiation of sporangium dehiscence.
Collapse
Affiliation(s)
- Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Graduate School of Infection Control Sciences, Kitasato University, Minato-ku, Tokyo, Japan.
| | - Kyota Mitsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Risa Date
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
2
|
Guo Y, Xiang Y, Liu G, Chen Y, Liu Y, Song M, Li Y, Shi J, Hu L, Yin Y, Cai Y, Jiang G. "Trojan Horse" Type Internalization Increases the Bioavailability of Mercury Sulfide Nanoparticles and Methylation after Intracellular Dissolution. ACS NANO 2023; 17:1925-1934. [PMID: 36688800 DOI: 10.1021/acsnano.2c05657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mercury sulfide nanoparticles (HgSNP), as natural metal-containing nanoparticles, are the dominant Hg species in anoxic zones. Although the microbial Hg methylation of HgSNP has been previously reported, the importance of this process in Hg methylation has yet to be clarified due to the lack of knowledge on the internalization and transformation of HgSNP. Here, we investigated the internalization and transformation of HgSNP in microbial methylator Geobacter sulfurreducens PCA through total Hg analysis and different Hg species quantification in medium and cytoplasm. We found that the microbial uptake of HgSNP, via a passive diffusion pathway, was significantly higher than that of the Hg2+-dissolved organic matter (Hg2+-DOM) complex. Internalized HgSNP were dissolved to Hg2+ in cytoplasm with a maximal dissolution of 41%, suggesting a "Trojan horse" mechanism. The intracellular Hg2+ from HgSNP exposure at the initial stage (8 h) was higher than that in Hg2+-DOM group, which led to higher methylation of HgSNP. Furthermore, no differences in methylmercury (MeHg) production from HgSNP were observed between the hgcAB gene knockout (ΔhgcAB) and wild-type strains, suggesting that HgSNP methylation may occur through HgcAB-independent pathways. Considering the possibility of a broad range of hgcAB-lacking microbes serving as methylators for HgSNP and the ubiquity of HgSNP in anoxic environments, this study highlights the importance of HgSNP internalization and methylation in MeHg production and demonstrates the necessity of understanding the assimilation and transformation of nutrient and toxic metal nanoparticles in general.
Collapse
Affiliation(s)
- Yingying Guo
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Yuping Xiang
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Guangliang Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Ying Chen
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanwei Liu
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Maoyong Song
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Yanbin Li
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education and College of Chemistry and Chemical Engineering, Ocean University of China, Qingdao 266100, China
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Ligang Hu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Yongguang Yin
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Yong Cai
- Laboratory of Environmental Nanotechnology and Health Effect, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| |
Collapse
|
3
|
Anaerobic Biodegradation of Polyaromatic Hydrocarbons by a Sulfate Reducing Bacteria C1Fd Strain. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.2.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
4
|
Regulation of Sporangium Formation by BldD in the Rare Actinomycete Actinoplanes missouriensis. J Bacteriol 2017; 199:JB.00840-16. [PMID: 28348024 DOI: 10.1128/jb.00840-16] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/19/2017] [Indexed: 11/20/2022] Open
Abstract
The rare actinomycete Actinoplanes missouriensis forms sporangia, including hundreds of flagellated spores that start swimming as zoospores after their release. Under conditions suitable for vegetative growth, zoospores stop swimming and germinate. A comparative proteome analysis between zoospores and germinating cells identified 15 proteins that were produced in larger amounts in germinating cells. They include an orthologue of BldD (herein named AmBldD [BldD of A. missouriensis]), which is a transcriptional regulator involved in morphological development and secondary metabolism in Streptomyces AmBldD was detected in mycelia during vegetative growth but was barely detected in mycelia during the sporangium-forming phase, in spite of the constant transcription of AmbldD throughout growth. An AmbldD mutant started to form sporangia much earlier than the wild-type strain, and the resulting sporangia were morphologically abnormal. Recombinant AmBldD bound a palindromic sequence, the AmBldD box, located upstream from AmbldD 3',5'-Cyclic di-GMP significantly enhanced the in vitro DNA-binding ability of AmBldD. A chromatin immunoprecipitation-sequencing analysis and an in silico search for AmBldD boxes revealed that AmBldD bound 346 genomic loci that contained the 19-bp inverted repeat 5'-NN(G/A)TNACN(C/G)N(G/C)NGTNA(C/T)NN-3' as the consensus AmBldD-binding sequence. The transcriptional analysis of 27 selected AmBldD target gene candidates indicated that AmBldD should repress 12 of the 27 genes, including bldM, ssgB, whiD, ddbA, and wblA orthologues. These genes are involved in morphological development in Streptomyces coelicolor A3(2). Thus, AmBldD is a global transcriptional regulator that seems to repress the transcription of tens of genes during vegetative growth, some of which are likely to be required for sporangium formation.IMPORTANCE The rare actinomycete Actinoplanes missouriensis undergoes complex morphological differentiation, including sporangium formation. However, almost no molecular biological studies have been conducted on this bacterium. BldD is a key global regulator involved in the morphological development of streptomycetes. BldD orthologues are highly conserved among sporulating actinomycetes, but no BldD orthologues, except one in Saccharopolyspora erythraea, have been studied outside the streptomycetes. Here, it was revealed that the BldD orthologue AmBldD is essential for normal developmental processes in A. missouriensis The AmBldD regulon seems to be different from the BldD regulon in Streptomyces coelicolor A3(2), but they share four genes that are involved in morphological differentiation in S. coelicolor A3(2).
Collapse
|
5
|
Abstract
The survival strategy of Actinoplanes is fascinating from an evolutionary perspective, combining a short motile phase in an otherwise nonmotile, filamentous life cycle and the somewhat paradoxical concept of spores-normally thought of as a resting stage-that swim. In the first paper to report a molecular genetic analysis of development in Actinoplanes, the authors identify a key regulator of the entry into development (Y. Mouri, K. Konishi, A. Fujita, T. Tezuka, Y. Ohnishi, J Bacteriol 199:e00840-16, 2017, https://doi.org/10.1128/JB.00840-16).
Collapse
|
6
|
Forss J, Lindh MV, Pinhassi J, Welander U. Microbial Biotreatment of Actual Textile Wastewater in a Continuous Sequential Rice Husk Biofilter and the Microbial Community Involved. PLoS One 2017; 12:e0170562. [PMID: 28114377 PMCID: PMC5256951 DOI: 10.1371/journal.pone.0170562] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/08/2017] [Indexed: 11/18/2022] Open
Abstract
Textile dying processes often pollute wastewater with recalcitrant azo and anthraquinone dyes. Yet, there is little development of effective and affordable degradation systems for textile wastewater applicable in countries where water technologies remain poor. We determined biodegradation of actual textile wastewater in biofilters containing rice husks by spectrophotometry and liquid chromatography mass spectrometry. The indigenous microflora from the rice husks consistently performed >90% decolorization at a hydraulic retention time of 67 h. Analysis of microbial community composition of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) gene fragments in the biofilters revealed a bacterial consortium known to carry azoreductase genes, such as Dysgonomonas, and Pseudomonas and the presence of fungal phylotypes such as Gibberella and Fusarium. Our findings emphasize that rice husk biofilters support a microbial community of both bacteria and fungi with key features for biodegradation of actual textile wastewater. These results suggest that microbial processes can substantially contribute to efficient and reliable degradation of actual textile wastewater. Thus, development of biodegradation systems holds promise for application of affordable wastewater treatment in polluted environments.
Collapse
Affiliation(s)
- Jörgen Forss
- Faculty of Technology, Linnæus University, Växjö, Sweden
- * E-mail:
| | - Markus V. Lindh
- Centre for Ecology and Evolution in Microbial model Systems, Linnæus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems, Linnæus University, Kalmar, Sweden
| | | |
Collapse
|
7
|
Genetic and Transcriptional Analyses of the Flagellar Gene Cluster in Actinoplanes missouriensis. J Bacteriol 2016; 198:2219-27. [PMID: 27274031 DOI: 10.1128/jb.00306-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
UNLABELLED Actinoplanes missouriensis, a Gram-positive and soil-inhabiting bacterium, is a member of the rare actinomycetes. The filamentous cells produce sporangia, which contain hundreds of flagellated spores that can swim rapidly for a short period of time until they find niches for germination. These swimming cells are called zoospores, and the mechanism of this unique temporal flagellation has not been elucidated. Here, we report all of the flagellar genes in the bacterial genome and their expected function and contribution for flagellar morphogenesis. We identified a large flagellar gene cluster composed of 33 genes that encode the majority of proteins essential for assembling the functional flagella of Gram-positive bacteria. One noted exception to the cluster was the location of the fliQ gene, which was separated from the cluster. We examined the involvement of four genes in flagellar biosynthesis by gene disruption, fliQ, fliC, fliK, and lytA Furthermore, we performed a transcriptional analysis of the flagellar genes using RNA samples prepared from A. missouriensis grown on a sporangium-producing agar medium for 1, 3, 6, and 40 days. We demonstrated that the transcription of the flagellar genes was activated in conjunction with sporangium formation. Eleven transcriptional start points of the flagellar genes were determined using the rapid amplification of cDNA 5' ends (RACE) procedure, which revealed the highly conserved promoter sequence CTCA(N15-17)GCCGAA. This result suggests that a sigma factor is responsible for the transcription of all flagellar genes and that the flagellar structure assembles simultaneously. IMPORTANCE The biology of a zoospore is very interesting from the viewpoint of morphogenesis, survival strategy, and evolution. Here, we analyzed flagellar genes in A. missouriensis, which produces sporangia containing hundreds of flagellated spores each. Zoospores released from the sporangia swim for a short time before germination occurs. We identified a large flagellar gene cluster and an orphan flagellar gene (fliQ). These findings indicate that the zoospore flagellar components are typical of Gram-positive bacteria. However, the transcriptional analysis revealed that all flagellar genes are transcribed simultaneously during sporangium formation, a pattern differing from the orderly, regulated expression of flagellar genes in other bacteria, such as Salmonella and Escherichia coli These results suggest a novel regulatory mechanism for flagellar formation in A. missouriensis.
Collapse
|
8
|
Wetzels SU, Mann E, Metzler-Zebeli BU, Pourazad P, Qumar M, Klevenhusen F, Pinior B, Wagner M, Zebeli Q, Schmitz-Esser S. Epimural Indicator Phylotypes of Transiently-Induced Subacute Ruminal Acidosis in Dairy Cattle. Front Microbiol 2016; 7:274. [PMID: 26973642 PMCID: PMC4777738 DOI: 10.3389/fmicb.2016.00274] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/19/2016] [Indexed: 02/01/2023] Open
Abstract
The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a 1-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5 and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P < 0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P < 0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.
Collapse
Affiliation(s)
- Stefanie U Wetzels
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Evelyne Mann
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Barbara U Metzler-Zebeli
- Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine ViennaVienna, Austria
| | - Poulad Pourazad
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria
| | - Muhammad Qumar
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria
| | - Fenja Klevenhusen
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Beate Pinior
- Department for Farm Animals and Veterinary Public Health, Institute for Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria
| | - Martin Wagner
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Qendrim Zebeli
- Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria
| | - Stephan Schmitz-Esser
- Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department of Animal Science, Iowa State UniversityAmes, IA, USA
| |
Collapse
|
9
|
Visser M, Stams AJM, Frutschi M, Bernier-Latmani R. Phylogenetic comparison of Desulfotomaculum species of subgroup 1a and description of Desulfotomaculum reducens sp. nov. Int J Syst Evol Microbiol 2015; 66:762-767. [PMID: 26597812 DOI: 10.1099/ijsem.0.000786] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A genome and physiological comparison was made of the type strains of Desulfotomaculum species belonging to subgroup 1a and of 'Desulfotomaculum reducens' strain MI-1. Phenotypically, 'Desulfotomaculum reducens' strain MI-1 can be distinguished from the other described Desulfotomaculum species of subgroup 1a by its ability to grow with propionate and butyrate. In addition, the strain is able to use a variety of metals as electron acceptors. Metal reduction has not been tested in the other species, but seems likely based on our genome analysis. Phylogenetic 16S rRNA gene sequence analysis and the average nucleotide identity between the genomes of the species of subgroup 1a show that strain MI-1 represents a novel species within the Desulfotomaculum 1a subgroup, Desulfotomaculum reducens sp. nov. The type strain is MI-1T.
Collapse
Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Manon Frutschi
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, CH A1 375 Station 6, Lausanne CH-1015, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, CH A1 375 Station 6, Lausanne CH-1015, Switzerland
| |
Collapse
|
10
|
A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
Collapse
|
11
|
Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK, van Loosdrecht MCM, Chen GH. A review of biological sulfate conversions in wastewater treatment. WATER RESEARCH 2014; 65:1-21. [PMID: 25086411 DOI: 10.1016/j.watres.2014.06.043] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/26/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Treatment of waters contaminated with sulfur containing compounds (S) resulting from seawater intrusion, the use of seawater (e.g. seawater flushing, cooling) and industrial processes has become a challenging issue since around two thirds of the world's population live within 150 km of the coast. In the past, research has produced a number of bioengineered systems for remediation of industrial sulfate containing sewage and sulfur contaminated groundwater utilizing sulfate reducing bacteria (SRB). The majority of these studies are specific with SRB only or focusing on the microbiology rather than the engineered application. In this review, existing sulfate based biotechnologies and new approaches for sulfate contaminated waters treatment are discussed. The sulfur cycle connects with carbon, nitrogen and phosphorus cycles, thus a new platform of sulfur based biotechnologies incorporating sulfur cycle with other cycles can be developed, for the removal of sulfate and other pollutants (e.g. carbon, nitrogen, phosphorus and metal) from wastewaters. All possible electron donors for sulfate reduction are summarized for further understanding of the S related biotechnologies including rates and benefits/drawbacks of each electron donor. A review of known SRB and their environmental preferences with regard to bioreactor operational parameters (e.g. pH, temperature, salinity etc.) shed light on the optimization of sulfur conversion-based biotechnologies. This review not only summarizes information from the current sulfur conversion-based biotechnologies for further optimization and understanding, but also offers new directions for sulfur related biotechnology development.
Collapse
Affiliation(s)
- Tian-wei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peng-yu Xiang
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hamish R Mackey
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Kun Chi
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hui Lu
- SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China
| | - Ho-kwong Chui
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
12
|
Morais-Silva FO, Rezende AM, Pimentel C, Santos CI, Clemente C, Varela-Raposo A, Resende DM, da Silva SM, de Oliveira LM, Matos M, Costa DA, Flores O, Ruiz JC, Rodrigues-Pousada C. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus. Microbiologyopen 2014; 3:513-30. [PMID: 25055974 PMCID: PMC4287179 DOI: 10.1002/mbo3.184] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/30/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022] Open
Abstract
Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh.
Collapse
Affiliation(s)
- Fabio O Morais-Silva
- Instituto de Tecnologia Quómica e Biológica - Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República - Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Kuever J, Visser M, Loeffler C, Boll M, Worm P, Sousa DZ, Plugge CM, Schaap PJ, Muyzer G, Pereira IAC, Parshina SN, Goodwin LA, Kyrpides NC, Detter J, Woyke T, Chain P, Davenport KW, Rohde M, Spring S, Klenk HP, Stams AJM. Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium. Stand Genomic Sci 2014; 9:821-39. [PMID: 25197466 PMCID: PMC4148979 DOI: 10.4056/sigs.5209235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes.
Collapse
Affiliation(s)
- Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Michael Visser
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Claudia Loeffler
- Albert-Ludwigs-University Freiburg, Institute of Biology II, Freiburg, Germany
| | - Matthias Boll
- Albert-Ludwigs-University Freiburg, Institute of Biology II, Freiburg, Germany
| | - Petra Worm
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Diana Z Sousa
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Caroline M Plugge
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Peter J Schaap
- Wageningen University, Laboratory of Systems and Synthetic Biology, Wageningen, The Netherlands
| | - Gerard Muyzer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Ines A C Pereira
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofiya N Parshina
- Winogradsky Institute of Microbiology Russian Academy of Sciences, Moscow, Russia
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | | | - Janine Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alfons J M Stams
- Wageningen University, Laboratory of Microbiology, Wageningen, The Netherlands ; University of Minho, Centre of Biological Engineering, Braga, Portugal
| |
Collapse
|
14
|
Visser M, Parshina SN, Alves JI, Sousa DZ, Pereira IAC, Muyzer G, Kuever J, Lebedinsky AV, Koehorst JJ, Worm P, Plugge CM, Schaap PJ, Goodwin LA, Lapidus A, Kyrpides NC, Detter JC, Woyke T, Chain P, Davenport KW, Spring S, Rohde M, Klenk HP, Stams AJM. Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. Stand Genomic Sci 2014; 9:655-75. [PMID: 25197452 PMCID: PMC4149029 DOI: 10.4056/sigs.4718645] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.
Collapse
Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Sofiya N Parshina
- Wingradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands ; Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Gerard Muyzer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | | | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Petra Worm
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | | | - Janine C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hans Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands ; Centre of Biological Engineering, University of Minho, Braga, Portugal
| |
Collapse
|
15
|
Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies. Animal 2013; 7 Suppl 2:235-43. [PMID: 23739466 DOI: 10.1017/s1751731113000700] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ruminant-derived methane (CH4), a potent greenhouse gas, is a consequence of microbial fermentation in the digestive tract of livestock. Development of mitigation strategies to reduce CH4 emissions from farmed animals is currently the subject of both scientific and environmental interest. Methanogens are the sole producers of ruminant CH4, and therefore CH4 abatement strategies can either target the methanogens themselves or target the other members of the rumen microbial community that produce substrates necessary for methanogenesis. Understanding the relationship that methanogens have with other rumen microbes is crucial when considering CH4 mitigation strategies for ruminant livestock. Genome sequencing of rumen microbes is an important tool to improve our knowledge of the processes that underpin those relationships. Currently, several rumen bacterial and archaeal genome projects are either complete or underway. Genome sequencing is providing information directly applicable to CH4 mitigation strategies based on vaccine and small molecule inhibitor approaches. In addition, genome sequencing is contributing information relevant to other CH4 mitigation strategies. These include the selection and breeding of low CH4-emitting animals through the interpretation of large-scale DNA and RNA sequencing studies and the modification of other microbial groups within the rumen, thereby changing the dynamics of microbial fermentation.
Collapse
|
16
|
Satou R, Izumikawa M, Katsuyama Y, Matsui M, Takagi M, Shin-ya K, Ohnishi Y. Isolation, structural elucidation and biosynthesis of 3-hydroxy-6-dimethylallylindolin-2-one, a novel prenylated indole derivative from Actinoplanes missouriensis. J Antibiot (Tokyo) 2013; 67:231-6. [DOI: 10.1038/ja.2013.116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 10/01/2013] [Accepted: 10/04/2013] [Indexed: 11/09/2022]
|