1
|
Mara P, Geller-McGrath D, Suter E, Taylor GT, Pachiadaki MG, Edgcomb VP. Plasmid-Borne Biosynthetic Gene Clusters within a Permanently Stratified Marine Water Column. Microorganisms 2024; 12:929. [PMID: 38792759 PMCID: PMC11123730 DOI: 10.3390/microorganisms12050929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Plasmids are mobile genetic elements known to carry secondary metabolic genes that affect the fitness and survival of microbes in the environment. Well-studied cases of plasmid-encoded secondary metabolic genes in marine habitats include toxin/antitoxin and antibiotic biosynthesis/resistance genes. Here, we examine metagenome-assembled genomes (MAGs) from the permanently-stratified water column of the Cariaco Basin for integrated plasmids that encode biosynthetic gene clusters of secondary metabolites (smBGCs). We identify 16 plasmid-borne smBGCs in MAGs associated primarily with Planctomycetota and Pseudomonadota that encode terpene-synthesizing genes, and genes for production of ribosomal and non-ribosomal peptides. These identified genes encode for secondary metabolites that are mainly antimicrobial agents, and hence, their uptake via plasmids may increase the competitive advantage of those host taxa that acquire them. The ecological and evolutionary significance of smBGCs carried by prokaryotes in oxygen-depleted water columns is yet to be fully elucidated.
Collapse
Affiliation(s)
- Paraskevi Mara
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA;
| | - David Geller-McGrath
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; (D.G.-M.); (M.G.P.)
| | - Elizabeth Suter
- Biology, Chemistry and Environmental Science Department, Molloy University, New York, NY 11570, USA;
| | - Gordon T. Taylor
- School of Marine, Atmospheric and Sustainability Sciences, Stony Brook University, New York, NY 11794, USA;
| | - Maria G. Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; (D.G.-M.); (M.G.P.)
| | - Virginia P. Edgcomb
- Geology & Geophysics Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA;
| |
Collapse
|
2
|
Quiñonero-Coronel MDM, Devos DP, Garcillán-Barcia MP. Specificities and commonalities of the Planctomycetes plasmidome. Environ Microbiol 2024; 26:e16638. [PMID: 38733104 DOI: 10.1111/1462-2920.16638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.
Collapse
Affiliation(s)
| | - Damien Paul Devos
- Centro Andaluz de Biología del Desarrollo (CABD, CSIC-Universidad Pablo de Olavide), Sevilla, Spain
| | - M Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC, CSIC-Universidad de Cantabria), Cantabria, Spain
| |
Collapse
|
3
|
Human Gut Metagenomes Encode Diverse GH156 Sialidases. Appl Environ Microbiol 2022; 88:e0175522. [PMID: 36394327 PMCID: PMC9746317 DOI: 10.1128/aem.01755-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The intestinal lining is protected by a mucous barrier composed predominantly of complex carbohydrates. Gut microbes employ diverse glycoside hydrolases (GHs) to liberate mucosal sugars as a nutrient source to facilitate host colonization. Intensive catabolism of mucosal glycans, however, may contribute to barrier erosion, pathogen encroachment, and inflammation. Sialic acid is an acidic sugar featured at terminal positions of host glycans. Characterized sialidases from the microbiome belong to the GH33 family, according to CAZy (Carbohydrate-Active enZYmes Database). In 2018 a functional metagenomics screen using thermal spring DNA uncovered the founding member of the GH156 sialidase family, the presence of which has yet to be reported in the context of the human microbiome. A subset of GH156 sequences from the CAZy database containing key sialidase residues was used to build a hidden Markov model. HMMsearch against public databases revealed ~10× more putative GH156 sialidases than currently cataloged by CAZy. Represented phyla include Bacteroidota, Verrucomicrobiota, and Firmicutes_A from human microbiomes, all of which play notable roles in carbohydrate fermentation. Analyses of metagenomic data sets revealed that GH156s are frequently encoded in metagenomes, with a greater variety and abundance of GH156 genes observed in traditional hunter-gatherer or agriculturalist societies than in industrialized societies, particularly relative to individuals with inflammatory bowel disease (IBD). Nineteen GH156s were recombinantly expressed and assayed for sialidase activity. The five GH156 sialidases identified here share limited sequence identity to each other or the founding GH156 family member and are representative of a large subset of the family. IMPORTANCE Sialic acids occupy terminal positions of human glycans where they act as receptors for microbes, toxins, and immune signaling molecules. Microbial enzymes that remove sialic acids, sialidases, are abundant in the human microbiome where they may contribute to shaping the microbiota community structure or contribute to pathology. Furthermore, sialidases have proven to hold therapeutic potential for cancer therapy. Here, we examined the sequence space of a sialidase family of enzymes, GH156, previously unknown in the human gut environment. Our analyses suggest that human populations with disparate dietary practices harbor distinct varieties and abundances of GH156-encoding genes. Furthermore, we demonstrate the sialidase activity of 5 gut-derived GH156s. These results expand the diversity of sialidases that may contribute to host glycan degradation, and these sequences may have biotechnological or clinical utility.
Collapse
|
4
|
Pontiller B, Martínez-García S, Joglar V, Amnebrink D, Pérez-Martínez C, González JM, Lundin D, Fernández E, Teira E, Pinhassi J. Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system. THE ISME JOURNAL 2022; 16:2360-2372. [PMID: 35804052 PMCID: PMC9478159 DOI: 10.1038/s41396-022-01273-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/01/2022] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Coastal upwelling zones are hotspots of oceanic productivity, driven by phytoplankton photosynthesis. Bacteria, in turn, grow on and are the principal remineralizers of dissolved organic matter (DOM) produced in aquatic ecosystems. However, the molecular processes that key bacterial taxa employ to regulate the turnover of phytoplankton-derived DOM are not well understood. We therefore carried out comparative time-series metatranscriptome analyses of bacterioplankton in the Northwest Iberian upwelling system, using parallel sampling of seawater and mesocosms with in situ-like conditions. The mesocosm experiment uncovered a taxon-specific progression of transcriptional responses from bloom development (characterized by a diverse set of taxa in the orders Cellvibrionales, Rhodobacterales, and Pelagibacterales), over early decay (mainly taxa in the Alteromonadales and Flavobacteriales), to senescence phases (Flavobacteriales and Saprospirales taxa). Pronounced order-specific differences in the transcription of glycoside hydrolases, peptidases, and transporters were found, supporting that functional resource partitioning is dynamically structured by temporal changes in available DOM. In addition, comparative analysis of mesocosm and field samples revealed a high degree of metabolic plasticity in the degradation and uptake of carbohydrates and nitrogen-rich compounds, suggesting these gene systems critically contribute to modulating the stoichiometry of the labile DOM pool. Our findings suggest that cascades of transcriptional responses in gene systems for the utilization of organic matter and nutrients largely shape the fate of organic matter on the time scales typical of upwelling-driven phytoplankton blooms.
Collapse
|
5
|
Morvan S, Paré MC, Schmitt A, Lafond J, Hijri M. Limited effect of thermal pruning on wild blueberry crop and its root-associated microbiota. FRONTIERS IN PLANT SCIENCE 2022; 13:954935. [PMID: 36035689 PMCID: PMC9408806 DOI: 10.3389/fpls.2022.954935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Thermal pruning was a common pruning method in the past but has progressively been replaced by mechanical pruning for economic reasons. Both practices are known to enhance and maintain high yields; however, thermal pruning was documented to have an additional sanitation effect by reducing weeds and fungal diseases outbreaks. Nevertheless, there is no clear consensus on the optimal fire intensity required to observe these outcomes. Furthermore, fire is known to alter the soil microbiome as it impacts the soil organic layer and chemistry. Thus far, no study has investigated into the effect of thermal pruning intensity on the wild blueberry microbiome in agricultural settings. This project aimed to document the effects of four gradual thermal pruning intensities on the wild blueberry performance, weeds, diseases, as well as the rhizosphere fungal and bacterial communities. A field trial was conducted using a block design where agronomic variables were documented throughout the 2-year growing period. MiSeq amplicon sequencing was used to determine the diversity as well as the structure of the bacterial and fungal communities. Overall, yield, fruit ripeness, and several other agronomical variables were not significantly impacted by the burning treatments. Soil phosphorus was the only parameter with a significant albeit temporary change (1 month after thermal pruning) for soil chemistry. Our results also showed that bacterial and fungal communities did not significantly change between burning treatments. The fungal community was dominated by ericoid mycorrhizal fungi, while the bacterial community was mainly composed of Acidobacteriales, Isosphaerales, Frankiales, and Rhizobiales. However, burning at high intensities temporarily reduced Septoria leaf spot disease in the season following thermal pruning. According to our study, thermal pruning has a limited short-term influence on the wild blueberry ecosystem but may have a potential impact on pests (notably Septoria infection), which should be explored in future studies to determine the burning frequency necessary to control this disease.
Collapse
Affiliation(s)
- Simon Morvan
- Institut de Recherche en Biologie Vègétale, Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | - Maxime C. Paré
- Laboratoire sur les écosystèmes boréaux terrestres (EcoTer), Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Anne Schmitt
- Laboratoire sur les écosystèmes boréaux terrestres (EcoTer), Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC, Canada
| | - Jean Lafond
- Direction générale des sciences et de la technologie, Agriculture et Agroalimentaire Canada, Gouvernement du Canada, Normandin, QC, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Vègétale, Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| |
Collapse
|
6
|
Naumoff DG, Kulichevskaya IS, Dedysh SN. Genetic Determinants of Xylan Utilization in Humisphaera borealis M1803T, a Planctomycete of the Class Phycisphaerae. Microbiology (Reading) 2022. [DOI: 10.1134/s002626172230004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Abstract—
Planctomycetes of the class Phycisphaerae are aerobic and anaerobic heterotrophic bacteria that colonize a wide range of marine and terrestrial habitats. Their functional roles in the environment, however, are still poorly understood. Humisphaera borealis M1803T is one of the very few characterized planctomycetes of this class. It is also the first described representative of the previously uncultured group WD2101, which is commonly detected in soils and peatlands. This work analyzed the genetic determinants that define the ability of Humisphaera borealis M1803T to grow on xylan, one of the plant cell wall polymers. The whole genome sequence analysis of this planctomycete resulted in identification of five genes encoding the proteins homologous to previously described endo-β-xylanases. For two of these proteins, evolutionarily closer experimentally characterized homologs with other substrate specificities were found. In a member of the GH10 family of glycoside hydrolases, the active center of the enzyme was destroyed. We consider two proteins from GH62 and GH141 families as the most likely candidates for the role of β-xylanase responsible for xylan utilization. Phylogenetic analysis of proteins of GH10, GH62, and GH141 families was carried out. The role of lateral transfers in the evolution of the genes for glycoside hydrolases and their close homologs is discussed.
Collapse
|
7
|
Bacterial communities in peat swamps reflect changes associated with catchment urbanisation. Urban Ecosyst 2022. [DOI: 10.1007/s11252-022-01238-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractLike many peat wetlands around the world, Temperate Highland Peat Swamps on Sandstone (THPSS), located in the Sydney Basin, Australia, have been impacted by urban development. In this paper, we used Illumina 16S rRNA DNA amplicon sequencing to characterise and compare the bacterial communities of surface (top 0–2 cm) and deep (50 cm) sediments in peat swamps that occur in both urbanised and non-urbanised catchments. Proteobacteria (32.2% of reads), Acidobacteria (23.6%) and Chloroflexi (10.7%) were the most common phyla of the dataset. There were significant differences in the bacterial community structure between catchment types and depths apparent at the phyla level. Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia made up a greater proportion of the reads in the surface sediments than the deeper sediments, while Chloroflexi and Nitrospirae were relatively more common in the deeper than the surface sediment. By catchment type, Acidobacteria were more common in swamps occurring in non-urbanised catchments, while Nitrospirae, Bacteroidetes and Actinobacteria were more common in those in urbanised catchments. Microbial community structure was significantly correlated with sediment pH, as was the relative abundance of several phyla, including Acidobacteria (negative correlation) and Bacteroidetes (positive correlation). As an indicator of trophic shift from oligotrophic to copiotrophic conditions associated with urbanised catchment, we found significant differences ratios of β-Proteobacteria to Acidobacteria and Bacteriodetes to Acidobacteria between the catchment types. Based on SIMPER results we suggest the relative abundance of Nitrosomonadaceae family as a potential indicator of urban degradation. As the first study to analyse the bacterial community structure of THPSS using sequencing of 16S rDNA, we reveal the utility of such analyses and show that urbanisation in the Blue Mountains is impacting the microbial ecology of these important peatland ecosystems.
Collapse
|
8
|
Zuo YW, Zhang JH, Ning DH, Zeng YL, Li WQ, Xia CY, Zhang H, Deng HP. Comparative Analyses of Rhizosphere Bacteria Along an Elevational Gradient of Thuja sutchuenensis. Front Microbiol 2022; 13:881921. [PMID: 35591985 PMCID: PMC9111514 DOI: 10.3389/fmicb.2022.881921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
Thuja sutchuenensis Franch. is an endangered species in southwestern China, primarily distributed in 800-2,100 m of inaccessible mountainous areas. Rhizosphere soil physicochemical properties and bacterial communities play an essential role in managing plant growth and survival. Nonetheless, the study investigating rhizosphere soil properties and bacterial communities of T. sutchuenensis is limited. The present study investigated soil properties, including soil pH, organic matter, water content, nitrogen, phosphorus, and potassium contents, and bacterial communities in nearly all extant T. sutchuenensis populations at five elevational gradients. Our results demonstrated that the increase in elevation decreased rhizosphere and bulk soil phosphorus content but increased potassium content. In addition, the elevational gradient was the dominant driver for the community composition differentiation of soil bacterial community. Proteobacteria and Acidobacteria were the dominant bacterial phyla distributed in the rhizosphere and bulk soils. Co-occurrence network analysis identified key genera, including Bradyrhizobium, Acidicapsa, Catenulispora, and Singulisphaera, that displayed densely connected interactions with many genera in the rhizosphere soil. The dominant KEGG functional pathways of the rhizosphere bacteria included ABC transporters, butanoate metabolism, and methane metabolism. Further correlation analysis found that soil phosphorus and potassium were the dominant drivers for the diversity of soil bacteria, which were distinctively contributed to the phylum of Planctomycetes and the genera of Blastopirellula, Planctomycetes, and Singulisphaera. Collectively, this comprehensive study generated multi-dimensional perspectives for understanding the soil bacterial community structures of T. sutchuenensis, and provided valuable findings for species conservation at large-scale views.
Collapse
Affiliation(s)
- You-wei Zuo
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Jia-hui Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Deng-hao Ning
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Yu-lian Zeng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Wen-qiao Li
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Chang-ying Xia
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Huan Zhang
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
| | - Hong-ping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Institute of Resources Botany, Southwest University, Chongqing, China
- Chongqing Academy of Science and Technology, Low Carbon and Ecological Environment Protection Research Center, Chongqing, China
| |
Collapse
|
9
|
Dom SP, Ikenaga M, Lau SYL, Radu S, Midot F, Yap ML, Chin MY, Lo ML, Jee MS, Maie N, Melling L. Linking prokaryotic community composition to carbon biogeochemical cycling across a tropical peat dome in Sarawak, Malaysia. Sci Rep 2021; 11:6416. [PMID: 33742002 PMCID: PMC7979770 DOI: 10.1038/s41598-021-81865-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Tropical peat swamp forest is a global store of carbon in a water-saturated, anoxic and acidic environment. This ecosystem holds diverse prokaryotic communities that play a major role in nutrient cycling. A study was conducted in which a total of 24 peat soil samples were collected in three forest types in a tropical peat dome in Sarawak, Malaysia namely, Mixed Peat Swamp (MPS), Alan Batu (ABt), and Alan Bunga (ABg) forests to profile the soil prokaryotic communities through meta 16S amplicon analysis using Illumina Miseq. Results showed these ecosystems were dominated by anaerobes and fermenters such as Acidobacteria, Proteobacteria, Actinobacteria and Firmicutes that cover 80-90% of the total prokaryotic abundance. Overall, the microbial community composition was different amongst forest types and depths. Additionally, this study highlighted the prokaryotic communities' composition in MPS was driven by higher humification level and lower pH whereas in ABt and ABg, the less acidic condition and higher organic matter content were the main factors. It was also observed that prokaryotic diversity and abundance were higher in the more oligotrophic ABt and ABg forest despite the constantly waterlogged condition. In MPS, the methanotroph Methylovirgula ligni was found to be the major species in this forest type that utilize methane (CH4), which could potentially be the contributing factor to the low CH4 gas emissions. Aquitalea magnusonii and Paraburkholderia oxyphila, which can degrade aromatic compounds, were the major species in ABt and ABg forests respectively. This information can be advantageous for future study in understanding the underlying mechanisms of environmental-driven alterations in soil microbial communities and its potential implications on biogeochemical processes in relation to peatland management.
Collapse
Affiliation(s)
- Simon Peter Dom
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Makoto Ikenaga
- Research Field in Agriculture, Agriculture Fisheries and Veterinary Medicine Area, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Sharon Yu Ling Lau
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Son Radu
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Frazer Midot
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Lan Yap
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei-Yee Chin
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mei Lieng Lo
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Mui Sie Jee
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Nagamitsu Maie
- School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan
| | - Lulie Melling
- Sarawak Tropical Peat Research Institute, Lot 6035, Kuching-Samarahan Expressway, 94300, Kota Samarahan, Sarawak, Malaysia
| |
Collapse
|
10
|
Furusawa G, Azami NA, Teh AH. Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4. PeerJ 2021; 9:e10929. [PMID: 33732545 PMCID: PMC7953866 DOI: 10.7717/peerj.10929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Oligosaccharides from polysaccharides containing uronic acids are known to have many useful bioactivities. Thus, polysaccharide lyases (PLs) and glycoside hydrolases (GHs) involved in producing the oligosaccharides have attracted interest in both medical and industrial settings. The numerous polysaccharide lyases and glycoside hydrolases involved in producing the oligosaccharides were isolated from soil and marine microorganisms. Our previous report demonstrated that an agar-degrading bacterium, Catenovulum sp. CCB-QB4, isolated from a coastal area of Penang, Malaysia, possessed 183 glycoside hydrolases and 43 polysaccharide lyases in the genome. We expected that the strain might degrade and use uronic acid-containing polysaccharides as a carbon source, indicating that the strain has a potential for a source of novel genes for degrading the polysaccharides. METHODS To confirm the expectation, the QB4 cells were cultured in artificial seawater media with uronic acid-containing polysaccharides, namely alginate, pectin (and saturated galacturonate), ulvan, and gellan gum, and the growth was observed. The genes involved in degradation and utilization of uronic acid-containing polysaccharides were explored in the QB4 genome using CAZy analysis and BlastP analysis. RESULTS The QB4 cells were capable of using these polysaccharides as a carbon source, and especially, the cells exhibited a robust growth in the presence of alginate. 28 PLs and 22 GHs related to the degradation of these polysaccharides were found in the QB4 genome based on the CAZy database. Eleven polysaccharide lyases and 16 glycoside hydrolases contained lipobox motif, indicating that these enzymes play an important role in degrading the polysaccharides. Fourteen of 28 polysaccharide lyases were classified into ulvan lyase, and the QB4 genome possessed the most abundant ulvan lyase genes in the CAZy database. Besides, genes involved in uronic acid metabolisms were also present in the genome. These results were consistent with the cell growth. In the pectin metabolic pathway, the strain had genes for three different pathways. However, the growth experiment using saturated galacturonate exhibited that the strain can only use the pathway related to unsaturated galacturonate.
Collapse
Affiliation(s)
- Go Furusawa
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Nor Azura Azami
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| |
Collapse
|
11
|
"Candidatus Laterigemmans baculatus" gen. nov. sp. nov., the first representative of rod shaped planctomycetes with lateral budding in the family Pirellulaceae. Syst Appl Microbiol 2021; 44:126188. [PMID: 33647766 DOI: 10.1016/j.syapm.2021.126188] [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: 09/24/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 01/27/2023]
Abstract
Two axenic cultures of Planctomycetes were isolated from distinct geographical regions of the east coast of India. The two closely related strains (JC640 and CH01) showed <93.3% 16S rRNA gene sequence identity with members of the genus Roseimaritima followed by Rhodopirellula (<91%). Both strains displayed non-canonical cell morphology of Planctomycetes, such as rod shaped cells with division by lateral budding. Both strains showed crateriform structures on their surfaces and cells lack fimbriae. The genomes have a size of about 5.76 Mb and DNA G+C content of 63.6mol%. Phylogenetic analysis based on 16S rRNA gene sequence and 92 core genes based RAxML phylogenetic tree place both the strains in the family Pirellulaceae and indicated Roseimaritima sediminicola as their closest relative. The AAI and POCP values differentiate both strains from rest of the members of the family Pirellulaceae. The axenic cultures of both strains were able to grow up to 8-10 passages and subsequently the cells became non-viable with pleomorphic shapes. Supported by genomic, phylogenetic and morphological differences, we conclude that both strains belong to a novel genus. However, since the new isolates lost their viability on passaging, we propose the novel genus as "Candidatus Laterigemmans" gen. nov. and the novel species as "Candidatus Laterigemmans baculatus" sp. nov.
Collapse
|
12
|
Jogler C, Wiegand S, Boedeker C, Heuer A, Peeters SH, Jogler M, Jetten MSM, Rohde M, Kallscheuer N. Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago. Antonie Van Leeuwenhoek 2020; 113:1889-1900. [PMID: 32399714 PMCID: PMC7716859 DOI: 10.1007/s10482-020-01424-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
A novel planctomycetal strain, designated ElPT, was isolated from an alga in the shallow hydrothermal vent system close to Panarea Island in the Tyrrhenian Sea. Cells of strain ElPT are spherical, form pink colonies and display typical planctomycetal characteristics including division by budding and presence of crateriform structures. Strain ElPT has a mesophilic (optimum at 30 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. It reaches a generation time of 29 h (µmax = 0.024 h-1). The strain has a genome size of 9.40 Mb with a G + C content of 71.1% and harbours five plasmids, the highest number observed in the phylum Planctomycetes thus far. Phylogenetically, the strain represents a novel species of the recently described genus Tautonia in the family Isosphaeraceae. A characteristic feature of the strain is its tendency to attach strongly to a range of plastic surfaces. We thus propose the name Tautonia plasticadhaerens sp. nov. for the novel species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).
Collapse
Affiliation(s)
- Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | | |
Collapse
|
13
|
Salbreiter M, Waqqas M, Jogler M, Kallscheuer N, Wiegand S, Peeters SH, Heuer A, Jetten MSM, Boedeker C, Rast P, Rohde M, Jogler C. Three Planctomycetes isolated from biotic surfaces in the Mediterranean Sea and the Pacific Ocean constitute the novel species Symmachiella dynata gen. nov., sp. nov. and Symmachiella macrocystis sp. nov. Antonie Van Leeuwenhoek 2020; 113:1965-1977. [PMID: 32833165 PMCID: PMC7716862 DOI: 10.1007/s10482-020-01464-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
Abstract
Planctomycetes is a phylum of environmentally important bacteria, which also receive significant attention due to their fascinating cell biology. Access to axenic Planctomycete cultures is crucial to study cell biological features within this phylum in further detail. In this study, we characterise three novel strains, Mal52T, Pan258 and CA54T, which were isolated close to the coasts of the islands Mallorca (Spain) and Panarea (Italy), and from Monterey Bay, CA, USA. The three isolates show optimal growth at temperatures between 22 and 24 °C and at pH 7.5, divide by polar budding, lack pigmentation and form strong aggregates in liquid culture. Analysis of five phylogenetic markers suggests that the strains constitute two novel species within a novel genus in the family Planctomycetaceae. The strains Mal52T (DSM 101177T = VKM B-3432T) and Pan258 were assigned to the species Symmachiella dynata gen nov., sp. nov., while strain CA54T (DSM 104301T = VKM B-3450T) forms a separate species of the same genus, for which we propose the name Symmachiella macrocystis sp. nov.
Collapse
Affiliation(s)
- Markus Salbreiter
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany
| | - Muhammad Waqqas
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany
| | - Mareike Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany
| | | | - Sandra Wiegand
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein- Leopoldshafen, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christian Jogler
- Department of Microbial Interactions, Friedrich-Schiller-University, Jena, Germany.
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
| |
Collapse
|
14
|
Aqeel H, Liss SN. Autotrophic Fixed-Film Systems Treating High Strength Ammonia Wastewater. Front Microbiol 2020; 11:551925. [PMID: 33013783 PMCID: PMC7506033 DOI: 10.3389/fmicb.2020.551925] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/12/2020] [Indexed: 01/04/2023] Open
Abstract
The aim of the study was enrichment of nitrifying bacteria and to investigate the potential of autotrophic fixed-film and hybrid bioreactors to treat high strength ammonia wastewater (up to 1,000 mg N/L). Two types of fixed-film systems [moving bed biofilm reactor (MBBR) and BioCordTM] in two different configurations [sequencing batch reactor (SBR) and a continuous stirred tank reactor (CSTR)] were operated for 306 days. The laboratory-scale bioreactors were seeded with activated sludge from a municipal wastewater treatment plant and fed synthetic wastewater with no organics. Strategies for acclimation included biomass reseeding (during bioreactor start-up), and gradual increase in the influent ammonia concentration [from 130 to 1,000 mg N/L (10% every 5 days)]. Stable ammonia removal was observed up to 750 mg N/L from 45 to 145 days in the MBBR SBR (94-100%) and CSTR (72-100%), and BioCordTM SBR (96-100%) and CSTR (92-100%). Ammonia removal declined to 87% ± 6, in all bioreactors treating 1,000 mg N/L (on day 185). Following long-term operation at 1,000 mg N/L (on day 306), ammonia removal was 93-94% in both the MBBR SBR and BioCordTM CSTR; whereas, ammonia removal was relatively lower in MBBR CSTR (20-35%) and BioCordTM SBR (45-54%). Acclimation to increasing concentrations of ammonia led to the enrichment of nitrifying (Nitrosomonas, Nitrospira, and Nitrobacter) and denitrifying (Comamonas, OLB8, and Rhodanobacter) bacteria [16S rRNA gene sequencing (Illumina)] in all bioreactors. In the hybrid bioreactor, the nitrifying and denitrifying bacteria were relatively more abundant in flocs and biofilms, respectively. The presence of dead cells (in biofilms) suggests that in the absence of an organic substrate, endogenous decay is a likely contributor of nutrients for denitrifying bacteria. The nitrite accumulation and abundance of denitrifying bacteria indicate partial denitrification in fixed-film bioreactors operated under limited carbon conditions. Further studies are required to assess the contribution of organic material produced in autotrophic biofilms (by endogenous decay and soluble microbial products) to the overall treatment process. Furthermore, the possibility of sustaining autotrophic nitrogen in high strength waste-streams in the presence of organic substrates warrants further investigation.
Collapse
Affiliation(s)
- Hussain Aqeel
- School of Environmental Studies, Queen's University, Kingston, ON, Canada
| | - Steven N Liss
- School of Environmental Studies, Queen's University, Kingston, ON, Canada.,Department of Chemistry and Biology, Ryerson University, Toronto, ON, Canada.,Department of Microbiology, Stellenbosch University, Stellenbosch, South Africa
| |
Collapse
|
15
|
Belova SE, Saltykova VA, Dedysh SN. Antimicrobial Activity of a Novel Freshwater Planctomycete Lacipirellula parvula PX69T. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720050045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
16
|
Kaushik R, Sharma M, Gaurav K, Jagadeeshwari U, Shabbir A, Sasikala C, Ramana CV, Pandit MK. Paludisphaera soli sp. nov., a new member of the family Isosphaeraceae isolated from high altitude soil in the Western Himalaya. Antonie van Leeuwenhoek 2020; 113:1663-1674. [PMID: 32936355 DOI: 10.1007/s10482-020-01471-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/01/2020] [Indexed: 11/28/2022]
Abstract
A novel strain of Planctomycetes, designated JC670T, was isolated from a high altitude (~ 2900 m above sea level) soil sample collected from Garhwal region in the Western Himalaya. Colonies of this strain were observed to be light pink coloured with spherical to oval shaped cells having crateriform structures distributed all over the cell surface. The cells divide by budding. Strain JC670T was found to grow well at pH 7.0 and pH 8.0 and to tolerate up to 2% NaCl (w/v). MK6 was the only respiratory quinone identified. The major fatty acids of strain JC670T were identified as C18:1ω9c, C18:0 and C16:0, and phosphatidylcholine, two unidentified phospholipids and six unidentified lipids are present as the polar lipids. The polyamines putrescine and sym-homospermidine were detected. Strain JC670T shows high 16S rRNA gene sequence identity (95.4%) with Paludisphaera borealis PX4T. The draft genome size of strain JC670T is 7.97 Mb, with G + C content of 70.4 mol%. Based on phylogenetic analyses with the sequences of ninety-two core genes, low dDDH value (20.6%), low gANI (76.8%) and low AAI (69.1%) results, differential chemotaxonomic and physiological properties, strain JC670T (= KCTC 72850T = NBRC 114339T) is recognised as the type strain of a new species of the genus Paludisphaera, for which we propose the name Paludisphaera soli sp. nov.
Collapse
Affiliation(s)
- Rishabh Kaushik
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India
| | - Meesha Sharma
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India
| | - Kumar Gaurav
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - U Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085, India
| | - A Shabbir
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India
| | - Ch Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University Hyderabad, Kukatpally, Hyderabad, 500085, India
| | - Ch V Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad, 500046, India.
| | - Maharaj K Pandit
- Department of Environmental Studies, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
17
|
Cai Y, Chen H, Yuan R, Wang F, Chen Z, Zhou B. Metagenomic analysis of soil microbial community under PFOA and PFOS stress. ENVIRONMENTAL RESEARCH 2020; 188:109838. [PMID: 32798955 DOI: 10.1016/j.envres.2020.109838] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/29/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Perfluorinated compounds (PFCs) contamination of soil has attracted global attention in recent years but influences of PFCs on microorganisms in the soil environment have not been fully described. In this study, the effects of perfluorooctane sulphonate (PFOS) and perfluoroctanoic acid (PFOA) on bacterial communities were determined by Illumina Miseq sequencing and Illumina Hiseq Xten. The stimulation of PFCs pollutants on soil bacterial richness and community diversity were observed. Sequencing information indicated that Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Gemmatimonadetes were the dominant bacterial phyla. Two genera, Bacillus and Sphingomonas, exhibited adverse responses toward PFCs pollution. Carbohydrate-active enzymes (CAZy), Kyoto Encyclopedia of Genes and Genomes (KEGG) and NCBI databases were used to elucidate the proteins and function action of soil microbial to PFCs pollution. Pathways such as Carbohydrate metabolism, Global and overview maps and Membrane transport in the soil microbes were affected by PFCs stress. CAZy analysis revealed that glycosyl transferases (GTs) in PFCs-polluted soils showed more active, while glycoside hydrolases (GHs) were inhibited severely.
Collapse
Affiliation(s)
- Yanping Cai
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Huilun Chen
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| | - Rongfang Yuan
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Fei Wang
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Zhongbing Chen
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500, Prague, Czech Republic
| | - Beihai Zhou
- Beijing Key Laboratory of Resource-oriented Treatment of Industrial Pollutants, School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
| |
Collapse
|
18
|
Kulichevskaya IS, Naumoff DG, Miroshnikov KK, Ivanova AA, Philippov DA, Hakobyan A, Rijpstra WIC, Damsté JSS, Liesack W, Dedysh SN. Limnoglobus roseus gen. nov., sp. nov., a novel freshwater planctomycete with a giant genome from the family Gemmataceae. Int J Syst Evol Microbiol 2020; 70:1240-1249. [PMID: 31800383 PMCID: PMC7397252 DOI: 10.1099/ijsem.0.003904] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/16/2019] [Indexed: 11/18/2022] Open
Abstract
The family Gemmataceae accommodates aerobic, chemoorganotrophic planctomycetes, which inhabit various freshwater ecosystems, wetlands and soils. Here, we describe a novel member of this family, strain PX52T, which was isolated from a boreal eutrophic lake in Northern Russia. This isolate formed pink-pigmented colonies and was represented by spherical cells that occurred singly, in pairs or aggregates and multiplied by budding. Daughter cells were highly motile. PX52T was an obligate aerobic chemoorganotroph, which utilized various sugars and some heteropolysaccharides. Growth occurred at pH 5.0-7.5 (optimum pH 6.5) and at temperatures between 10 and 30 °C (optimum 20-25 °C). The major fatty acids were C18 : 1ɷ7c, C18 : 0 and βOH-C16:0; the major intact polar lipid was trimethylornithine, and the quinone was MK-6. The complete genome of PX52T was 9.38 Mb in size and contained nearly 8000 potential protein-coding genes. Among those were genes encoding a wide repertoire of carbohydrate-active enzymes (CAZymes) including 33 glycoside hydrolases (GH) and 87 glycosyltransferases (GT) affiliated with 17 and 12 CAZy families, respectively. DNA G+C content was 65.6 mol%. PX52T displayed only 86.0-89.8 % 16S rRNA gene sequence similarity to taxonomically described Gemmataceae planctomycetes and differed from them by a number of phenotypic characteristics and by fatty acid composition. We, therefore, propose to classify it as representing a novel genus and species, Limnoglobus roseus gen. nov., sp. nov. The type strain is strain PX52T (=KCTC 72397T=VKM B-3275T).
Collapse
Affiliation(s)
- Irina S. Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Daniil G. Naumoff
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Kirill K. Miroshnikov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A. Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Dmitriy A. Philippov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok 152742, Russia
| | - Anna Hakobyan
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - W. Irene C. Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Jaap S. Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
- Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Werner Liesack
- Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany
| | - Svetlana N. Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| |
Collapse
|
19
|
Dedysh SN, Ivanova AA. Planctomycetes in boreal and subarctic wetlands: diversity patterns and potential ecological functions. FEMS Microbiol Ecol 2019; 95:5195516. [PMID: 30476049 DOI: 10.1093/femsec/fiy227] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/18/2018] [Indexed: 12/13/2022] Open
Abstract
Members of the phylum Planctomycetes are common inhabitants of boreal Sphagnum peat bogs and lichen-dominated tundra wetlands. These bacteria colonize both oxic and anoxic peat layers and reach the population size of 107 cells per gram of wet peat. The 16S rRNA gene sequences from planctomycetes comprise 5%-22% of total 16S rRNA gene reads retrieved from peat samples. Most abundant peat-inhabiting planctomycetes affiliate with the families Isosphaeraceae and Gemmataceae, and with as-yet-uncultured Phycisphaera-related group WD2101. The use of metatranscriptomics to assess the functional role of planctomycetes in peatlands suggested the presence of versatile hydrolytic capabilities in these bacteria. This evidence was further confirmed by the analysis of genome-encoded capabilities of isolates from wetlands. Large (up to 12 Mbp) genomes of planctomycetes encode wide repertoires of carbohydrate-active enzymes including many unclassified putative glycoside hydrolases, which suggests the presence of extremely high glycolytic potential in these bacteria. Experimental tests confirmed their ability to grow on xylan, pectin, starch, lichenan, cellulose, chitin and polysaccharides of microbial origin. These results provide an insight into the ecological roles of peat-inhabiting planctomycetes and suggest their participation in degradation of plant-derived polymers, exoskeletons of peat-inhabiting arthropods as well as exopolysaccharides produced by other bacteria.
Collapse
Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Leninsky prospect 33-2, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Leninsky prospect 33-2, Russia
| |
Collapse
|
20
|
Rhodopirellula heiligendammensis sp. nov., Rhodopirellula pilleata sp. nov., and Rhodopirellula solitaria sp. nov. isolated from natural or artificial marine surfaces in Northern Germany and California, USA, and emended description of the genus Rhodopirellula. Antonie van Leeuwenhoek 2019; 113:1737-1750. [DOI: 10.1007/s10482-019-01366-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023]
|
21
|
Kohn T, Wiegand S, Boedeker C, Rast P, Heuer A, Jetten MSM, Schüler M, Becker S, Rohde C, Müller RW, Brümmer F, Rohde M, Engelhardt H, Jogler M, Jogler C. Planctopirus ephydatiae, a novel Planctomycete isolated from a freshwater sponge. Syst Appl Microbiol 2019; 43:126022. [PMID: 31785948 DOI: 10.1016/j.syapm.2019.126022] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 01/28/2023]
Abstract
The microbiome of freshwater sponges is rarely studied, and not a single novel bacterial species has been isolated and subsequently characterized from a freshwater sponge to date. A previous study showed that 14.4% of the microbiome from Ephydatia fluviatilis belong to the phylum Planctomycetes. Therefore, we sampled an Ephydatia sponge from a freshwater lake and employed enrichment techniques targeting bacteria from the phylum Planctomycetes. The obtained strain spb1T was subject to genomic and phenomic characterization and found to represent a novel planctomycetal species proposed as Planctopirus ephydatiae sp. nov. (DSM 106606 = CECT 9866). In the process of differentiating spb1T from its next relative Planctopirus limnophila DSM 3776T, we identified and characterized the first phage - Planctopirus phage vB_PlimS_J1 - infecting planctomycetes that was only mentioned anecdotally before. Interestingly, classical chemotaxonomic methods would have failed to distinguish Planctopirus ephydatiae strain spb1T from Planctopirus limnophila DSM 3776T. Our findings demonstrate and underpin the need for whole genome-based taxonomy to detect and differentiate planctomycetal species.
Collapse
Affiliation(s)
- T Kohn
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - S Wiegand
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - C Boedeker
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - P Rast
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - A Heuer
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - M S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, Netherlands
| | - M Schüler
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - S Becker
- University of Veterinary Medicine Hannover, Germany
| | - C Rohde
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - R-W Müller
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Germany
| | - F Brümmer
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Germany
| | - M Rohde
- Central Facility for Microscopy, Helmholtz-Centre for Infection Research (HZI), Braunschweig, Germany
| | - H Engelhardt
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - M Jogler
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - C Jogler
- Department of Microbiology, Radboud University, Nijmegen, Netherlands; Department of Microbial Interactions, Friedrich Schiller Universität Jena, Germany.
| |
Collapse
|
22
|
Kulichevskaya IS, Naumoff DG, Ivanova AA, Rakitin AL, Dedysh SN. Detection of Chitinolytic Capabilities in the Freshwater Planctomycete Planctomicrobium piriforme. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719040076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
23
|
Ma J, Zhu D, Chen QL, Ding J, Zhu YG, Sheng GD, Qiu YP. Exposure to tetracycline perturbs the microbiome of soil oligochaete Enchytraeus crypticus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:643-650. [PMID: 30447602 DOI: 10.1016/j.scitotenv.2018.11.154] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/09/2018] [Accepted: 11/10/2018] [Indexed: 06/09/2023]
Abstract
Microbial symbiosis is essential for the normal development and growth of hosts. Past attention has mostly been paid to its effects on plants and vertebrates. The effects of environmental pressures such as antibiotics on the microbiome of soil fauna remain largely elusive. We used bacterial 16S rRNA gene high-throughput sequencing to examine the response of microbiome of soil invertebrate Enchytraeus crypticus to oral tetracycline exposure. After two-week exposure, tetracycline-free oat was used as food to monitor the restoration of E. crypticus microbiome. The results showed that Proteobacteria, Actinobacteria and Planctomycetes were the three dominant phyla in all samples, Rhizobiaceae and Kaistia were the most abundant family and genus in all samples, respectively. After 14 days tetracycline exposure, Planctomycetes declined dramatically from 33.05% to 3.28% (P = 0.016), but Actinobacteria elevated substantially from 2.47% to 23.65% (P = 0.004). The alpha-diversity of microbial community increased significantly after tetracycline exposure compared to the control (P = 0.014). Terminating tetracycline exposure led to the recovery of E. crypticus microbiome back to the background level within 14 days. Our results suggest that while tetracycline can disturb the microbiome in E. crypticus significantly, the effects of the antibiotic on E. crypticus microbiome may not be permanent but reversibly diminish after stopping exposure for a period of time. The results may contribute to extending our understanding of the effect of antibiotics on microbiome of soil invertebrates. CAPSULE: The microbiome of E. crypticus exposed to tetracycline is perturbed and reversibly restored after terminating the exposure.
Collapse
Affiliation(s)
- Jun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Dong Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jing Ding
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - G Daniel Sheng
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China.
| | - Yu-Ping Qiu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| |
Collapse
|
24
|
Naumoff DG, Dedysh SN. Bacteria from Poorly Studied Phyla as a Potential Source of New Enzymes: β-Galactosidases from Planctomycetes and Verrucomicrobia. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718060127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
25
|
Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| |
Collapse
|
26
|
Franke JD, Blomberg WR, Todd RT, Thomas RW, Selmecki AM. Assembly of a complete genome sequence for Gemmata obscuriglobus reveals a novel prokaryotic rRNA operon gene architecture. Antonie van Leeuwenhoek 2018; 111:2095-2105. [DOI: 10.1007/s10482-018-1102-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/16/2018] [Indexed: 11/28/2022]
|
27
|
Genome Analysis of Fimbriiglobus ruber SP5 T, a Planctomycete with Confirmed Chitinolytic Capability. Appl Environ Microbiol 2018; 84:AEM.02645-17. [PMID: 29374042 DOI: 10.1128/aem.02645-17] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 01/21/2018] [Indexed: 11/20/2022] Open
Abstract
Members of the bacterial order Planctomycetales have often been observed in associations with Crustacea. The ability to degrade chitin, however, has never been reported for any of the cultured planctomycetes although utilization of N-acetylglucosamine (GlcNAc) as a sole carbon and nitrogen source is well recognized for these bacteria. Here, we demonstrate the chitinolytic capability of a member of the family Gemmataceae, Fimbriiglobus ruber SP5T, which was isolated from a peat bog. As revealed by metatranscriptomic analysis of chitin-amended peat, the pool of 16S rRNA reads from F. ruber increased in response to chitin availability. Strain SP5T displayed only weak growth on amorphous chitin as a sole source of carbon but grew well with chitin as a source of nitrogen. The genome of F. ruber SP5T is 12.364 Mb in size and is the largest among all currently determined planctomycete genomes. It encodes several enzymes putatively involved in chitin degradation, including two chitinases affiliated with the glycoside hydrolase (GH) family GH18, GH20 family β-N-acetylglucosaminidase, and the complete set of enzymes required for utilization of GlcNAc. The gene encoding one of the predicted chitinases was expressed in Escherichia coli, and the endochitinase activity of the recombinant enzyme was confirmed. The genome also contains genes required for the assembly of type IV pili, which may be used to adhere to chitin and possibly other biopolymers. The ability to use chitin as a source of nitrogen is of special importance for planctomycetes that inhabit N-depleted ombrotrophic wetlands.IMPORTANCE Planctomycetes represent an important part of the microbial community in Sphagnum-dominated peatlands, but their potential functions in these ecosystems remain poorly understood. This study reports the presence of chitinolytic potential in one of the recently described peat-inhabiting members of the family Gemmataceae, Fimbriiglobus ruber SP5T This planctomycete uses chitin, a major constituent of fungal cell walls and exoskeletons of peat-inhabiting arthropods, as a source of nitrogen in N-depleted ombrotrophic Sphagnum-dominated peatlands. This study reports the chitin-degrading capability of representatives of the order Planctomycetales.
Collapse
|
28
|
Metatranscriptomics reveals the hydrolytic potential of peat-inhabiting Planctomycetes. Antonie van Leeuwenhoek 2017; 111:801-809. [PMID: 29134393 DOI: 10.1007/s10482-017-0973-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/31/2017] [Indexed: 10/18/2022]
Abstract
Members of the phylum Planctomycetes are common inhabitants of northern Sphagnum-dominated wetlands. Evidence is accumulating that, in these environments, some planctomycetes may be involved in degrading polymeric organic matter. The experimental data, however, remain scarce due to the low number of characterized representatives of this phylum. In a previous study, we used metatranscriptomics to assess the activity response of peat-inhabiting microorganisms to biopolymers abundantly present in native peat. The community responses to cellulose, xylan, pectin, and chitin availability were analysed relative to unamended controls. Here, we re-analysed these metatranscriptomes and retrieved a total of 1,602,783 rRNA and 35,522 mRNA sequences affiliated with the Planctomycetes. Each of the four polymers induced specific planctomycete responses. These were most pronounced on chitin. The two groups with increased 16S rRNA transcript pools were Gemmata- and Phycisphaera-like planctomycetes. Among uncultivated members of the Planctomycetaceae, two increased transcript pools were detected in pectin-amended samples and belonged to Pirellula-like bacteria. The analysis of taxonomically assigned mRNA reads confirmed the specific response of Gemmata-related planctomycetes to chitin amendment suggesting the presence of chitinolytic capabilities in these bacteria.
Collapse
|
29
|
Kulichevskaya IS, Ivanova AA, Detkova EN, Rijpstra WIC, Sinninghe Damsté JS, Dedysh SN. Tundrisphaera lichenicola gen. nov., sp. nov., a psychrotolerant representative of the family Isosphaeraceae from lichen-dominated tundra soils. Int J Syst Evol Microbiol 2017; 67:3583-3589. [PMID: 28829024 DOI: 10.1099/ijsem.0.002172] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of aerobic, budding, pink-pigmented bacteria, P12T and P515, were isolated from a lichen-dominated peatland and a forested tundra soil of north-western Siberia, respectively. Cells of these isolates were represented by non-motile spheres that occurred singly or were arranged in short chains and aggregates. While growing on solid media, cells of strains P12T and P515 attached to the surface by means of holdfast-like appendages. These isolates were mildly acidophilic (optimum growth at pH 5.5-6.0), psychrotolerant bacteria, which displayed tolerance of low temperatures (4-15 °C), grew optimally at 15-22 °C and did not grow at temperatures above 28 °C. The preferred growth substrates were sugars and some heteropolysaccharides. The major fatty acids were C18 : 1ω9c, C16 : 0 and C14 : 0. Trimethylornithine lipid was the major polar lipid. The only quinone was MK-6, and the G+C content of the DNA was 61.2-62.2 mol%. Strains P12T and P515 possessed identical 16S rRNA gene sequences, which affiliated them with the family Isosphaeraceae, order Planctomycetales, and these displayed the highest similarity (93-94 %) to 16S rRNA gene sequences from members of the genus Singulisphaera. However, the signature fatty acid of species of the genus Singulisphaera, i.e. C18 : 2ω6c,12c, was absent in cells of strains P12T and P515. They also differed from members of the genus Singulisphaera by substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Tundrisphaera lichenicola gen. nov., sp. nov, is proposed. The type strain is P12T (=LMG 29571T=VKM B-3044T).
Collapse
Affiliation(s)
- Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Ekaterina N Detkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, PO Box 59, 1790 AB Den Burg, The Netherlands.,Department of Earth Sciences, Geochemistry, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| |
Collapse
|