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Guden RM, Haegeman A, Ruttink T, Moens T, Derycke S. Nematodes alter the taxonomic and functional profiles of benthic bacterial communities: A metatranscriptomic approach. Mol Ecol 2024; 33:e17331. [PMID: 38533629 DOI: 10.1111/mec.17331] [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: 06/21/2023] [Revised: 02/25/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024]
Abstract
Marine sediments cover 70% of the Earth's surface, and harbour diverse bacterial communities critical for marine biogeochemical processes, which affect climate change, biodiversity and ecosystem functioning. Nematodes, the most abundant and species-rich metazoan organisms in marine sediments, in turn, affect benthic bacterial communities and bacterial-mediated ecological processes, but the underlying mechanisms by which they affect biogeochemical cycles remain poorly understood. Here, we demonstrate using a metatranscriptomic approach that nematodes alter the taxonomic and functional profiles of benthic bacterial communities. We found particularly strong stimulation of nitrogen-fixing and methane-oxidizing bacteria in the presence of nematodes, as well as increased functional activity associated with methane metabolism and degradation of various carbon compounds. This study provides empirical evidence that the presence of nematodes results in taxonomic and functional shifts in active bacterial communities, indicating that nematodes may play an important role in benthic ecosystem processes.
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Affiliation(s)
- Rodgee Mae Guden
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Moens
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
| | - Sofie Derycke
- Marine Biology Unit, Department of Biology, Ghent University, Ghent, Belgium
- Aquatic Environment and Quality, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Oostende, Belgium
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2
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Oceaniferula marina gen.nov., sp.nov., an anti-fluoroquinolone bacterium isolated from marine sediment. Antonie van Leeuwenhoek 2021; 114:1855-1865. [PMID: 34468960 DOI: 10.1007/s10482-021-01645-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/16/2021] [Indexed: 10/20/2022]
Abstract
A Gram-stain-negative, aerobic, rod-shaped, non-gliding and non-motile bacterium designated as N1E253T, was isolated from marine sediments collected from the coast of Weihai, PR China. N1E253T was found to grow at pH 7.0-9.0 (optimum, pH 7.5), 15-37 °C (optimum, 30 °C) in the presence of 1.5-5.0% (w/v) NaCl (optimum, 3.0%). The major polar lipids of strain N1E253T were phosphatidylethanolamine, diphosphatidylglycerol and one unidentified phospholipid. The sole respiratory quinone was MK-9. The major cellular fatty acids (> 10.0%) were iso-C14: 0, C16: 0 and Summed Feature 3 (C16:1 ω7c and/or C16:1 ω6c). The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this novel isolate to the family Verrucomicrobiaceae, with Persicirhabdus sediminis KCTC 22039 T being its closest relative with 92.1% sequence similarity. Genome sequencing revealed a genome size of 5,073,947 bp, DNA G + C content of 52.0% and two protein-coding genes related to the resistance of fluoroquinolones. Based on physiological, genomic, biochemical and chemotaxonomic characteristics, we propose that strain N1E253T represents a novel species of a novel genus within the family Verrucomicrobiaceae, for which the name Oceaniferula marina gen. nov., sp. nov. is proposed. The type strain is N1E253T (= KCTC 72800 T = MCCC 1H00405T).
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Complete Genome Sequence of the Novel Roseimicrobium sp. Strain ORNL1, a Verrucomicrobium Isolated from the Populus deltoides Rhizosphere. Microbiol Resour Announc 2020; 9:9/27/e00617-20. [PMID: 32616646 PMCID: PMC7330248 DOI: 10.1128/mra.00617-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Roseimicrobium sp. strain ORNL1 is a soil bacterium that belongs to the phylum Verrucomicrobia and was isolated from the rhizosphere of a forest Eastern cottonwood tree, Populus deltoides, in Tennessee. Its 7.9-Mb chromosome was completely sequenced using PacBio long reads and is predicted to encode 6,288 proteins and 76 RNAs. Roseimicrobium sp. strain ORNL1 is a soil bacterium that belongs to the phylum Verrucomicrobia and was isolated from the rhizosphere of a forest Eastern cottonwood tree, Populus deltoides, in Tennessee. Its 7.9-Mb chromosome was completely sequenced using PacBio long reads and is predicted to encode 6,288 proteins and 76 RNAs.
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Szuróczki S, Abbaszade G, Szabó A, Bóka K, Schumann P, Tóth E. Phragmitibacter flavus gen. nov., sp. nov. a new member of the family Verrucomicrobiaceae. Int J Syst Evol Microbiol 2020; 70:2108-2114. [DOI: 10.1099/ijsem.0.004025] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-stain-negative, aerobic, non-motile, oxidase- and catalase-positive, rod-shaped yellow-coloured bacterial strain MG-N-17T was isolated from a water sample of Lake Fertő/Neusiedler See (Hungary). Results of phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain forms a distinct linage within the family
Verrucomicrobiaceae
of the phylum
Verrucomicrobia
, and its closest relatives are
Verrucomicrobium spinosum
DSM 4136T (94.38 %) and
Roseimicrobium gellanilyticum
DC2a-G7T (91.55 %). The novel bacterial strain prefers a weak alkaline environment and grows optimally between 22–28 °C in the absence of NaCl. The major isoprenoid quinones are MK-10, MK-11, MK-12 and MK-9. The major cellular fatty acids are anteiso-C15 : 0, C16 : 0, C16 : 1ω5c and iso-C14 : 0. The polar lipid profile contains phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified glycolipids. The assembled draft genome of strain MG-N-17T had 44 contigs with an N50 value 348255 nt, 56.5× genome coverage, total length of 5 910 933 bp and G+C content of 56.9 mol%. Strain MG-N-17T (=DSM 106674T=NCAIM B.02643T) is proposed as the type strain of a new genus and species in the family
Verrucomicrobiaceae
, for which the name Phragmitibacter flavus gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Sára Szuróczki
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Gorkhmaz Abbaszade
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Attila Szabó
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Faculty of Science, Eötvös Loránd University, Budapest, Pázmány Péter stny. 1/C, H-1117, Hungary
| | - Peter Schumann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124, Braunschweig, Germany
| | - Erika Tóth
- Department of Microbiology, Faculty of Science, Eötvös Loránd University, Pázmány Péter stny. 1/C, H-1117 Budapest, Hungary
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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He S, Stevens SLR, Chan LK, Bertilsson S, Glavina del Rio T, Tringe SG, Malmstrom RR, McMahon KD. Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes. mSphere 2017; 2:e00277-17. [PMID: 28959738 PMCID: PMC5615132 DOI: 10.1128/msphere.00277-17] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/05/2017] [Indexed: 11/20/2022] Open
Abstract
Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called "Planctomycete-specific" cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called "Planctomycete-specific" cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling.
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Affiliation(s)
- Shaomei He
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Geoscience, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Sarah L. R. Stevens
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | | | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | | | | | - Katherine D. McMahon
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Civil and Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Pepe-Ranney C, Campbell AN, Koechli CN, Berthrong S, Buckley DH. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil. Front Microbiol 2016; 7:703. [PMID: 27242725 PMCID: PMC4867679 DOI: 10.3389/fmicb.2016.00703] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/27/2016] [Indexed: 11/13/2022] Open
Abstract
We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either (13)C-xylose or (13)C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for (13)C-incorporation into DNA from (13)C-xylose and (13)C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated (13)C in the (13)C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These (13)C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes.
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Affiliation(s)
| | | | | | - Sean Berthrong
- Department of Biological Sciences, Butler UniversityIndianapolis, IN, USA
| | - Daniel H. Buckley
- School of Integrative Plant Sciences, Cornell UniversityIthaca, NY, USA
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Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class ‘Spartobacteria’ in the phylum Verrucomicrobia, isolated from a rice paddy field. Int J Syst Evol Microbiol 2014; 64:1718-1723. [DOI: 10.1099/ijs.0.060244-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly anaerobic, mesophilic, carbohydrate-fermenting bacterium, designated NM-5T, was isolated from a rice paddy field. Cells of strain NM-5T were Gram-stain-negative, non-motile, non-spore-forming, short rods (0.5–0.7 µm×0.6–1.2 µm). The strain grew optimally at 37 °C (growth range 20–40 °C) and pH 7.0 (pH 5.5–8.0). The strain could grow fermentatively on arabinose, xylose, fructose, galactose, glucose, ribose, mannose, cellobiose, lactose, maltose and sucrose. The main end-products of glucose fermentation were acetate and propionate. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required but stimulated the growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The DNA G+C content was 46.3 mol%. The major cellular fatty acids were iso-C14 : 0, C18 : 0 and C16 : 0. 16S rRNA gene sequence analysis revealed that strain NM-5T belongs to the class ‘S
partobacteria’, subdivision 2 of the bacterial phylum
Verrucomicrobia
. Phylogenetically, the closest species was ‘Chthoniobacter flavus’ (89.6 % similarity in 16S rRNA gene sequence). A novel genus and species, Terrimicrobium sacchariphilum gen. nov., sp. nov., is proposed. The type strain of the type species is NM-5T ( = JCM 17479T = CGMCC 1.5168T).
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Otsuka S, Suenaga T, Vu HT, Ueda H, Yokota A, Senoo K. Brevifollis gellanilyticus gen. nov., sp. nov., a gellan-gum-degrading bacterium of the phylum
Verrucomicrobia. Int J Syst Evol Microbiol 2013; 63:3075-3078. [DOI: 10.1099/ijs.0.048793-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic properties of strain DC2c-G4T, a Gram-staining-negative, ovoid, gellan-gum-degrading bacterial isolate, were examined. Phylogenetic analysis based on 16S rRNA gene sequences identified this isolate as a member of the phylum
Verrucomicrobia
and closest to the genus
Prosthecobacter
. The 16S rRNA gene sequence similarities between this isolate and any of the type strains of species of the genus
Prosthecobacter
were less than 95 %. In addition, the absence of a single prostheca and the predominant menaquinone MK-7(H2) supported the differentiation of this isolate from the genus
Prosthecobacter
. Here, we propose Brevifollis gellanilyticus gen. nov., sp. nov. to accommodate the isolate. The type strain of the type species is DC2c-G4T ( = NBRC 108608T = CIP 110457T).
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Affiliation(s)
- Shigeto Otsuka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Taku Suenaga
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hoan Thi Vu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Hiroyuki Ueda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Keishi Senoo
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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