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Wassel MA, Makabe-Kobayashi Y, Iqbal MM, Takatani T, Sakakura Y, Hamasaki K. The impact of tetrodotoxin (TTX) on the gut microbiome in juvenile tiger pufferfish, Takifugu rubripes. Sci Rep 2024; 14:16684. [PMID: 39085277 PMCID: PMC11291987 DOI: 10.1038/s41598-024-66112-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: 03/16/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Tetrodotoxin (TTX) is a potent neurotoxin that accumulates in Takifugu rubripes, commonly known as pufferfish, through the ingestion of TTX-bearing organisms as part of their food chain. Although researchers believe that pufferfish use TTX to relieve stress, data are not currently available on how TTX affects the gut microbiota of pufferfish. To address this gap, our study aimed to investigate whether administering TTX to fish could alter their gut microbiota and overall health under various salinity conditions, including 30.0 ppt, 8.5 ppt, and 1.7 ppt salinity, which represent full-strength, isosmotic, and low-salinity stress, respectively. We analyzed the effect of TTX ingestion on the community structure, core microbiome, and metabolic capabilities of the gut microbiome using high-throughput sequencing technologies. The predominant bacterial taxa within the gut microbiome were Firmicutes (21-85%), Campilobacterota (2.8-67%), Spirochaetota (0.5-14%), and Proteobacteria (0.7-9.8%), with Mycoplasma, uncultured Arcobacteraceae, Brevinema, Vibrio, Rubritalea, and uncultured Pirellulaceae as core genera. Our findings indicated that the impact of TTX on high-abundance genera at 30.0 ppt and 8.5 ppt salinity levels was negligible, indicating their stability and resilience to TTX ingestion. However, at 1.7 ppt, TTX-fed fish showed a significant increase in uncultured Arcobacteraceae. Furthermore, our analysis of TTX-fed fish revealed taxonomic alterations in low-abundance taxa, which altered the predicted functions of the gut microbiota at all salinity levels. These results suggest that TTX administration could cause subtle effects on the metabolic functions of gut microbial communities. Overall, our study provides insights into the complex relationship between a TTX-accumulating animal, T. rubripes, and its gut microbiota.
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Affiliation(s)
- Mai A Wassel
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
- Genetics and Genetic Engineering Research Group, National Institute of Oceanography and Fisheries, NIOF, Cairo, Egypt.
| | - Yoko Makabe-Kobayashi
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Md Mehedi Iqbal
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
| | - Tomohiro Takatani
- Graduate School of Integrated Science and Technology, Nagasaki University, 1‑14 Bunkyo, Nagasaki, 852‑8521, Japan
| | - Yoshitaka Sakakura
- Graduate School of Integrated Science and Technology, Nagasaki University, 1‑14 Bunkyo, Nagasaki, 852‑8521, Japan
| | - Koji Hamasaki
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
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Vesamäki JS, Laine MB, Nissinen R, Taipale SJ. Plastic and terrestrial organic matter degradation by the humic lake microbiome continues throughout the seasons. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13302. [PMID: 38852938 PMCID: PMC11162827 DOI: 10.1111/1758-2229.13302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
Boreal freshwaters go through four seasons, however, studies about the decomposition of terrestrial and plastic compounds often focus only on summer. We compared microbial decomposition of 13C-polyethylene, 13C-polystyrene, and 13C-plant litter (Typha latifolia) by determining the biochemical fate of the substrate carbon and identified the microbial decomposer taxa in humic lake waters in four seasons. For the first time, the annual decomposition rate including separated seasonal variation was calculated for microplastics and plant litter in the freshwater system. Polyethylene decomposition was not detected, whereas polystyrene and plant litter were degraded in all seasons. In winter, decomposition rates of polystyrene and plant litter were fivefold and fourfold slower than in summer, respectively. Carbon from each substrate was mainly respired in all seasons. Plant litter was utilized efficiently by various microbial groups, whereas polystyrene decomposition was limited to Alpha- and Gammaproteobacteria. The decomposition was not restricted only to the growth season, highlighting that the decomposition of both labile organic matter and extremely recalcitrant microplastics continues throughout the seasons.
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Affiliation(s)
- Jussi S. Vesamäki
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Miikka B. Laine
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Riitta Nissinen
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Sami J. Taipale
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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Taipale SJ, Vesamäki J, Kautonen P, Kukkonen JVK, Biasi C, Nissinen R, Tiirola M. Biodegradation of microplastic in freshwaters: A long-lasting process affected by the lake microbiome. Environ Microbiol 2023; 25:2669-2680. [PMID: 36054230 DOI: 10.1111/1462-2920.16177] [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: 04/11/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022]
Abstract
Plastics have been produced for over a century, but definitive evidence of complete plastic biodegradation in different habitats, particularly freshwater ecosystems, is still missing. Using 13 C-labelled polyethylene microplastics (PE-MP) and stable isotope analysis of produced gas and microbial membrane lipids, we determined the biodegradation rate and fate of carbon in PE-MP in different freshwater types. The biodegradation rate in the humic-lake waters was much higher (0.45% ± 0.21% per year) than in the clear-lake waters (0.07% ± 0.06% per year) or the artificial freshwater medium (0.02% ± 0.02% per year). Complete biodegradation of PE-MP was calculated to last 100-200 years in humic-lake waters, 300-4000 years in clear-lake waters, and 2000-20,000 years in the artificial freshwater medium. The concentration of 18:1ω7, characteristic phospholipid fatty acid in Alpha- and Gammaproteobacteria, was a predictor of faster biodegradation of PE. Uncultured Acetobacteraceae and Comamonadaceae among Alpha- and Gammaproteobacteria, respectively, were major bacteria related to the biodegradation of PE-MP. Overall, it appears that microorganisms in humic lakes with naturally occurring refractory polymers are more adept at decomposing PE than those in other waters.
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Affiliation(s)
- Sami J Taipale
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Jussi Vesamäki
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Petra Kautonen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Jussi V K Kukkonen
- Department of Environmental and Biological Science, University of Eastern Finland, Finland
| | - Christina Biasi
- Department of Environmental and Biological Science, University of Eastern Finland, Finland
| | - Riitta Nissinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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Golder HM, Denman SE, McSweeney C, Celi P, Lean IJ. Effects of feed additives on rumen function and bacterial and archaeal communities during a starch and fructose challenge. J Dairy Sci 2023; 106:8787-8808. [PMID: 37678787 DOI: 10.3168/jds.2023-23486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/18/2023] [Indexed: 09/09/2023]
Abstract
The objective of this study was to improve understandings of the rumen microbial ecosystem during ruminal acidosis and responses to feed additives to improve prudent use strategies for ruminal acidosis control. Rumen bacterial and archaeal community composition (BCC) and its associations with rumen fermentation measures were examined in Holstein heifers fed feed additives and challenged with starch and fructose. Heifers (n = 40) were randomly allocated to 5 treatment groups: (1) control (no additives); (2) virginiamycin (VM; 200 mg/d); (3) monensin (MT; 200 mg/d) + tylosin (110 mg/d); (4) monensin (MLY; 220 mg/d) + live yeast (5.0 × 1012 cfu/d); (5) sodium bicarbonate (BUF; 200 g/d) + magnesium oxide (30 g/d). Heifers were fed twice daily a 62% forage:38% concentrate total mixed ration at 1.25% of body weight (BW) dry matter (DM)/d for a 20-d adaptation period with their additive(s). Fructose (0.1% of BW/d) was added to the ration for the last 10 d of adaptation. On d 21 heifers were challenged once with a ration consisting of 1.0% of BW DM wheat and 0.2% of BW fructose plus their additive(s). A rumen sample was collected from each heifer via stomach tube weekly (d 0, 7, 14) and 5 times over a 3.6 h period at 5, 65, 115, 165, and 215 min after consumption of the challenge ration (d 21) and analyzed for pH, and ammonia, d- and l-lactate, volatile fatty acids (VFA), and histamine concentrations and total bacteria and archaea. The 16S rRNA gene spanning the V4 region was PCR amplified and sequenced. Alpha and β diversity and associations of relative abundances of taxa with rumen fermentation measures were evaluated. Rumen BCC shifted among treatment groups in the adaptation period and across the challenge sampling period, indicating the feed additives had different modes of action. The monensin-containing treatment groups, MT and MLY often had similar relative abundances of rumen bacterial phyla and families. The MLY treatment group was characterized in the challenge period by increased relative abundances of the lactate utilizing genera Anaerovibrio and Megasphaera. The MLY treatment group also had increased diversity of ruminal bacteria which may provide resilience to changes in substrates. The control and BUF treatment groups were most similar in BCC. A redundancy analysis showed the MLY treatment group differed from all other treatment groups and concentrations of histamine and valerate in the rumen were associated with the most variation in the microbiota, 5.3% and 4.8%, respectively. It was evident from the taxa common to all treatment groups that cattle have a core microbiota. Functional redundancy of rumen bacteria which was reflected in the greater sensitivity for the rumen BCC than rumen fermentation measures likely provide resilience to changes in substrate. This functional redundancy of microbes in cattle suggests that there is no single optimal ruminal microbial population and no universally superior feed additive(s). In summary, differences in modes of action suggest the potential for more targeted and improved prudent use of feed additives with no single feed additive(s) providing an optimal BCC in all heifers.
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Affiliation(s)
- H M Golder
- Scibus, Camden, New South Wales, 2570, Australia; Dairy Science Group, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia, 2567.
| | - S E Denman
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | - C McSweeney
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD 4067, Australia
| | - P Celi
- Melbourne School of Land and Environment, The University of Melbourne, Parkville, VIC 3052, Australia
| | - I J Lean
- Scibus, Camden, New South Wales, 2570, Australia; Dairy Science Group, School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camden, New South Wales, Australia, 2567
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Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
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Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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Ruiz A, Scicchitano D, Palladino G, Nanetti E, Candela M, Furones D, Sanahuja I, Carbó R, Gisbert E, Andree KB. Microbiome study of a coupled aquaponic system: unveiling the independency of bacterial communities and their beneficial influences among different compartments. Sci Rep 2023; 13:19704. [PMID: 37952071 PMCID: PMC10640640 DOI: 10.1038/s41598-023-47081-0] [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: 08/06/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023] Open
Abstract
To understand the microbiome composition and interplay among bacterial communities in different compartments of a coupled freshwater aquaponics system growing flathead grey mullet (Mugil cephalus) and lettuces (Lactuca sativa), 16S rRNA gene amplicon sequencing of the V3-V4 region was analysed from each compartment (fish intestine, water from the sedimentation tank, bioballs from the biological filter, water and biofilm from the hydroponic unit, and lettuce roots). The bacterial communities of each sample group showed a stable diversity during all the trial, except for the fish gut microbiota, which displayed lower alpha diversity values. Regarding beta diversity, the structure of bacterial communities belonging to the biofilm adhering to the hydroponic tank walls, bioballs, and lettuce roots resembled each other (weighted and unweighted UniFrac distances), while bacteria from water samples also clustered together. However, both of the above-mentioned bacterial communities did not resemble those of fish gut. We found a low or almost null number of shared Amplicon Sequence Variants (ASVs) among sampled groups which indicated that each compartment worked as an independent microbiome. Regarding fish health and food safety, the microbiome profile did not reveal neither fish pathogens nor bacterial species potentially pathogenic for food health, highlighting the safety of this sustainable food production system.
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Affiliation(s)
- Alberto Ruiz
- Aquaculture Program, Institute for Research and Technology in Agroalimentaries (IRTA), Ctra. Poble Nou. Km 5.5, 43540, Ràpita, Spain
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
| | - Enrico Nanetti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Viale Adriatico 1/N, 61032, Fano, Pesaro Urbino, Italy
| | - Dolors Furones
- Aquaculture Program, Institute for Research and Technology in Agroalimentaries (IRTA), Ctra. Poble Nou. Km 5.5, 43540, Ràpita, Spain
| | - Ignasi Sanahuja
- Aquaculture Program, Institute for Research and Technology in Agroalimentaries (IRTA), Ctra. Poble Nou. Km 5.5, 43540, Ràpita, Spain
| | - Ricard Carbó
- Aquaculture Program, Institute for Research and Technology in Agroalimentaries (IRTA), Ctra. Poble Nou. Km 5.5, 43540, Ràpita, Spain
| | - Enric Gisbert
- Aquaculture Program, Institute for Research and Technology in Agroalimentaries (IRTA), Ctra. Poble Nou. Km 5.5, 43540, Ràpita, Spain.
| | - Karl B Andree
- Aquaculture Program, Institute for Research and Technology in Agroalimentaries (IRTA), Ctra. Poble Nou. Km 5.5, 43540, Ràpita, Spain
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Rankins DR, Herrera MJ, Christensen MP, Chen A, Hood NZ, Heras J, German DP. When digestive physiology doesn't match "diet": Lumpenus sagitta (Stichaeidae) is an "omnivore" with a carnivorous gut. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111508. [PMID: 37625480 DOI: 10.1016/j.cbpa.2023.111508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/21/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
What an animal ingests and what it digests can be different. Thus, we examined the nutritional physiology of Lumpenus sagitta, a member of the family Stichaeidae, to better understand whether it could digest algal components like its better studied algivorous relatives. Although L. sagitta ingests considerable algal content, we found little evidence of algal digestion. This fish species has a short gut that doesn't show positive allometry with body size, low amylolytic activity that actually decreases as the fish grow, no ontogenetic changes in digestive enzyme gene expression, elevated N-acetyl-glucosaminidase activity (indicative of chitin breakdown), and an enteric microbial community that is consistent with carnivory and differs from members of its family that consume and digest algae. Hence, we are left concluding that L. sagitta is not capable of digesting the algae it consumes, and instead, are likely targeting epibionts on the algae itself, and other invertebrates consumed with the algae. Our study expands the coverage of dietary and digestive information for the family Stichaeidae, which is becoming a model for fish digestive physiology and genomics, and shows the power of moving beyond gut content analyses to better understand what an animal can actually digest and use metabolically.
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Affiliation(s)
- Daniel R Rankins
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA.
| | - Michelle J Herrera
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Michelle P Christensen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Alisa Chen
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Newton Z Hood
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Joseph Heras
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
| | - Donovan P German
- Department of Ecology and Evolutionary Biology, University of California, Irvine, 321 Steinhaus Hall, Irvine, CA 92697-2525, USA
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Blastopirellula sediminis sp. nov. a new member of Pirellulaceae isolated from the Andaman and Nicobar Islands. Antonie Van Leeuwenhoek 2023; 116:463-475. [PMID: 36867270 DOI: 10.1007/s10482-023-01818-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/22/2023] [Indexed: 03/04/2023]
Abstract
Two cream-coloured strains (JC732T, JC733) of Gram-stain negative, mesophilic, catalase and oxidase positive, aerobic bacteria which divide by budding, form crateriform structures, and cell aggregates were isolated from marine habitats of Andaman and Nicobar Islands, India. Both strains had genome size of 7.1 Mb and G + C content of 58.9%. Both strains showed highest 16S rRNA gene-based similarity with Blastopirellula retiformator Enr8T (98.7%). Strains JC732T and JC733 shared 100% identity of 16S rRNA gene and genome sequences. The coherence of both strains with the genus Blastopirellula was supported by the 16S rRNA gene based and the phylogenomic trees. Further, the chemo-taxonomic characters and the genome relatedness indices [ANI (82.4%), AAI (80.4%) and dDDH (25.2%)] also support the delineation at the species level. Both strains have the capability to degrade chitin and genome analysis shows the ability to fix N2. Based on the phylogenetic, phylogenomic, comparative genomic, morphological, physiological, and biochemical characteristics, strain JC732T is described as a new species of the genus Blastopirellula for which the name Blastopirellula sediminis sp. nov. is proposed, with strain JC733 as an additional strain.
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9
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Suarez C, Hackl T, Wilen BM, Persson F, Hagelia P, Jetten MSM, Dalcin Martins P. Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel. FEMS Microbiol Lett 2023; 370:fnad049. [PMID: 37291701 PMCID: PMC10732223 DOI: 10.1093/femsle/fnad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 06/10/2023] Open
Abstract
The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.
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Affiliation(s)
- Carolina Suarez
- Division of Water Resources Engineering, Faculty of Engineering LTH, Lund University, Lund 221 00, Sweden
| | - Thomas Hackl
- Microbial Ecology Cluster, GELIFES, University of Groningen, Groningen 9747 AG, Netherlands
| | - Britt-Marie Wilen
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Frank Persson
- Division of Water Environment Technology, Department of Architecture and Civil Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Per Hagelia
- Construction Division, The Norwegian Public Roads, Administration, Oslo 0667, Norway
| | - Mike S M Jetten
- Department of Microbiology, RIBES, Radboud University, Nijmegen 6525 AJ, Netherlands
| | - Paula Dalcin Martins
- Microbial Ecology Cluster, GELIFES, University of Groningen, Groningen 9747 AG, Netherlands
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10
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Ravinath R, Das AJ, Usha T, Ramesh N, Middha SK. Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate. Arch Microbiol 2022; 204:481. [PMID: 35834016 DOI: 10.1007/s00203-022-03100-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p < 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.
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Affiliation(s)
- Renuka Ravinath
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
| | - Anupam J Das
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
- Basesolve Informatics Private Limited, Ellisbridge, Ahmedabad, 380006, Gujarat, India
| | - Talambedu Usha
- Department of Biotechnology, Maharani Lakshmi Ammani College for Women, Bangalore, 560012, Karnataka, India
| | - Nijalingappa Ramesh
- School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India
| | - Sushil Kumar Middha
- Department of Biotechnology, Maharani Lakshmi Ammani College for Women, Bangalore, 560012, Karnataka, India.
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11
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Chen JS, Tsai HC, Hsu YL, Nagarajan V, Su HY, Hussain B, Hsu BM. Comprehensive assessment of bacterial communities and their functional profiles in the Huang Gang Creek in the Tatun Volcano Group basin, Taiwan using 16S rRNA amplicon sequencing. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 234:113375. [PMID: 35278991 DOI: 10.1016/j.ecoenv.2022.113375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
The microbial characteristics of water bodies located in the outflow of hot springs may affect the water quality parameters of the associated river ecosystem. Using 16S rRNA amplicon sequencing, we investigated the bacterial diversity and functional profiles of the Huang Gang (HG) Creek, located in the trace metal-rich, acid-sulfate thermal springs zone of the Tatun Volcano Group (TVG). Biofilms and water samples were collected from the upstream, midstream, and geothermal valleys and downstream of the creek. The results showed that the biofilm and water samples had distinct bacterial diversity and abundance profiles. Acidophilic sulfur-oxidizing bacteria were found to be more abundant in water samples, whereas aquatic photosynthetic bacterial communities were dominant in biofilms. The water samples were contaminated with Legionella and Chlamydiae, which could contaminate the nearby river and cause clinical infections in humans. The upstream samples were highly unique and displayed higher diversity than the other sites. Moderate thermo-acidophiles were dominant in the upstream and midstream regions, whereas the geothermal valley and downstream samples were abundant in thermo-acidophiles. In addition, functional profiling revealed higher expression of sulfur, arsenic, and iron-related functions in water and lead-related functions in the biofilms of the creek. As described in previous studies, the hydrochemical properties of the HG Creek were influenced by the TVG hot springs. Our findings indicated that the hydrochemical properties of the HG Creek were highly correlated with the bacterial diversity and functional potential of running water as compared to biofilms.
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Affiliation(s)
- Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung, Taiwan
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien, Taiwan; Department of Psychiatry, Tzu-Chi General Hospital, Hualien, Taiwan
| | - Yu-Ling Hsu
- Department of Nuclear Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
| | - Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Hung-Yuan Su
- Department of Emergency Medicine, E-Da Hospital and I-Shou University, Kaohsiung, Taiwan; School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung, Taiwan
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan; Department of Biomedical Sciences, National Chung Cheng University, Chiayi, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi, Taiwan.
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12
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Nagarajan V, Tsai HC, Chen JS, Hussain B, Fan CW, Asif A, Hsu BM. The Evaluation of Bacterial Abundance and Functional Potentials in the Three Major Watersheds, Located in the Hot Spring Zone of the Tatun Volcano Group Basin, Taiwan. Microorganisms 2022; 10:microorganisms10030500. [PMID: 35336075 PMCID: PMC8949176 DOI: 10.3390/microorganisms10030500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/10/2022] Open
Abstract
The Tatun Volcanic Group (TVG), located in northern Taiwan, is characterized by acidic hot springs where the outflow of the hot springs may affect the properties of the associated lotic water bodies. We investigated the bacterial diversity and functional profiles of the Peihuang (PHC), HuangGang (HGC), and Nanhuang Creeks (NHC) located in the TVG basin using 16S rRNA gene sequencing coupled with statistical analyses. Water samples were collected from various streams of the creeks for two months of the year. The NHC showed the highest diversity, richness, and a unique number of phyla, which was followed by the HGC. A reduced number of phyla and a lower diversity was noticed in the PHC. The NHC was found to be abundant in the genera Armatimonas, Prosthecobacter, Pirellula, and Bdellovibrio, whereas the HGC was rich in Thiomonas, Acidiphilium, Prevotella, Acidocella, Acidithiobacillus, and Metallibacterium. The PHC was abundant in Thiomonsa, Legionella, Acidocella, and Sulfuriferula. The samples did not show any strong seasonal variations with the bacterial diversity and abundance; however, the relative abundance of each sampling site varied within the sampling months. The iron transport protein- and the sulfur metabolism-related pathways were predicted to be the key functions in all the creeks, whereas the heavy metal-related functions, such as the cobalt/nickel transport protein and the cobalt–zinc–cadmium efflux system were found to be abundant in the HGC and PHC, respectively. The abundance of Bdellovibrio in the NHC, Diplorickettsia in the HGC, and Legionella in the PHC samples indicated a higher anthropogenic impact over the creek water quality. This study provides the data to understand the distinct bacterial community structure, as well as the functional potentials of the three major watersheds, and helps the knowledge of the impact of the physicochemical properties of the TVG hot springs upon the watersheds.
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Affiliation(s)
- Viji Nagarajan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Hsin-Chi Tsai
- Department of Psychiatry, School of Medicine, Tzu Chi University, Hualien 970, Taiwan;
- Department of Psychiatry, Tzu-Chi General Hospital, Hualien 970, Taiwan
| | - Jung-Sheng Chen
- Department of Medical Research, E-Da Hospital, Kaohsiung 824, Taiwan;
| | - Bashir Hussain
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 621, Taiwan
| | - Cheng-Wei Fan
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
| | - Aslia Asif
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Doctoral Program in Science, Technology, Environment and Mathematics (STEM), National Chung Cheng University, Chiayi 621, Taiwan
| | - Bing-Mu Hsu
- Department of Earth and Environmental Sciences, National Chung Cheng University, Chiayi 621, Taiwan; (V.N.); (B.H.); (C.-W.F.); (A.A.)
- Correspondence: ; Tel.: +886-52-720-411 (ext. 66218)
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13
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Vitorino IR, Lage OM. The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes. Antonie van Leeuwenhoek 2022; 115:169-201. [PMID: 35037113 DOI: 10.1007/s10482-021-01699-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 01/21/2023]
Abstract
The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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14
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Vitorino I, Santos JDN, Godinho O, Vicente F, Vasconcelos V, Lage OM. Novel and Conventional Isolation Techniques to Obtain Planctomycetes from Marine Environments. Microorganisms 2021; 9:2078. [PMID: 34683399 PMCID: PMC8541047 DOI: 10.3390/microorganisms9102078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Bacteria from the distinctive Planctomycetes phylum are well spread around the globe; they are capable of colonizing many habitats, including marine, freshwater, terrestrial, and even extreme habitats such as hydrothermal vents and hot springs. They can also be found living in association with other organisms, such as macroalgae, plants, and invertebrates. While ubiquitous, only a small fraction of the known diversity includes axenic cultures. In this study, we aimed to apply conventional techniques to isolate, in diverse culture media, planctomycetes from two beaches of the Portuguese north-coast by using sediments, red, green, and brown macroalgae, the shell of the mussel Mytilus edulis, an anemone belonging to the species Actinia equina, and seawater as sources. With this approach, thirty-seven isolates closely related to seven species from the families Planctomycetaceae and Pirellulaceae (class Planctomycetia) were brought into pure culture. Moreover, we applied an iChip inspired in-situ culturing technique to successfully retrieve planctomycetes from marine sediments, which resulted in the isolation of three additional strains, two affiliated to the species Novipirellula caenicola and one to a putative novel Rubinisphaera. This work enlarges the number of isolated planctomycetal strains and shows the adequacy of a novel methodology for planctomycetes isolation.
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Affiliation(s)
- Inês Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (J.D.N.S.); (O.G.); (V.V.); (O.M.L.)
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, 4450-208 Matosinhos, Portugal
| | - José Diogo Neves Santos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (J.D.N.S.); (O.G.); (V.V.); (O.M.L.)
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, 4450-208 Matosinhos, Portugal
| | - Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (J.D.N.S.); (O.G.); (V.V.); (O.M.L.)
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, 4450-208 Matosinhos, Portugal
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, 18016 Granada, Spain;
| | - Vítor Vasconcelos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (J.D.N.S.); (O.G.); (V.V.); (O.M.L.)
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, 4450-208 Matosinhos, Portugal
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal; (J.D.N.S.); (O.G.); (V.V.); (O.M.L.)
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, 4450-208 Matosinhos, Portugal
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15
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Bali R, Pineault J, Chagnon PL, Hijri M. Fresh Compost Tea Application Does Not Change Rhizosphere Soil Bacterial Community Structure, and Has No Effects on Soybean Growth or Yield. PLANTS (BASEL, SWITZERLAND) 2021; 10:1638. [PMID: 34451683 PMCID: PMC8399032 DOI: 10.3390/plants10081638] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023]
Abstract
Soil bacteria drive key ecosystem functions, including nutrient mobilization, soil aggregation and crop bioprotection against pathogens. Bacterial diversity is thus considered a key component of soil health. Conventional agriculture reduces bacterial diversity in many ways. Compost tea has been suggested as a bioinoculant that may restore bacterial community diversity and promote crop performance under conventional agriculture. Here, we conducted a field experiment to test this hypothesis in a soybean-maize rotation. Compost tea application had no influence on bacterial diversity or community structure. Plant growth and yield were also unresponsive to compost tea application. Combined, our results suggest that our compost tea bacteria did not thrive in the soil, and that the positive impacts of compost tea applications reported elsewhere may be caused by different microbial groups (e.g., fungi, protists and nematodes) or by abiotic effects on soil (e.g., contribution of nutrients and dissolved organic matter). Further investigations are needed to elucidate the mechanisms through which compost tea influences crop performance.
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Affiliation(s)
- Rana Bali
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada;
| | - Jonathan Pineault
- Écomestible Inc., 470 Rue Constable, McMasterVille, QC J3G 1N6, Canada;
| | - Pierre-Luc Chagnon
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada;
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, QC H1X 2B2, Canada;
- African Genome Center, Mohammed VI Polytechnic University (UM6P), Lot 660, Hay Moulay Rachid, Ben Guerir 43150, Morocco
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16
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Bergsveinson J, Lawrence J, Schebel A, Wasserscheid J, Roy J, Conly FM, Sanschagrin S, Korber DR, Tremblay J, Greer CW, Droppo IG. Impact of sample collection on prokaryotic and eukaryotic diversity of niche environments of the oil-sand mining impacted Athabasca River. Can J Microbiol 2021; 67:813-826. [PMID: 34171204 DOI: 10.1139/cjm-2021-0058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microbial communities are an important aspect of overall riverine ecology; however, appreciation of the effects of anthropogenic activities on unique riverine microbial niches, and how the collection of these samples affects the observed diversity and community profile is lacking. We analyzed prokaryotic and eukaryotic communities from surface water, biofilm, suspended load niches along a gradient of oil sands-related contamination in the Athabasca River (Alberta, Canada), with suspended load or particle-associated communities collected either via Kenney Sampler or centrifugation manifold. At the level of phyla, different niche communities were highly similar to one another and across locations. However, there were significant differences in the abundance of specific genera amongst different niches and across sampling locations. A generalized linear model revealed that use of the Kenney Sampler resulted in more diverse bacterial and eukaryotic suspended load community than centrifugal collection, though "suspended load" communities collected by any means remained stably diverse across locations. Though there was influence of water quality parameters on community composition, all sampled sites support diverse bacterial and eukaryotic communities regardless of the degree of contamination, highlighting the need to look beyond ecological diversity as means of assessing ecological perturbations, and consider collecting samples from multiple niche environments.
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Affiliation(s)
- Jordyn Bergsveinson
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - John Lawrence
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - Alixandra Schebel
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - Jessica Wasserscheid
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Julie Roy
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - F Malcom Conly
- Environment and Climate Change Canada, Watershed Hydrology and Ecology Research Division, Saskatoon, Saskatchewan, Canada;
| | - Sylvie Sanschagrin
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Darren R Korber
- University of Saskatchewan, Department of Food and Bioproduct Science, Saskatoon, Saskatchewan, Canada;
| | - Julien Tremblay
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Charles W Greer
- National Research Council, Energy, Mining and Environment Research Centre, Montreal, Quebec, Canada;
| | - Ian G Droppo
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, Ontario, Canada;
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17
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Godinho O, Botelho R, Albuquerque L, Wiegand S, Kallscheuer N, da Costa MS, Lobo-da-Cunha A, Jogler C, Lage OM. Bremerella alba sp. nov., a novel planctomycete isolated from the surface of the macroalga Fucus spiralis. Syst Appl Microbiol 2021; 44:126189. [PMID: 33852992 DOI: 10.1016/j.syapm.2021.126189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/19/2021] [Accepted: 02/22/2021] [Indexed: 11/25/2022]
Abstract
A bacterial strain, designated FF15T, was isolated from the thallus surface of the macroalga Fucus spiralis sampled on a rocky beach in Porto, Portugal. Based on the 16S rRNA gene sequence, strain FF15T was affiliated to the phylum Planctomycetes. This strain forms white colonies on modified M13 medium and the cells are pear-shaped, can form rosettes, divide by polar budding and are motile. The novel isolate is mesophilic and neutrophilic with an optimum growth temperature of about 30 °C and an optimum pH for growth between 6.5 and 7.5. It showed growth over a broad range of salinities (0-9% NaCl - optimum at 1.5%). No additional vitamins are required for growth. It is cytochrome c oxidase and catalase positive. The major respiratory quinone was menaquinone 6 (MK-6). Genome sequencing revealed a genome size of 6.37 Mbp and a DNA G + C content of 54.2%. Analysis of phylogenetic markers, including similarities of the 16S rRNA gene sequence, rpoB gene sequence, as well as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI), suggest the affiliation of strain FF15T to "Bremerella", a recently described genus in the family Pirellulaceae. Based on the genotypic, phylogenetic, chemotaxonomic, physiological and biochemical characterization, we described a new species represented by strain FF15T (=CECT 8078T = LMG 31936T), for which we propose the name Bremerella alba snov.
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Affiliation(s)
- Ofélia Godinho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal
| | - Raquel Botelho
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Luciana Albuquerque
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-504 Coimbra, Portugal
| | - Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands; Institute for Biological Surfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Milton S da Costa
- Centro de Neurociências e Biologia Celular, Universidade de Coimbra, 3004-504 Coimbra, Portugal; Departamento de Ciências da Vida, Universidade de Coimbra, 3000-456 Coimbra, Portugal
| | - Alexandre Lobo-da-Cunha
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands; Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal.
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18
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Kalinowska A, Jankowska K, Fudala-Ksiazek S, Pierpaoli M, Luczkiewicz A. The microbial community, its biochemical potential, and the antimicrobial resistance of Enterococcus spp. in Arctic lakes under natural and anthropogenic impact (West Spitsbergen). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 763:142998. [PMID: 33213908 DOI: 10.1016/j.scitotenv.2020.142998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
The sustainable management of small human communities in the Arctic is challenging. In this study, both a water supply system (Lake 1) under the natural impact of a bird-nesting area, and a wastewater receiver (Lake 2) were analysed in the vicinity of the Polish Polar Station on West Spitsbergen. Microbial community composition, abundance and activity were assessed in samples of the treated wastewater, lake water and sediments using next-generation sequencing and direct microscope counts. Special attention was given to the faecal indicator, Enterococcus spp., whose occurrence and antimicrobial resistance were tested in water and wastewater samples. The results indicate that Lake 1, at a tundra stream discharge (L-TS) and a water supply point (L-WS) were dominated by three phyla: Proteobacteria (57-58%) Bacteroidetes (27-29%) and Actinobacteria (9-10%), showing similar microbial composition up to the genus level. This suggests that nutrient-rich runoff from the bird colony was retained by surrounding tundra vegetation and reached Lake 1 at L-TS to a limited extent. Lake 2, being the wastewater recipient (WW-R), mirrors to some extent the core phyla of treated wastewater (WW-E), but in different shares. This suggests the possible washout of wastewater-related bacteria with activated sludge flocs, which was also supported by the microscopic observations. Compared to Lake 1, in WW-R an increase in all tested parameters was noted: total prokaryotic cell number, average cell volume, prokaryotic biomass and live cell percentage. The presence of Enterococcus spp. antibiotic resistance patterns highlight the importance of human associated microbiome and resistome dissemination via wastewater discharge. Moreover, it can be expected that temperature-related biochemical processes (e.g. nutrient cycling) may be accelerated by the ongoing climate change. Thus, proper wastewater treatment requires locally adapted solutions in increasingly visited and inhabited polar regions. Additionally, microbial community discharged to the environment with the treated wastewater, requires critical attention.
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Affiliation(s)
- Agnieszka Kalinowska
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
| | - Katarzyna Jankowska
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Sylwia Fudala-Ksiazek
- Department of Sanitary Engineering, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Mattia Pierpaoli
- Department of Metrology and Optoelectronics, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland
| | - Aneta Luczkiewicz
- Department of Water and Wastewater Technology, Faculty of Civil and Environmental Engineering, Gdansk University of Technology, 11/12 Narutowicza St., Gdansk 80-233, Poland.
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10207367] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas.
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Diet type influences the gut microbiome and nutrient assimilation of Genetically Improved Farmed Tilapia (Oreochromis niloticus). PLoS One 2020; 15:e0237775. [PMID: 32813739 PMCID: PMC7446784 DOI: 10.1371/journal.pone.0237775] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
Nile tilapia, Oreochromis niloticus is the third most commonly farmed finfish species in the world, accounting for nearly 5% of global aquaculture production. In the past few decades much of the success of this species has been attributed to the development and distribution of Genetically Improved Farmed Tilapia (GIFT). Despite the increasing availability of GIFT, the productivity of small-scale farming remains highly variable, particularly in developing nations. Commercial fish-feed pellets can increase fish farm productivity; however, many small-scale farmers rely on other means of feeding fish due to the high cost and limited availability of commercial fish feed pellets. Therefore, understanding how locally-sourced feeds affect the production of GIFT is an important step towards improving feeding practices, particularly for farmers with low financial capital. This study used stable isotope analysis (SIA) and 16S rRNA gene sequencing to compare the effects of a locally-sourced vegetable-based diet and commercial pellet-based diets on the relative condition, nutrient assimilation patterns and gastrointestinal microbiota of GIFT. GIFT fed a locally-sourced diet were smaller, and in a significantly poorer condition than those fed with commercial fish feeds. SIA showed no differences in dietary carbon between the two diets; however, δ13C, poor fish condition and the abundance of specific bacterial taxa (of such as Fusobacteria) were correlated. SIA revealed that GIFT fed locally-sourced diets that predominantly consisted of vegetables were significantly enriched in δ15N despite a perceived lack of dietary protein. This enrichment suggests that GIFT fed a locally-sourced diet may be supplementing their diet via cannibalism, a behaviour representative of poor farming practice. Overall this study highlights the need to increase the availability of suitable GIFT feeds in developing nations. The development a low-cost feed alternative could improve the success of small-scale GIFT farmers in PNG, increasing both food and income security within the region.
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Planctomycetes as a Vital Constituent of the Microbial Communities Inhabiting Different Layers of the Meromictic Lake Sælenvannet (Norway). Microorganisms 2020; 8:microorganisms8081150. [PMID: 32751313 PMCID: PMC7464441 DOI: 10.3390/microorganisms8081150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/17/2020] [Accepted: 07/26/2020] [Indexed: 12/20/2022] Open
Abstract
Meromictic lakes are permanently stratified lakes that display steep gradients in salinity, oxygen and sulphur compounds tightly linked to bacterial community structure and diversity. Lake Sælenvannet is a meromictic lake located south of Bergen, Norway. The 26 m deep lake is connected to the open sea and permanently stratified into two layers separated by a chemocline. The upper water layer is brackish with major input from water runoff from the surroundings. The bottom layer consists of old saline water with low or no oxygen concentrations. Bacteria from phylum Planctomycetes are reported to be ubiquitous in lake environments. They are involved in the degradation of complex carbon sources in aquatic environments and are also linked to anaerobic processes such as fermentation and sulphur reduction. To study Planctomycete distribution along a chemical gradient, we sampled the water column throughout Lake Sælenvannet in 2012 and profiled the microbial community using 16S rRNA amplicon sequencing (metabarcoding) with 454 pyrosequencing. Planctomycetes related 16S rRNA gene sequences were found to be present both in the oxic and anoxic parts of the lake and showed an uneven distribution throughout the water column, with the highest relative abundance of 10% found in the saline anoxic layer at 15 m depth. In a follow-up study in 2014, samples from eight different depths were collected for enrichment and isolation of novel Planctomycetes. This study resulted in successful isolation in pure culture of 10 isolates affiliated to four different genera from the family Planctomycetaceae. One strain closely related to Blastopirellula cremea was isolated from 9 m depth, and two novel strains affiliated to the genera Stieleria and Gimesia were isolated at 7 and 9 m depths, respectively. Furthermore, seven isolates with identical 16S rRNA gene sequences were retrieved from seven different depths which varied greatly in salinity and chemical composition. These isolates likely represent a new species affiliated to Rubinisphaera. The adaptation of this novel Planctomycete to water depths spanning the entire chemical gradient could indicate a high phenotypic plasticity and/or a very efficient survival strategy. Overall, our results show the presence of a diverse group of Planctomycetes in Lake Sælenvannet, with a strong potential for novel adaptations to chemical stress factors.
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van Vliet DM, Lin Y, Bale NJ, Koenen M, Villanueva L, Stams AJM, Sánchez-Andrea I. Pontiella desulfatans gen. nov., sp. nov., and Pontiella sulfatireligans sp. nov., Two Marine Anaerobes of the Pontiellaceae fam. nov. Producing Sulfated Glycosaminoglycan-like Exopolymers. Microorganisms 2020; 8:microorganisms8060920. [PMID: 32570748 PMCID: PMC7356697 DOI: 10.3390/microorganisms8060920] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/11/2020] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
Recently, we isolated two marine strains, F1T and F21T, which together with Kiritimatiella glycovorans L21-Fru-ABT are the only pure cultures of the class Kiritimatiellae within the phylum Verrucomicrobiota. Here, we present an in-depth genome-guided characterization of both isolates with emphasis on their exopolysaccharide synthesis. The strains only grew fermentatively on simple carbohydrates and sulfated polysaccharides. Strains F1T, F21T and K. glycovorans reduced elemental sulfur, ferric citrate and anthraquinone-2,6-disulfonate during anaerobic growth on sugars. Both strains produced exopolysaccharides during stationary phase, probably with intracellularly stored glycogen as energy and carbon source. Exopolysaccharides included N-sulfated polysaccharides probably containing hexosamines and thus resembling glycosaminoglycans. This implies that the isolates can both degrade and produce sulfated polysaccharides. Both strains encoded an unprecedently high number of glycoside hydrolase genes (422 and 388, respectively), including prevalent alpha-L-fucosidase genes, which may be necessary for degrading complex sulfated polysaccharides such as fucoidan. Strain F21T encoded three putative glycosaminoglycan sulfotransferases and a putative sulfate glycosaminoglycan biosynthesis gene cluster. Based on phylogenetic and chemotaxonomic analyses, we propose the taxa Pontiella desulfatans F1T gen. nov., sp. nov. and Pontiella sulfatireligans F21T sp. nov. as representatives of the Pontiellaceae fam. nov. within the class Kiritimatiellae.
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Affiliation(s)
- Daan M. van Vliet
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands;
| | - Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ) and Utrecht University, Landsdiep 4, 1797 SZ ’t Horntje (Texel), The Netherlands; (N.J.B.); (M.K.); (L.V.)
| | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
- Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Irene Sánchez-Andrea
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands; (D.M.v.V.); (A.J.M.S.)
- Correspondence: ; Tel.: +31-317-483486
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Chen YG, Zhang ZH, Luo HW, Li Z, Zhang LJ, Huang H. Distinct Characteristics of Bacterial Community in the Soil of Nanshazhou Island, South China Sea. Curr Microbiol 2020; 77:1292-1300. [PMID: 32140834 DOI: 10.1007/s00284-020-01933-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/22/2020] [Indexed: 11/29/2022]
Abstract
Characterizing soil bacterial community is important to understand microbial distribution affected by environmental factors. Here, we investigated the bacterial communities distributed from different location on Nanshazhou island, South China Sea. We collected and compared soil bacterial communities from central island, intertidal island, and inshore island. Results showed no difference in the bacterial richness and diversity for the soils from the three different locations. However, weighted and unweighted UniFrac distances analysis revealed that the three soil samples were clearly separated from each other. Five bacterial phyla, including Proteobacteria, Bacteroidetes, Verrucomicrobia, Spirochaetes and Tenericutes were more abundant in the inshore island sample; while Deinococcus-Thermus was more abundant in the intertidal island sample; and the central island sample had more abundant Gemmatimonadetes and Planctomycetes. Bacterial structure showed significantly positive relationships with organic matter content, but it was significantly negatively correlated with sodium content. Furthermore, a network analysis based on Spearman correlation coefficients showed that there were similar numbers of positive and negative correlations within the bacterial community of Nanshazhou island. Our results revealed that the soil bacterial communities in the three sampling sites were easily affected by environmental fluctuations.
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Affiliation(s)
- Yong-Gan Chen
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, 572022, China.,Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Zhen-Hua Zhang
- Key Laboratory of Biosafety, Nanjing Institute of Environmental Sciences, Nanjing, 210042, China
| | - Hong-Wei Luo
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Zhen Li
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Lai-Jun Zhang
- Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Hai Huang
- Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources (Hainan Tropical Ocean University), Ministry of Education, Sanya, 572022, China. .,Hainan Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources, Hainan Tropical Ocean University, Sanya, 572022, China.
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25
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Schwob G, Cabrol L, Poulin E, Orlando J. Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii. Front Microbiol 2020; 11:308. [PMID: 32184772 PMCID: PMC7058685 DOI: 10.3389/fmicb.2020.00308] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/11/2020] [Indexed: 12/25/2022] Open
Abstract
Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia, were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed.
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Affiliation(s)
- Guillaume Schwob
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Léa Cabrol
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France
| | - Elie Poulin
- Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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26
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Pradel N, Fardeau ML, Tindall BJ, Spring S. Anaerohalosphaera lusitana gen. nov., sp. nov., and Limihaloglobus sulfuriphilus gen. nov., sp. nov., isolated from solar saltern sediments, and proposal of Anaerohalosphaeraceae fam. nov. within the order Sedimentisphaerales. Int J Syst Evol Microbiol 2020; 70:1321-1330. [DOI: 10.1099/ijsem.0.003919] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Nathalie Pradel
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Marie-Laure Fardeau
- Aix-Marseille Université, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Brian J. Tindall
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Stefan Spring
- Department Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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27
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Taipale SJ, Peltomaa E, Kukkonen JVK, Kainz MJ, Kautonen P, Tiirola M. Tracing the fate of microplastic carbon in the aquatic food web by compound-specific isotope analysis. Sci Rep 2019; 9:19894. [PMID: 31882692 PMCID: PMC6934716 DOI: 10.1038/s41598-019-55990-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 12/04/2019] [Indexed: 02/05/2023] Open
Abstract
Increasing abundance of microplastics (MP) in marine and freshwaters is currently one of the greatest environmental concerns. Since plastics are fairly resistant to chemical decomposition, breakdown and reutilization of MP carbon complexes requires microbial activity. Currently, only a few microbial isolates have been shown to degrade MPs, and direct measurements of the fate of the MP carbon are still lacking. We used compound-specific isotope analysis to track the fate of fully labelled 13C-polyethylene (PE) MP carbon across the aquatic microbial-animal interface. Isotopic values of respired CO2 and membrane lipids showed that MP carbon was partly mineralized and partly used for cell growth. Microbial mineralization and assimilation of PE-MP carbon was most active when inoculated microbes were obtained from highly humic waters, which contain recalcitrant substrate sources. Mixotrophic algae (Cryptomonas sp.) and herbivorous zooplankton (Daphnia magna) used microbial mediated PE-MP carbon in their cell membrane fatty acids. Moreover, heteronanoflagellates and mixotrophic algae sequestered MP carbon for synthesizing essential ω-6 and ω-3 polyunsaturated fatty acids. Thus, this study demonstrates that aquatic micro-organisms can produce, biochemically upgrade, and trophically transfer nutritionally important biomolecules from PE-MP.
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Affiliation(s)
- S J Taipale
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, P.O. Box 35 (YA), 40014, Jyväskylä, Finland.
| | - E Peltomaa
- Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research programme, University of Helsinki, Niemenkatu 73, Lahti, FI-15140, Finland.,Institute of Atmospheric and Earth System Research (INAR)/Forest Sciences, University of Helsinki, Helsinki, Finland
| | - J V K Kukkonen
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland, P.O. Box 1627, FI-70211, Kuopio, Finland
| | - M J Kainz
- WasserCluster - Biological Station Lunz, Danube University Krems, Dr. Carl Kupelwieser Promenade 5, A-3293, Lunz am See, Austria
| | - P Kautonen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, P.O. Box 35 (YA), 40014, Jyväskylä, Finland
| | - M Tiirola
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, P.O. Box 35 (YA), 40014, Jyväskylä, Finland
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Hamdan HZ, Salam DA, Saikaly PE. Characterization of the microbial community diversity and composition of the coast of Lebanon: Potential for petroleum oil biodegradation. MARINE POLLUTION BULLETIN 2019; 149:110508. [PMID: 31425842 DOI: 10.1016/j.marpolbul.2019.110508] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/22/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
In this study, the shoreline of Lebanon, which extends over 225 km along the eastern side of the Mediterranean Sea, was characterized for its sediment microbial community diversity and composition using 16S rRNA gene sequencing with Illumina MiSeq technology. Non-metric multidimensional scaling (NMDS) analysis showed no clear grouping among nearby sampled sites along the shoreline. Insignificant diversion between the wet and dry season microbial communities was observed along the coast at each sampling site. A high variation at the genus level was observed, with several novel genera identified at high relative abundance in certain locations, such as JTB255 marine benthic groups OTU_4 (5.4%) and OTU_60 (3.2%), and BD7-8 marine group OTU_5 (2.9%).
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Affiliation(s)
- Hamdan Z Hamdan
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon
| | - Darine A Salam
- Department of Civil and Environmental Engineering, Maroun Semaan Faculty of Engineering and Architecture, American University of Beirut, Beirut, Lebanon.
| | - Pascal E Saikaly
- Division of Biological and Environmental Sciences and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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29
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Dang Q, Tan W, Zhao X, Li D, Li Y, Yang T, Li R, Zu G, Xi B. Linking the response of soil microbial community structure in soils to long-term wastewater irrigation and soil depth. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 688:26-36. [PMID: 31233911 DOI: 10.1016/j.scitotenv.2019.06.138] [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: 04/09/2019] [Revised: 06/04/2019] [Accepted: 06/08/2019] [Indexed: 05/08/2023]
Abstract
Irrigation with treated wastewater (TWW) has become a prevailing agricultural practice due to the scarcity of fresh water resources, which may have a significant impact on the microbial communities that are critical to many biogeochemical processes in soils. However, it is unclear whether there are links between soil microbial responses to long-term irrigation with different sources of wastewater and soil depth. Here we assess the influence of treated domestic (DTWW), leather industry (LTWW) and pharmaceutical (PTWW) wastewater on microbial communities in vertical soil profiles using high-throughput sequencing based on 16S rRNA and internal transcribed spacer (ITS) gene profiling. We found that microbial α-diversity in the vertical profiles of soils was significantly influenced by TWW irrigation. Bacteria and fungi in different soil depths showed distinct responses to TWW; irrigation with TWW markedly increased abundance of bacterial OTUs and inhibited abundance of fungal OTUs. β-diversity analysis showed that the effect of TWW irrigation on microbial communities was greater than the effect of soil depth, and microbes in subsurface soil were more sensitive to different sources of irrigation water. We also found that, based on β-diversity analysis, irrigation with treated industrial wastewater, including LTWW and PTWW, had a greater impact on microbial community structures than DTWW. TWW irrigation significantly affected the composition of indigenous soil microbial communities at different depths and might introduce exogenous microbes into the soil environment. Our work explicitly demonstrates the vertical responses of bacterial and fungal communities in soils to irrigation with TWW from different sources, which can provides insights into the microbial-dominated geochemical processes from the perspective of the entire soil profile under the context of wastewater irrigation.
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Affiliation(s)
- Qiuling Dang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China; State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Wenbing Tan
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Xinyu Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Dan Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Yanping Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Tianxue Yang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Renfei Li
- State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Guofeng Zu
- Groundwater Pollution Control and Remediation Industry Alliance, Beijing 100012, China
| | - Beidou Xi
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; State Environmental Protection Key Laboratory of Simulation and Control of Groundwater Pollution, Chinese Research Academy of Environmental Sciences, Beijing 100012, China.
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Aepfler RF, Bühring SI, Elvert M. Substrate characteristic bacterial fatty acid production based on amino acid assimilation and transformation in marine sediments. FEMS Microbiol Ecol 2019; 95:5555570. [PMID: 31504469 DOI: 10.1093/femsec/fiz131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/23/2019] [Indexed: 01/25/2023] Open
Abstract
Polar lipid-derived fatty acids (PLFAs) and their stable carbon isotopes are frequently combined to characterize microbial populations involved in the degradation of organic matter, offering a link to biogeochemical processes and carbon sources used. However, PLFA patterns derive from multiple species and may be influenced by substrate types. Here, we investigated such dependencies by monitoring the transformation of position-specifically 13C-labeled amino acids (AAs) in coastal marine sediments dominated by heterotrophic bacteria. Alanine was assimilated into straight-chain FAs, while valine and leucine incorporation led to the characteristic production of even- and odd-numbered iso-series FAs. This suggests that identical microbial communities adjust lipid biosynthesis according to substrate availability. Transformation into precursor molecules for FA biosynthesis was manifested in increased 13C recoveries of the corresponding volatiles acetate, isobutyrate and isovalerate of up to 39.1%, much higher than for PLFAs (<0.9%). A significant fraction of 13C was found in dissolved inorganic carbon (up to 37.9%), while less was recovered in total organic carbon (up to 17.3%). We observed a clear discrimination against the carboxyl C, whereby C2 and C3 positions were preferentially incorporated into PLFAs. Therefore, position-specific labeling is an appropriate tool for reconstructing the metabolic fate of protein-derived AAs in marine environments.
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Affiliation(s)
- Rebecca F Aepfler
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, 28359 Bremen, Germany.,Hydrothermal Geomicrobiology Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 13, 28359 Bremen, Germany
| | - Solveig I Bühring
- Hydrothermal Geomicrobiology Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 13, 28359 Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Strasse 8, 28359 Bremen, Germany
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Dyksma S, Gallert C. Candidatus Syntrophosphaera thermopropionivorans: a novel player in syntrophic propionate oxidation during anaerobic digestion. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:558-570. [PMID: 30985964 DOI: 10.1111/1758-2229.12759] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Propionate is an important intermediate in the anaerobic mineralization of organic matter. In methanogenic environments, its degradation relies on syntrophic associations between syntrophic propionate-oxidizing bacteria (SPOB) and Archaea. However, only 10 isolated species have been identified as SPOB so far. We report syntrophic propionate oxidation in thermophilic enrichments of Candidatus Syntrophosphaera thermopropionivorans, a novel representative of the candidate phylum Cloacimonetes. In enrichment culture, methane was produced from propionate, while Ca. S. thermopropionivorans contributed 63% to total bacterial cells. The draft genome of Ca. S. thermopropionivorans encodes genes for propionate oxidation via methymalonyl-CoA. Phylogenetically, Ca. S. thermopropionivorans affiliates with the uncultured Cloacimonadaceae W5 and is more distantly related (86.4% 16S rRNA gene identity) to Ca. Cloacimonas acidaminovorans. Although Ca. S. thermopropionivorans was enriched from a thermophilic biogas reactor, Ca. Syntrophosphaera was in particular associated with mesophilic anaerobic digestion systems. 16S rRNA gene amplicon sequencng and a novel genus-specific quantitative PCR assay consistently identified Ca. Syntrophosphaera/Cloacimonadaceae W5 in 9 of 12 tested full-scale biogas reactors thereby outnumbering other SPOB such as Pelotomaculum, Smithella and Syntrophobacter. Taken together the ubiquity and abundance of Ca. Syntrophosphaera, those SPOB might be key players for syntrophic propionate metabolism that have been overlooked before.
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Affiliation(s)
- Stefan Dyksma
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
| | - Claudia Gallert
- Faculty of Technology, Microbiology - Biotechnology, University of Applied Sciences Emden/Leer, Emden, Germany
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32
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Zhuang M, Sanganyado E, Li P, Liu W. Distribution of microbial communities in metal-contaminated nearshore sediment from Eastern Guangdong, China. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 250:482-492. [PMID: 31026695 DOI: 10.1016/j.envpol.2019.04.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/22/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Nearshore environments are a critical transitional zone that connects the marine and terrestrial/freshwater ecosystems. The release of anthropogenic chemicals into nearshore ecosystems pose a human and environmental health risk. We investigated the microbial diversity, abundance and function in metal-contaminated sediments collected from the Rongjiang, Hanjiang and Lianjiang River estuaries and adjacent coastal areas using high throughput sequencing. The concentration of nutrients (NO3-N, NO2-N, NH4-N, PO4-P) and metal (Cu, Zn, Cd, Pb, As, Hg) contaminants were higher at the mouth of the rivers compared to the coastal lines, and this was confirmed using cluster analysis. Estimates obtained using geoaccumulation index showed that about 38.9% of the sites were contaminated with Pb and the pollution load index showed that sediment from the mouth of Hanjiang River Estuary was moderately polluted with metals. In the nearshore sediment samples collected, Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria were the dominant phylum with relative abundances of 46.6%, 8.05%, 6.47%, 5.26%, and 4.59%, respectively. There was no significant correlation between environmental variables and microbial abundance and diversity except for total organic carbon (TOC) (diversity; r = 0.569, p < 0.05) and Cr (diversity; r = 0.581, p < 0.05). At phyla level, Nitrospirae had a significant negative correlation with all metals except Cr, while OD1 had a significant positive correlation with all the metals. Overall, changes in nearshore sediment microbial communities by environmental factors were observed, and these may affect biogeochemical cycling.
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Affiliation(s)
- Mei Zhuang
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Edmond Sanganyado
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Ping Li
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong Province, China.
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Effect of Dietary Carbohydrate-to-Protein Ratio on Gut Microbiota in Atlantic Salmon ( Salmo salar). Animals (Basel) 2019; 9:ani9030089. [PMID: 30862122 PMCID: PMC6466077 DOI: 10.3390/ani9030089] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Carbohydrates, in the form of energy reserve polysaccharides, are major food components that supply low-cost energy in farm animal feed formulation. Most of these compounds are obtained from plant ingredients (i.e., cereal grains). As the aquaculture industry moves towards formulating marine-derived ingredients free diets, the inclusion of plant ingredients is expected to continuously increase, and thus the amount of carbohydrates in aquafeed formulation will increase as well. Carnivorous fish, including salmonids, show a slow blood glucose clearance rate and suboptimal growth performance when fed rich carbohydrate meals. The role of gut microbial communities on carbohydrate utilization has been poorly explored in salmonids. Hence, we conducted an experiment to evaluate the effect of feeding a high carbohydrate diet to Atlantic salmon (Salmo salar) on gut microbiota composition. Our results suggest increasing the level of digestible carbohydrate mostly affects low-abundance bacteria in favor of those capable of using carbohydrates as a major energy-yielding substrate. Further study for a better understanding of the role of gut microbiota in carbohydrate utilization in carnivorous fish is required. Abstract Atlantic salmon (Salmo salar) is a carnivorous fish species whose productive performance tends to be suboptimal when fed low-cost carbohydrate rich meals. It is of interest to study the dynamics of gut microbiota communities in salmonids fed high carbohydrate diets since gut microbes are referred to as key players that influence the metabolism and physiology of the host. A study was conducted to determine the effect of feeding a high carbohydrate diet to Atlantic salmon in gut microbiota communities. A medium carbohydrate (15% wheat starch)/medium protein (MC/MP) diet or a high carbohydrate (30% wheat starch)/low protein (HC/LP) diet was fed to triplicate tanks (28 fish each) during four weeks. We conducted an in-depth characterization of the distal intestine digesta microbiota using high-throughput sequencing of the V4 region of the 16S rRNA gene. Firmicutes, Actinobacteria and Proteobacteria were the major phyla determined in either experimental group. Phylum Planctomycetes, class Planctomycetia, order Planctomycetales and genus Lactococcus were significantly more abundant in fish fed the HC/LP diet compared with fish fed the MC/MP diet. Our study suggests feeding a carbohydrate rich meal to salmon exerts a low impact on the structure of gut microbial communities, affecting mostly low-abundance bacteria capable of metabolizing anaerobically carbohydrates as a major energy-yielding substrate.
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Candidatus Krumholzibacterium zodletonense gen. nov., sp nov, the first representative of the candidate phylum Krumholzibacteriota phyl. nov. recovered from an anoxic sulfidic spring using genome resolved metagenomics. Syst Appl Microbiol 2018; 42:85-93. [PMID: 30477901 DOI: 10.1016/j.syapm.2018.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 11/23/2022]
Abstract
The accumulation of genomes of uncultured organisms has highlighted the need for devising a taxonomic and nomenclature scheme to validate names and prevent redundancies. We here report on the recovery and analysis of four phylogenetically related genomes recovered from an anoxic sulfide and sulfur-rich spring (Zodletone spring) in southwestern Oklahoma. Phylogenetic analysis based on 120 single copy markers attested to their position as a novel distinct bacterial phylum. Genomic analysis suggests Gram-negative flagellated organisms that possess type IV pili. The organisms are predicted to be rod-shaped, slow-growers, with an anoxic, heterotrophic, and fermentative lifestyle. Predicted substrate utilization pattern includes multiple amino acids, dipeptides, tripeptides, and oligpopeptides; as well as few sugars. Predicted auxotrophies include proline, vitamin B6, lipoic acid, biotin, and vitamin B12. Assessment of the putative global distribution pattern of this novel lineage suggests its preference to anoxic marine, terrestrial, hydrocarbon-impacted, and freshwater habitats. We propose the candidatus name Krumholzibacterium zodletonense gen. nov, sp. nov. for Zgenome0171T, with the genome serving as the type material for the novel family Krumholzibacteriaceae fam. nov., order Krumholzibacteriales ord. nov., class Krumholzibacteria class nov., and phylum Krumholzibacteriota phyl. nov. The type material genome assembly is deposited in GenBank under accession number QTKG01000000.
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35
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Spring S, Bunk B, Spröer C, Rohde M, Klenk H. Genome biology of a novel lineage of planctomycetes widespread in anoxic aquatic environments. Environ Microbiol 2018; 20:2438-2455. [DOI: 10.1111/1462-2920.14253] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/22/2023]
Affiliation(s)
- Stefan Spring
- Department MicroorganismsLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
| | - Boyke Bunk
- Department BioinformaticsLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
| | - Cathrin Spröer
- Department Central ServicesLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection ResearchBraunschweig Germany
| | - Hans‐Peter Klenk
- Department MicroorganismsLeibniz Institute DSMZ‐German Collection of Microorganisms and Cell CulturesBraunschweig Germany
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36
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Delgado Vela J, Dick GJ, Love NG. Sulfide inhibition of nitrite oxidation in activated sludge depends on microbial community composition. WATER RESEARCH 2018; 138:241-249. [PMID: 29604576 DOI: 10.1016/j.watres.2018.03.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/19/2018] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
Increasingly, technologies that use sulfide as an electron donor are being considered for nitrogen removal; however, our understanding of how sulfide affects microbial communities in nitrifying treatment processes is limited. In this study, we used batch experiments to quantify sulfide inhibition of both ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) using activated sludge from two full-scale treatment plants with distinct treatment processes. The batch experiments showed that NOB were more vulnerable to sulfide inhibition than AOB, and that inhibition constants (KI) for NOB were distinct between the two treatment plants, which also had distinct nitrite oxidizing microbial communities. A Nitrospira-rich, less diverse NOB community was inhibited more by sulfide than a more diverse community rich in Nitrotoga and Nitrobacter. Therefore, sulfide-induced nitritation may be more successful in less diverse, Nitrospira-rich communities. Additionally, sulfide significantly influenced the activity of non-nitrifying microbial community members, as measured by 16S rRNA cDNA sequencing. Overall, these results indicate that sulfide has a strong impact on both nitrification and the activity of the underlying microbial communities, and that the response is community-specific.
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Affiliation(s)
- Jeseth Delgado Vela
- Department of Civil and Environmental Engineering, University of Michigan, USA
| | - Gregory J Dick
- Department of Earth and Environmental Sciences, University of Michigan, USA
| | - Nancy G Love
- Department of Civil and Environmental Engineering, University of Michigan, USA.
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37
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Mustapha NA, Hu A, Yu CP, Sharuddin SS, Ramli N, Shirai Y, Maeda T. Seeking key microorganisms for enhancing methane production in anaerobic digestion of waste sewage sludge. Appl Microbiol Biotechnol 2018; 102:5323-5334. [DOI: 10.1007/s00253-018-9003-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/04/2018] [Accepted: 04/07/2018] [Indexed: 11/24/2022]
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38
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Storesund JE, Lanzèn A, García-Moyano A, Reysenbach AL, Øvreås L. Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific). Antonie van Leeuwenhoek 2018; 111:841-858. [PMID: 29423768 DOI: 10.1007/s10482-018-1026-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these deep ocean environments.
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Affiliation(s)
- Julia Endresen Storesund
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway
| | - Anders Lanzèn
- AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110, Pasaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
| | - Antonio García-Moyano
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway
| | | | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway.
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39
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Bray AW, Stewart DI, Courtney R, Rout SP, Humphreys PN, Mayes WM, Burke IT. Sustained Bauxite Residue Rehabilitation with Gypsum and Organic Matter 16 years after Initial Treatment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:152-161. [PMID: 29182867 DOI: 10.1021/acs.est.7b03568] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Bauxite residue is a high volume byproduct of alumina manufacture which is commonly disposed of in purpose-built bauxite residue disposal areas (BRDAs). Natural waters interacting with bauxite residue are characteristically highly alkaline, and have elevated concentrations of Na, Al, and other trace metals. Rehabilitation of BRDAs is therefore often costly and resource/infrastructure intensive. Data is presented from three neighboring plots of bauxite residue that was deposited 20 years ago. One plot was amended 16 years ago with process sand, organic matter, gypsum, and seeded (fully treated), another plot was amended 16 years ago with process sand, organic matter, and seeded (partially treated), and a third plot was left untreated. These surface treatments lower alkalinity and salinity, and thus produce a substrate more suitable for biological colonisation from seeding. The reduction of pH leads to much lower Al, V, and As mobility in the actively treated residue and the beneficial effects of treatment extend passively 20-30 cm below the depth of the original amendment. These positive rehabilitation effects are maintained after 2 decades due to the presence of an active and resilient biological community. This treatment may provide a lower cost solution to BRDA end of use closure plans and orphaned BRDA rehabilitation.
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Affiliation(s)
- Andrew W Bray
- School of Earth and Environment, University of Leeds , Leeds LS2 9JT, U.K
| | - Douglas I Stewart
- School of Civil Engineering, University of Leeds , Leeds LS2 9JT, U.K
| | - Ronan Courtney
- Department of Biological Sciences & The Bernal Institute, University of Limerick , Limerick, Ireland
| | - Simon P Rout
- Department of Chemical and Biological Sciences, University of Huddersfield , Huddersfield HD1 3DH, U.K
| | - Paul N Humphreys
- Department of Chemical and Biological Sciences, University of Huddersfield , Huddersfield HD1 3DH, U.K
| | - William M Mayes
- School of Environmental Sciences, University of Hull , Hull HU6 7RX, U.K
| | - Ian T Burke
- School of Earth and Environment, University of Leeds , Leeds LS2 9JT, U.K
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40
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Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb. Proteomes 2017; 5:proteomes5040036. [PMID: 29258228 PMCID: PMC5748571 DOI: 10.3390/proteomes5040036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 01/23/2023] Open
Abstract
The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composition and metabolic functions, although low amounts of microbial proteins could be identified in the small intestinal and mucosal samples. Our data suggest that a 30-day lamb has already developed mature microbial functions in the forestomachs, while the effect of the milky diet appears to be more evident in the remaining GITs. We also report the distribution and the relative abundance of the host functions, active at the GIT level, with a special focus on those involved in digestive processes. In conclusion, this pilot study supports the suitability of a metaproteogenomic approach to the characterization of microbial and host functions of the lamb GITs, opening the way to further studies aimed at investigating the impact of early dietary interventions on the GIT microbiota of small ruminants.
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41
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Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc. Extremophiles 2017; 22:13-27. [DOI: 10.1007/s00792-017-0971-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/03/2017] [Indexed: 01/28/2023]
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42
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Jasmin C, Anas A, Tharakan B, Jaleel A, Puthiyaveettil V, Narayanane S, Lincy J, Nair S. Diversity of sediment-associated Planctomycetes in the Arabian Sea oxygen minimum zone. J Basic Microbiol 2017; 57:1010-1017. [DOI: 10.1002/jobm.201600750] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 08/23/2017] [Accepted: 08/30/2017] [Indexed: 11/12/2022]
Affiliation(s)
| | - Abdulaziz Anas
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | - Balu Tharakan
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | - Abdul Jaleel
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | | | - Saravanane Narayanane
- Centre for Marine Living Resource and Ecology; Ministry of Earth Sciences; Kakkanad, Kochi, Kerala India
| | - Jovitha Lincy
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
| | - Shanta Nair
- CSIR-National Institute of Oceanography; Regional Centre Kochi; Kerala India
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43
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Saad S, Bhatnagar S, Tegetmeyer HE, Geelhoed JS, Strous M, Ruff SE. Transient exposure to oxygen or nitrate reveals ecophysiology of fermentative and sulfate-reducing benthic microbial populations. Environ Microbiol 2017; 19:4866-4881. [PMID: 28836729 PMCID: PMC5763382 DOI: 10.1111/1462-2920.13895] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/07/2017] [Accepted: 08/15/2017] [Indexed: 12/01/2022]
Abstract
For the anaerobic remineralization of organic matter in marine sediments, sulfate reduction coupled to fermentation plays a key role. Here, we enriched sulfate‐reducing/fermentative communities from intertidal sediments under defined conditions in continuous culture. We transiently exposed the cultures to oxygen or nitrate twice daily and investigated the community response. Chemical measurements, provisional genomes and transcriptomic profiles revealed trophic networks of microbial populations. Sulfate reducers coexisted with facultative nitrate reducers or aerobes enabling the community to adjust to nitrate or oxygen pulses. Exposure to oxygen and nitrate impacted the community structure, but did not suppress fermentation or sulfate reduction as community functions, highlighting their stability under dynamic conditions. The most abundant sulfate reducer in all cultures, related to Desulfotignum balticum, appeared to have coupled both acetate‐ and hydrogen oxidation to sulfate reduction. We describe a novel representative of the widespread uncultured candidate phylum Fermentibacteria (formerly candidate division Hyd24‐12). For this strictly anaerobic, obligate fermentative bacterium, we propose the name ‘USabulitectum silens’ and identify it as a partner of sulfate reducers in marine sediments. Overall, we provide insights into the function of fermentative, as well as sulfate‐reducing microbial communities and their adaptation to a dynamic environment.
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Affiliation(s)
- Sainab Saad
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Srijak Bhatnagar
- UC Davis Genome Center, University of California Davis, Davis, CA, USA
| | - Halina E Tegetmeyer
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Jeanine S Geelhoed
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Ecosystem Studies, NIOZ Royal Netherlands Institute for Sea Research, Yerseke, The Netherlands
| | - Marc Strous
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Institute for Genome Research and Systems Biology, Center for Biotechnology, University of Bielefeld, Bielefeld, Germany.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
| | - S Emil Ruff
- Max Planck Institute for Marine Microbiology, Bremen, Germany.,Department of Geoscience, University of Calgary, Calgary, AB, Canada
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44
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Lindh MV, Maillot BM, Shulse CN, Gooday AJ, Amon DJ, Smith CR, Church MJ. From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean. Front Microbiol 2017; 8:1696. [PMID: 28943866 PMCID: PMC5596108 DOI: 10.3389/fmicb.2017.01696] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/23/2017] [Indexed: 11/13/2022] Open
Abstract
Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae (Alphaproteobacteria) had higher relative abundances in the nodule and sediment habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had higher relative abundance in nodule samples, but were less abundant in sediment and water column samples. Bacterial communities in sediments and associated with nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial OTUs clustering among Prochlorococcus and Synechococcus were detected in both sediments and nodules, with greater representation among nodule samples. Such results suggest that vertical export of typically abundant photic-zone microbes may be an important process in delivery of water column microorganisms to abyssal habitats, potentially influencing the structure and function of communities in polymetallic nodule fields.
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Affiliation(s)
- Markus V Lindh
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at MānoaHonolulu, HI, United States
| | - Brianne M Maillot
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at MānoaHonolulu, HI, United States
| | - Christine N Shulse
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at MānoaHonolulu, HI, United States
| | - Andrew J Gooday
- National Oceanography Centre, University of Southampton Waterfront CampusSouthampton, United Kingdom
| | - Diva J Amon
- Department of Oceanography, University of Hawai'i at MānoaHonolulu, HI, United States
| | - Craig R Smith
- Department of Oceanography, University of Hawai'i at MānoaHonolulu, HI, United States
| | - Matthew J Church
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai'i at MānoaHonolulu, HI, United States.,Department of Oceanography, University of Hawai'i at MānoaHonolulu, HI, United States
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45
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Factors affecting distribution patterns of organic carbon in sediments at regional and national scales in China. Sci Rep 2017; 7:5497. [PMID: 28710452 PMCID: PMC5511284 DOI: 10.1038/s41598-017-06035-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/06/2017] [Indexed: 11/20/2022] Open
Abstract
Wetlands are an important carbon reservoir pool in terrestrial ecosystems. Light fraction organic carbon (LFOC), heavy fraction organic carbon (HFOC), and dissolved organic carbon (DOC) were fractionated in sediment samples from the four wetlands (ZR: Zhaoniu River; ZRCW: Zhaoniu River Constructed Wetland; XR: Xinxue River; XRCW: Xinxue River Constructed Wetland). Organic carbon (OC) from rivers and coasts of China were retrieved and statistically analyzed. At regional scale, HFOC stably dominates the deposition of OC (95.4%), whereas DOC and LFOC in ZR is significantly higher than in ZRCW. Concentration of DOC is significantly higher in XRCW (30.37 mg/l) than that in XR (13.59 mg/l). DOC and HFOC notably distinguish between two sampling campaigns, and the deposition of carbon fractions are limited by low nitrogen input. At the national scale, OC attains the maximum of 2.29% at precipitation of 800 mm. OC has no significant difference among the three climate zones but significantly higher in river sediments than in coasts. Coastal OC increases from Bohai Sea (0.52%) to South Sea (0.70%) with a decrease in latitude. This study summarizes the factors affecting organic carbon storage in regional and national scale, and have constructive implications for carbon assessment, modelling, and management.
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Andrade AC, Fróes A, Lopes FÁC, Thompson FL, Krüger RH, Dinsdale E, Bruce T. Diversity of Microbial Carbohydrate-Active enZYmes (CAZYmes) Associated with Freshwater and Soil Samples from Caatinga Biome. MICROBIAL ECOLOGY 2017; 74:89-105. [PMID: 28070679 DOI: 10.1007/s00248-016-0911-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/05/2016] [Indexed: 06/06/2023]
Abstract
Semi-arid and arid areas occupy about 33% of terrestrial ecosystems. However, little information is available about microbial diversity in the semi-arid Caatinga, which represents a unique biome that extends to about 11% of the Brazilian territory and is home to extraordinary diversity and high endemism level of species. In this study, we characterized the diversity of microbial genes associated with biomass conversion (carbohydrate-active enzymes, or so-called CAZYmes) in soil and freshwater of the Caatinga. Our results showed distinct CAZYme profiles in the soil and freshwater samples. Glycoside hydrolases and glycosyltransferases were the most abundant CAZYme families, with glycoside hydrolases more dominant in soil (∼44%) and glycosyltransferases more abundant in freshwater (∼50%). The abundances of individual glycoside hydrolase, glycosyltransferase, and carbohydrate-binding module subfamilies varied widely between soil and water samples. A predominance of glycoside hydrolases was observed in soil, and a higher contribution of enzymes involved in carbohydrate biosynthesis was observed in freshwater. The main taxa associated with the CAZYme sequences were Planctomycetia (relative abundance in soil, 29%) and Alphaproteobacteria (relative abundance in freshwater, 27%). Approximately 5-7% of CAZYme sequences showed low similarity with sequences deposited in non-redundant databases, suggesting putative homologues. Our findings represent a first attempt to describe specific microbial CAZYme profiles for environmental samples. Characterizing these enzyme groups associated with the conversion of carbohydrates in nature will improve our understanding of the significant roles of enzymes in the carbon cycle. We identified a CAZYme signature that can be used to discriminate between soil and freshwater samples, and this signature may be related to the microbial species adapted to the habitat. The data show the potential ecological roles of the CAZYme repertoire and associated biotechnological applications.
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Affiliation(s)
- Ana Camila Andrade
- Faculdade de Tecnologia e Ciências, Grupo de Biotecnologia Ambiental, Department of Bioenergy, Salvador, Brazil
| | - Adriana Fróes
- Laboratory of Microbiology, Institute of Biology, and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | - Fabiano L Thompson
- Laboratory of Microbiology, Institute of Biology, and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | | | - Thiago Bruce
- Faculdade de Tecnologia e Ciências, Grupo de Biotecnologia Ambiental, Department of Bioenergy, Salvador, Brazil.
- Department of Biology, San Diego State University, San Diego, CA, USA.
- Institute of Biology, Microbiology department, Universidade Federal da Bahia (UFBA), Rio de Janeiro, Brazil.
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47
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Jing Y, Wan J, Angelidaki I, Zhang S, Luo G. iTRAQ quantitative proteomic analysis reveals the pathways for methanation of propionate facilitated by magnetite. WATER RESEARCH 2017; 108:212-221. [PMID: 27817893 DOI: 10.1016/j.watres.2016.10.077] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/22/2016] [Accepted: 10/30/2016] [Indexed: 06/06/2023]
Abstract
Methanation of propionate requires syntrophic interaction of propionate-oxidizing bacteria and hydrogenotrophic methanogens, which is referred to as interspecies electron transfer. The present study showed that 10 mg/L conductive magnetite enhanced the methane production rate from propionate by around 44% in batch experiments, and both direct interspecies electron transfer and interspecies H2 transfer were thermodynamically feasible with the addition of magnetite. The methanation of propionate facilitated by magnetite was also demonstrated in a long-term operated continuous reactor. The methane production rate from acetate by the enriched mixed culture with magnetite was higher than that without magnetite, while similar methane production rates were found from H2/CO2 by the enriched mixed culture with and without magnetite. The ability to utilize molecular H2 indicated interspecies H2 transfer played a role in the enriched culture with magnetite, and propionate-oxidizing bacteria relating with interspecies H2 transfer were also detected by metagenomic sequencing. Metagenomic sequencing analysis also showed that Thauera, possibly relating with direct interspecies electron transfer, were enriched with the addition of magnetite. iTRAQ quantitative proteomic analysis, which was used in mixed culture for the first time, showed that magnetite induced the changes of protein expression levels involved in various pathways during the methanation of propionate. The up-regulation of proteins involved in propionate metabolism were found, and they were mainly originated from propionate-oxidizing bacteria which were not reported to be capable of direct interspecies electron transfer until now. Cytochrome c oxidase was also revealed as the possible protein relating with direct interspecies electron transfer considering its up-regulation with the addition of magnetite and origination from Thauera. Most of the up-regulated proteins in methane metabolism were originated from Methanosaeta, while most of the enzymes with down-regulated proteins were originated from Methanosarcina. However, the up-regulated proteins relating with hydrogenotrophic methanogenesis were originated from neither Methanosaeta nor Methanosarcina, indicating they were not involved in direct interspecies electron transfer. The hydrogenotrophic methanogens, e.g. Methanospirillum, Methanosphaerula et al., might be involved in direct interspecies electron transfer. Overall, the present study showed that both direct interspecies electron transfer and interspecies H2 transfer were present during methanation of propionate facilitated by magnetite.
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Affiliation(s)
- Yuhang Jing
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433, Shanghai, China
| | - Jingjing Wan
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433, Shanghai, China
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, DK-2800, Kgs Lyngby, Denmark
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433, Shanghai, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433, Shanghai, China.
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48
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Cao Q, Wang H, Chen X, Wang R, Liu J. Composition and distribution of microbial communities in natural river wetlands and corresponding constructed wetlands. ECOLOGICAL ENGINEERING 2017; 98:40-48. [DOI: 10.1016/j.ecoleng.2016.10.063] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
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49
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Ji Y, Angel R, Klose M, Claus P, Marotta H, Pinho L, Enrich-Prast A, Conrad R. Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. Environ Microbiol 2016; 18:5082-5100. [PMID: 27507000 DOI: 10.1111/1462-2920.13491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/06/2016] [Indexed: 11/28/2022]
Abstract
Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity.
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Affiliation(s)
- Yang Ji
- Jiangsu Key Laboratory of Agricultural Meteorology, College of Applied Meteorology, Nanjing University of Information Science & Technology, Ningliu Road 219, Nanjing, 210044, China.,Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Roey Angel
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Research Network Chemistry meets Microbiology, University of Vienna, Althanstrasse 14, Vienna, 1090, Austria
| | - Melanie Klose
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Peter Claus
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
| | - Humberto Marotta
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Graduated Program in Geosciences (Geochemistry), Graduated Program in Geography, Research Center on Biomass and Water Management (NAB/UFF), Sedimentary Environmental Processes Laboratory (LAPSA/UFF), International Laboratory of Global Change (LINC-Global), Fluminense Federal University (UFF), Niterói, Brazil
| | - Luana Pinho
- Department of Chemical Oceanography, Rio de Janeiro State University, Pavilhão João Lyra Filho, sala 4008 Bloco E, Rua São Francisco Xavier, 524, Maracanã-RJ, 20550-900, Brazil
| | - Alex Enrich-Prast
- Laboratório de Biogeoquímica, Departamento de Ecologia, Instituto de Biologia, University Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.,Department of Environmental Change, Linköping University, Linköping, Sweden
| | - Ralf Conrad
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, Marburg, 35043, Germany
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50
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Hamilton TL, Bovee RJ, Sattin SR, Mohr W, Gilhooly WP, Lyons TW, Pearson A, Macalady JL. Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria. Front Microbiol 2016; 7:598. [PMID: 27199928 PMCID: PMC4846661 DOI: 10.3389/fmicb.2016.00598] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/11/2016] [Indexed: 11/13/2022] Open
Abstract
Mahoney Lake in British Columbia is an extreme meromictic system with unusually high levels of sulfate and sulfide present in the water column. As is common in strongly stratified lakes, Mahoney Lake hosts a dense, sulfide-oxidizing phototrophic microbial community where light reaches the chemocline. Below this "plate," the euxinic hypolimnion is anoxic, eutrophic, saline, and rich in sulfide, polysulfides, elemental sulfur, and other sulfur intermediates. While much is known regarding microbial communities in sunlit portions of euxinic systems, the composition and genetic potential of organisms living at aphotic depths have rarely been studied. Metagenomic sequencing of samples from the hypolimnion and the underlying sediments of Mahoney Lake indicate that multiple taxa contribute to sulfate reduction below the chemocline and that the hypolimnion and sediments each support distinct populations of sulfate reducing bacteria (SRB) that differ from the SRB populations observed in the chemocline. After assembling and binning the metagenomic datasets, we recovered near-complete genomes of dominant populations including two Deltaproteobacteria. One of the deltaproteobacterial genomes encoded a 16S rRNA sequence that was most closely related to the sulfur-disproportionating genus Dissulfuribacter and the other encoded a 16S rRNA sequence that was most closely related to the fatty acid- and aromatic acid-degrading genus Syntrophus. We also recovered two near-complete genomes of Firmicutes species. Analysis of concatenated ribosomal protein trees suggests these genomes are most closely related to extremely alkaliphilic genera Alkaliphilus and Dethiobacter. Our metagenomic data indicate that these Firmicutes contribute to carbon cycling below the chemocline. Lastly, we recovered a nearly complete genome from the sediment metagenome which represents a new genus within the FCB (Fibrobacteres, Chlorobi, Bacteroidetes) superphylum. Consistent with the geochemical data, we found little or no evidence for organisms capable of sulfide oxidation in the aphotic zone below the chemocline. Instead, comparison of functional genes below the chemocline are consistent with recovery of multiple populations capable of reducing oxidized sulfur. Our data support previous observations that at least some of the sulfide necessary to support the dense population of phototrophs in the chemocline is supplied from sulfate reduction in the hypolimnion and sediments. These studies provide key insights regarding the taxonomic and functional diversity within a euxinic environment and highlight the complexity of biogeochemical carbon and sulfur cycling necessary to maintain euxinia.
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Affiliation(s)
- Trinity L Hamilton
- Department of Biological Sciences, University of Cincinnati Cincinnati, OH, USA
| | - Roderick J Bovee
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Sarah R Sattin
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Wiebke Mohr
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - William P Gilhooly
- Department of Earth Sciences, Indiana University-Purdue University Indianapolis Indianapolis, IN, USA
| | - Timothy W Lyons
- Department of Earth Sciences, University of California Riverside, CA, USA
| | - Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University Cambridge, MA, USA
| | - Jennifer L Macalady
- Penn State Astrobiology Research Center, Department of Geosciences, Pennsylvania State University University Park, TX, USA
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