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Yang T, Wang Y, Zhou T, Yang J, Liu M, Shang Y, Zhang Y, Hei P. Modeling microbial impact on macrophyte debris decomposition in macrophyte-dominated eutrophic lakes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174442. [PMID: 38964387 DOI: 10.1016/j.scitotenv.2024.174442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/13/2024] [Accepted: 06/30/2024] [Indexed: 07/06/2024]
Abstract
The decomposition of macrophytes plays a crucial role in the nutrient cycles of macrophyte-dominated eutrophication lakes. While research on plant decomposition mechanisms and microbial influences has rapid developed, it is curious that plant decomposition models have remained stagnant at the single-stage model from 50 years ago, without endeavor to consider any important factors. Our research conducted in-situ experiments and identified the optimal metrics for decomposition-related microbes, thereby establishing models for microbial impacts on decomposition rates (k_RDR). Using backward elimination in stepwise regression, we found that the optimal subset of independent variables-specifically Gammaproteobacteria-Q-L, Actinobacteriota-Q-L, and Ascomycota-Q-L-increased the adjusted R-squared (Ra2) to 0.93, providing the best modeling for decomposition rate (p = 0.002). Additionally, k_RDR can be modeled by synergic parameters of ACHB-Q-L, LDB-Q-L, and AB-Q-L for bacteria, and SFQ for fungi, albeit with a slightly lower Ra2 of 0.7-0.9 (p < 0.01). The primary contribution of our research lies in two key aspects. Firstly, we introduced optimal metrics for modeling microbes, opting for debris surface microbes over sediment microbes, and prioritizing absolute abundance over relative abundance. Secondly, our model represents a noteworthy advancement in debris modeling. Alongside elucidating the focus and innovative aspects of our work, we also addressed existing limitations and proposed directions for future research. SYNOPSIS: This study explores optimum metrics for decomposition-related microbes, offering precise microbial models for enhanced lake nutrient cycle simulation.
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Affiliation(s)
- Tingting Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yaqin Wang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Tong Zhou
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Jing Yang
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Manman Liu
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China
| | - Yizi Shang
- State Key Laboratory of Simulation and Regulation of Water Cycles in River Basins, China Institute of Water Resources and Hydropower Research, Beijing 100038, China
| | - Yingyuan Zhang
- Guizhou Academy of Testing and Analysis, Guiyang 550000, China
| | - Pengfei Hei
- College of Life and Environmental Science, Minzu University of China, Beijing 100081, China.
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2
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Jiménez-Morillo NT, Moreno J, Moreno F, Fatela F, Leorri E, De la Rosa JM. Composition and sources of sediment organic matter in a western Iberian salt marsh: Developing a novel prediction model of the bromine sedimentary pool. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:167931. [PMID: 37863236 DOI: 10.1016/j.scitotenv.2023.167931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/18/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Salt marshes are sensitive highly productive habitats crucial for carbon cycling. This study presents a comprehensive analysis of organic geochemical indicators and geochronology in the Mira salt marsh (SW Portugal) over eight centuries. The closely intertwined carbon and bromine (Br) biogeochemical cycles in these environments can influence the fluxes of volatile compounds such as ozone-depleting methyl bromide, emphasizing the importance of understanding sediment organic matter (OM) origin, budget, and composition in salt marshes. To characterize the strong Br-OM relationship, we used n-alkane signatures, bulk elemental data (total carbon, total nitrogen, Corg/Nat ratio), and stable isotopes (δ15N, δ13C) from a sediment core. Findings revealed a mixed composition of terrestrial and marine OM, posing challenges in distinguishing ex situ higher plant sources from in situ production by marsh vegetation. n-Alkanes (C15 to C31) were found in all the sediment samples, predominantly C25-C29. Changes in their presence were linked to marsh succession, evolving from a vegetation-free tidal flat to a C3 halophyte-dominated high marsh ecosystem. Despite the area's low industrial and population impact, regulation of water flow through the dam affected the balance between continental and marine waters. This study aimed to create a cost-effective predictive model for total Br, enhancing paleoclimatic studies using sedimentary samples. The n-alkane model had limited resolution, but an alternative infrared (IR) spectroscopy-based model, requiring less time and smaller sample sizes, was developed. Combining FT-IR spectra with statistical analysis enabled the creation of a reliable total Br concentration prediction model (mean absolute error = 14.39). These findings have implications for controlling Br enrichment in marsh environments and can be applied in various coastal wetlands with different mineralogical and organic characteristics.
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Affiliation(s)
- Nicasio T Jiménez-Morillo
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Avda. Reina Mercedes 10, 41012 Sevilla, Spain
| | - João Moreno
- Instituto Dom Luiz - IDL, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Filipa Moreno
- Independent Researcher, Caminho da Portela 97, 4940-061 Bico PCR, Portugal
| | - Francisco Fatela
- Instituto Dom Luiz - IDL, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Departamento de Geologia, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Eduardo Leorri
- Department of Geological Sciences, East Carolina University, Greenville, NC 27858-4353, USA
| | - Jose Maria De la Rosa
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS-CSIC), Avda. Reina Mercedes 10, 41012 Sevilla, Spain.
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3
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Frates ES, Spietz RL, Silverstein MR, Girguis P, Hatzenpichler R, Marlow JJ. Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment. Front Microbiol 2023; 14:1235906. [PMID: 37744927 PMCID: PMC10512730 DOI: 10.3389/fmicb.2023.1235906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.
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Affiliation(s)
- Erin S. Frates
- Department of Biology, Boston University, Boston, MA, United States
| | - Rachel L. Spietz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | | | - Peter Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, United States
- Thermal Biology Institute, Montana State University, Bozeman, MT, United States
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4
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Colette M, Guentas L, Patrona LD, Ansquer D, Callac N. Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds. ENVIRONMENTAL MICROBIOME 2023; 18:58. [PMID: 37438848 DOI: 10.1186/s40793-023-00512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species (Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata) on active sediment microbial communities and their implications on organic matter degradation. RESULTS Drying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture. CONCLUSION The efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.
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Affiliation(s)
- Marie Colette
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia.
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia.
| | - Linda Guentas
- Institute of Exact and Applied Sciences (ISEA), EA 7484, University of New Caledonia, Noumea, 98851, New Caledonia
| | - Luc Della Patrona
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Dominique Ansquer
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
| | - Nolwenn Callac
- French Institute for Research in the Science of the Sea (IFREMER), Research Institute for Development (IRD), University of New Caledonia, University of Reunion, CNRS, UMR 9220 ENTROPIE, Noumea, New Caledonia
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5
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Kim C, Staver LW, Chen X, Bulseco A, Cornwell JC, Malkin SY. Microbial Community Succession Along a Chronosequence in Constructed Salt Marsh Soils. MICROBIAL ECOLOGY 2023; 85:931-950. [PMID: 36764950 DOI: 10.1007/s00248-023-02189-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/02/2023] [Indexed: 05/04/2023]
Abstract
In this study, we examined the succession of soil microbial communities across a chronosequence of newly constructed salt marshes constructed primarily of fine-grained dredge material, using 16S rRNA amplicon sequences. Alpha diversity in the subsurface horizons was initially low and increased to reference levels within 3 years of marsh construction, while alpha diversity in the newly accumulating organic matter-rich surface soils was initially high and remained unchanged. Microbial community succession was fastest in the surface horizon (~ 24 years to reference equivalency) and became progressively slower with depth in the subsurface horizons (~ 30-67 years). Random forest linear regression analysis was used to identify important taxa driving the trajectories toward reference conditions. In the parent material, putative sulfate-reducers (Desulfobacterota), methanogens (Crenarchaeota, especially Methanosaeta), and fermenters (Chloroflexi and Clostridia) increased over time, suggesting an enrichment of these metabolisms over time, similar to natural marshes. Concurrently in the surface soils, the relative abundances of putative methane-, methyl-, and sulfide oxidizers, especially among Gammaproteobacteria, increased over time, suggesting the co-development of sulfide and methane removal metabolisms in marsh soils. Finally, we observed that the surface soil communities at one of the marshes did not follow the trajectory of the others, exhibiting a greater relative abundance of anaerobic taxa. Uniquely in this dataset, this marsh was developing signs of excessive inundation stress in terms of vegetation coverage and soil geochemistry. Therefore, we suggest that soil microbial community structure may be effective bioindicators of salt marsh inundation and are worthy of further targeted investigation.
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Affiliation(s)
- Carol Kim
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Lorie W Staver
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Xuan Chen
- Department of Biology, Salisbury University, Salisbury, MD, USA
| | | | - Jeffrey C Cornwell
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA
| | - Sairah Y Malkin
- Horn Point Laboratory, University of Maryland Center for Environmental Science (UMCES), Cambridge, MD, USA.
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6
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Zakavi M, Askari H, Shahrooei M. Maize growth response to different Bacillus strains isolated from a salt-marshland area under salinity stress. BMC PLANT BIOLOGY 2022; 22:367. [PMID: 35879654 PMCID: PMC9317119 DOI: 10.1186/s12870-022-03702-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Maize (Zea mays) growth performance has been hindered due to the high soil salinity. Salinity is one of the most severe abiotic stresses that has led to growth imbalance and profitability of harvests in arid and semi-arid regions. Plants have taken advantage of salt-tolerant bacteria as plant growth-promoters to enhance growth and reduce the adverse effects of salinity through the regulation of some biochemical, physiological, and molecular features. Preferences for non-chemical, eco-friendly, and economical approaches have caused the inquiry of the Bacillus genus as a joint group of plant growth-promoting rhizobacteria known to alleviate salt-stress impacts. In the present study, halotolerant Bacillus strains were isolated from salt-marshland soil and characterized for their physiological, molecular, and biochemical properties. Twenty-four bacterial isolates collected from high saline fields of salt marshland were analyzed by MALDI-TOF MS proteome analysis, which confirmed the taxonomic affiliation with Bacillus cereus, Bacillus subtilis, Bacillus atrophaeus, and Bacillus thorngiensis. Applying the isolates on maize plants as bio-inoculant bacteria obviously increased the growth parameters (P < 0.01). Pot experiments showed that isolates 74 and 90 were the most prominent strains to minimize the harmful effects of salinity. Its effects are heightening the potassium/sodium ratio and K-Na selectivity in shoots and roots measured by flame atomic absorption photometry (AAS). Accordingly, Bacillus cereus isolate 74 showed a maximum increase in dry weights of the shoot (133.89%), root (237.08%), length of the shoot (125%), and root (119.44%) compared to the control condition. Our findings suggest that bacteria isolated from marshland may be an economical and simple means to increase plant growth and resistance to high salinity soil conditions.
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Affiliation(s)
- Maryam Zakavi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Hossein Askari
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Shahrooei
- Department of Microbiology and Immunology, Clinical and Diagnostic Immunology, KU Leuven, Leuven, Belgium
- Medical Laboratory of Dr. Shahrooei, Tehran, Iran
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7
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Wang Y, Liu Y, Li Y, Sun J, Lai Q, Zhu H, Zhou H. Pseudemcibacter aquimaris gen. nov., sp. nov., isolated from an aquaculture farm. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005327] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A rod-shaped, Gram-stain-negative, aerobic and non-motile bacterium, designated strain Y4T, was isolated from an aquaculture farm in Xiamen, PR China. Strain Y4T had 94.8, 93.3 and 91.8 % 16S rRNA gene sequence similarity to
Paremcibacter congregatus
ZYLT,
Emcibacter nanhaiensis
HTCJW17T and
Luteithermobacter gelatinilyticus
MEBiC09520T, respectively. The genomic DNA G+C content of strain Y4T was 42.7 mol%. The average amino acid identity and percentage of conserved proteins values between strain Y4T and type strains of the family
Emcibacteraceae
were 57.9–58.6 % and 44.5–47.6 %, respectively. Optimal growth was observed at 28 °C, at pH 7.0 and with 2 % (w/v) NaCl. The novel strain Y4T required Ca2+, K+ and Mg2+ ions in addition to NaCl for growth. The dominant fatty acids of strain Y4T were summed feature 3 (C16 : 1
ω7c/C16 : 1
ω6c), summed feature 8 (C18 : 1
ω7c/C18 : 1
ω6c) and C14 : 0 2-OH. The polar lipid profile contained phosphatidylethanolamine, phosphatidyglycerol, three unidentified aminolipids, four unidentified aminophospholipids and two unidentified lipids. Cells contained exclusively ubiquinone Q-10. On the basis of the polyphasic analysis, strain Y4T (=MCCC 1K06278T=KCTC 82926T) is considered to represent a novel species in a novel genus of the family
Emcibacteraceae
, for which the name Pseudemcibacter aquimaris gen. nov., sp. nov. is proposed.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Yanbo Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Yanyan Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Jia Sun
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Hongmei Zhu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
| | - Hantao Zhou
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, PR China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, PR China
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8
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Pérez-Rodríguez I, Choi JK, Abuyen K, Tyler M, Ronkowski C, Romero E, Trujillo A, Tremblay J, Viney I, Savalia P, Amend JP. Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter. Int J Syst Evol Microbiol 2021; 71. [PMID: 33877046 DOI: 10.1099/ijsem.0.004739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-MT and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lō'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-MT grew between 25 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-20 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5-40 °C), 10 and 50 g l-1 NaCl (optimum, 15-25 g l-1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H2 as the primary electron donor, CO2 as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-MT and HR-1, respectively. Fe(OH)3, MnO2, AsO4 3-, SO4 2-, SeO4 2-, S2O3 2-, S0 and NO3 - were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-MT and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to Geothermobacter ehrlichii, within the class δ-Proteobacteria (now within the class Desulfuromonadia). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus Geothermobacter, for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-MT (=JCM 32109T=KCTC 15831T=ATCC TSD-173T) and strain HR-1 (=JCM 32110=KCTC 15832).
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Affiliation(s)
- Ileana Pérez-Rodríguez
- Geophysical Laboratory, Carnegie Institution of Washington, Washington, DC 20015, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica K Choi
- Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karla Abuyen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Madeline Tyler
- Present address: College of Pharmacy, Oregon State University, Corvallis, OR 97330, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Cynthia Ronkowski
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Eric Romero
- Present address: Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA.,Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Anthony Trujillo
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Jason Tremblay
- Community College Cultivation Cohort, University of Southern California, Los Angeles, CA 90089, USA
| | - Isabella Viney
- Present address: Department of Microbiology, University of Arizona, Tucson, AZ 85721, USA.,Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pratixaben Savalia
- Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Jan P Amend
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Department of Earth Sciences, University of Southern California, Los Angeles, CA 90089, USA
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9
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Molecular characterization of bacteria and archaea in a bioaugmented zero-water exchange shrimp pond. SN APPLIED SCIENCES 2021. [DOI: 10.1007/s42452-021-04392-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
AbstractIn the zero-water exchange shrimp culture pond maintained with the application of indigenous bioaugmentor, low levels of total ammonia–nitrogen were reported, indicating the relevance of indigenous microbial communities. Sediments (0–5 cm layer) were sampled from the pond (85th day) and the bacterial and archaeal communities; specifically, the ammonia oxidizers (ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and anaerobic ammonia-oxidizing bacteria) in the sediment metagenome of the pond were analysed using the 16S rRNA and functional genes. Bacterial and archaeal 16S rRNA genes showed the relative abundance of Delta-Proteobacteria and Bacteroidetes groups performing sulphur respiration and organic matter degradation, archaeal groups of anaerobic sulphur respiring Crenarchaeotae, and chemolithoautotrophic ammonia oxidizers belonging to Thaumarchaeota. The presence of these diverse bacterial and archaeal communities denotes their significant roles in the cycling the carbon, nitrogen, and sulphur thereby bringing out efficient bioremediation in the bioaugmented zero-water exchange shrimp culture pond. Similarly, the functional gene-specific study showed the predominance of Nitrosomonas sp. (ammonia-oxidizing bacteria), Nitrosopumilus maritimus (ammonia-oxidizing archaea), and Candidatus Kuenenia (anaerobic ammonia-oxidizing bacteria) in the system, which points to their importance in the removal of accumulated ammonia. Thus, this study paves the way for understanding the microbial communities, specifically the ammonia oxidizers responsible for maintaining healthy and optimal environmental conditions in the bioaugmented zero-water exchange shrimp culture pond.
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10
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Leadbeater DR, Oates NC, Bennett JP, Li Y, Dowle AA, Taylor JD, Alponti JS, Setchfield AT, Alessi AM, Helgason T, McQueen-Mason SJ, Bruce NC. Mechanistic strategies of microbial communities regulating lignocellulose deconstruction in a UK salt marsh. MICROBIOME 2021; 9:48. [PMID: 33597033 PMCID: PMC7890819 DOI: 10.1186/s40168-020-00964-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/06/2020] [Indexed: 05/29/2023]
Abstract
BACKGROUND Salt marshes are major natural repositories of sequestered organic carbon with high burial rates of organic matter, produced by highly productive native flora. Accumulated carbon predominantly exists as lignocellulose which is metabolised by communities of functionally diverse microbes. However, the organisms that orchestrate this process and the enzymatic mechanisms employed that regulate the accumulation, composition and permanence of this carbon stock are not yet known. We applied meta-exo-proteome proteomics and 16S rRNA gene profiling to study lignocellulose decomposition in situ within the surface level sediments of a natural established UK salt marsh. RESULTS Our studies revealed a community dominated by Gammaproteobacteria, Bacteroidetes and Deltaproteobacteria that drive lignocellulose degradation in the salt marsh. We identify 42 families of lignocellulolytic bacteria of which the most active secretors of carbohydrate-active enzymes were observed to be Prolixibacteracea, Flavobacteriaceae, Cellvibrionaceae, Saccharospirillaceae, Alteromonadaceae, Vibrionaceae and Cytophagaceae. These families secreted lignocellulose-active glycoside hydrolase (GH) family enzymes GH3, GH5, GH6, GH9, GH10, GH11, GH13 and GH43 that were associated with degrading Spartina biomass. While fungi were present, we did not detect a lignocellulolytic contribution from fungi which are major contributors to terrestrial lignocellulose deconstruction. Oxidative enzymes such as laccases, peroxidases and lytic polysaccharide monooxygenases that are important for lignocellulose degradation in the terrestrial environment were present but not abundant, while a notable abundance of putative esterases (such as carbohydrate esterase family 1) associated with decoupling lignin from polysaccharides in lignocellulose was observed. CONCLUSIONS Here, we identify a diverse cohort of previously undefined bacteria that drive lignocellulose degradation in the surface sediments of the salt marsh environment and describe the enzymatic mechanisms they employ to facilitate this process. Our results increase the understanding of the microbial and molecular mechanisms that underpin carbon sequestration from lignocellulose within salt marsh surface sediments in situ and provide insights into the potential enzymatic mechanisms regulating the enrichment of polyphenolics in salt marsh sediments. Video Abstract.
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Affiliation(s)
- Daniel R Leadbeater
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Nicola C Oates
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joseph P Bennett
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Adam A Dowle
- Bioscience Technology Facility, Department of Biology, University of York, York, YO10 5DD, UK
| | - Joe D Taylor
- School of Chemistry and Biosciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Juliana Sanchez Alponti
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Alexander T Setchfield
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | - Anna M Alessi
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK
| | | | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Neil C Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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11
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Huang Z, Wei X, Lai Q, Chen S, Yuan J. Pareuzebyella sediminis gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae, isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2020; 71. [PMID: 33300861 DOI: 10.1099/ijsem.0.004606] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two marine bacterial strains, designated S2-4-21T and MT2-5-19, were isolated from two tidal flat sediments of cordgrass Spartina alterniflora and adjacent oyster culture field in Quanzhou bay, China, respectively. Both strains were Gram-staining-negative, rod-shaped, non-flagellated, non-motile, aerobic, had NaCl requirements, and contained carotenoid and flexirubin pigments. The 16S rRNA gene sequence similarity (99.8%), average nucleotide identity value (99.4%) and average amino acid identity (99.3%) between strain S2-4-21T and strain MT2-5-19 strongly supported that they belonged to a single species. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-4-21T and strain MT2-5-19 formed a monophyletic branch affiliated to the family Flavobacteriaceae, sharing similarities of 94.6% with Euzebyella marina CY01T and E. saccharophila 7SM30T, and of 94.1 and 92.8% with E. algicola MEBiC 12267T and Pseudozobellia thermophile DSM 19858T, respectively. Phylogenomic analysis based on the whole genome sequences supported that the two strains formed a distinct monophyletic clade within Flavobacteriaceae members, which was phylogenetically different from the clades of Euzebyella and Pseudozobellia. The major respiratory quinone was menaquinone MK-6. The major fatty acids (>10%) consisted of C15 : 0 iso, C16 : 0, summed feature 9 (C17 : 1 iso ω9c/C16 : 0 10-methyl) and C17 : 0 iso 3-OH. The polar lipid profiles of strain S2-4-21T and strain MT2-5-19 are identical, including phosphatidylethanolamine, four unidentified aminolipids, and four unidentified lipids. The genomic size was 4.9-5.0 Mb with genomic DNA G+C content of 41.5 mol%. Based on the above characteristics, strains S2-4-21T and MT2-5-19 represented a novel species of a novel genus in the family Flavobacteriaceae. Thus, Pareuzebyella sediminis gen. nov. sp. nov. is proposed with type strain S2-4-21T (=MCCC 1K03818T=KCTC 72152T), and another strain MT2-5-19 (=KCTC 72539=MCCC 1K03874).
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Affiliation(s)
- Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China.,Key Laboratory of Inshore Resources Biotechnology (Quanzhou Normal University) Fujian Province University, Quanzhou, PR China
| | - Xiaomei Wei
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Shiyong Chen
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, PR China
| | - Jianjun Yuan
- Key Laboratory of Inshore Resources Biotechnology (Quanzhou Normal University) Fujian Province University, Quanzhou, PR China.,College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China
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12
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Park MJ, Namirimu T, Yang SH, Kwon KK. Description of Luteithermobacter gelatinilyticus gen. nov., sp. nov., and Paremcibacter congregatus gen. nov., comb. nov. via reclassification of the genus Emcibacter. Int J Syst Evol Microbiol 2020; 70:4691-4697. [PMID: 32697185 DOI: 10.1099/ijsem.0.004334] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MEBiC09520T, which was isolated from a tidal sediment in Incheon, Korea, is a pale yellow, rod-shaped bacterium, cells of which are 0.4-0.5 µm in width and 1.5-2 µm in length. Strain MEBiC09520T shared 95.17 and 92.57% 16S rRNA gene sequence similarity with Emcibacter nanhaiensis and E. congregatus, respectively. It grew optimally at pH 6.0, at 55 °C and with 2.5-3.5% (w/v) NaCl. Its polar lipid components included phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), an unidentified phospholipid (PL), three unidentified aminolipids (ALs) and two unidentified lipids (L). The fatty acids C16:0, C19:0 cyclo ω8c, C14:0 2-OH and summed feature 8 (C18:1ω7c and/or C18:1ω6c) were predominantly present in its cell wall. Strain MEBiC09520T was thermophilic, while E. nanhaiensis and E. congregatus were mesophilic. Although E. nanhaiensis showed no nitrate reduction activity, MEBiC09520T and E. congregatus showed a positive reaction. These strains differed in carbohydrate utilization. In particular, E. congregatus was able to thrive on various carbohydrate substrates as compared to the other strains. The average nucleotide identity value was 69.92% between strain MEBiC09520T and E. congregatus ZYLT, 70.38% between E. congregatus ZYLT and E. nanhaiensis HTCJW17T, and 72.83% between strain MEBiC09520 and E. nanhaiensis HTCJW17T. Considering these differences, strain MEBiC09520T (=KCCM 43320T=MCCC 1K03920T) is suggested to represent and novel species of a new genus, Luteithermobacter gelatinilyticus gen. nov., sp. nov., and E. congregatus should be reclassified as Paremcibacter congregatus gen. nov., comb. nov.
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Affiliation(s)
- Mi-Jeong Park
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea.,Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Teddy Namirimu
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea.,Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- Major of Applied Ocean Science, University of Science and Technology, Daejeon, Republic of Korea.,Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea
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13
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Cragg SM, Friess DA, Gillis LG, Trevathan-Tackett SM, Terrett OM, Watts JEM, Distel DL, Dupree P. Vascular Plants Are Globally Significant Contributors to Marine Carbon Fluxes and Sinks. ANNUAL REVIEW OF MARINE SCIENCE 2020; 12:469-497. [PMID: 31505131 DOI: 10.1146/annurev-marine-010318-095333] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
More than two-thirds of global biomass consists of vascular plants. A portion of the detritus they generate is carried into the oceans from land and highly productive blue carbon ecosystems-salt marshes, mangrove forests, and seagrass meadows. This large detrital input receives scant attention in current models of the global carbon cycle, though for blue carbon ecosystems, increasingly well-constrained estimates of biomass, productivity, and carbon fluxes, reviewed in this article, are now available. We show that the fate of this detritus differs markedly from that of strictly marine origin, because the former contains lignocellulose-an energy-rich polymer complex of cellulose, hemicelluloses, and lignin that is resistant to enzymatic breakdown. This complex can be depolymerized for nutritional purposes by specialized marine prokaryotes, fungi, protists, and invertebrates using enzymes such as glycoside hydrolases and lytic polysaccharide monooxygenases to release sugar monomers. The lignin component, however, is less readily depolymerized, and detritus therefore becomes lignin enriched, particularly in anoxic sediments, and forms a major carbon sink in blue carbon ecosystems. Eventual lignin breakdown releases a wide variety of small molecules that may contribute significantly to the oceanic pool of recalcitrant dissolved organic carbon. Marine carbon fluxes and sinks dependent on lignocellulosic detritus are important ecosystem services that are vulnerable to human interventions. These services must be considered when protecting blue carbon ecosystems and planning initiatives aimed at mitigating anthropogenic carbon emissions.
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Affiliation(s)
- Simon M Cragg
- Institute of Marine Sciences, University of Portsmouth, Portsmouth PO4 9LY, United Kingdom;
| | - Daniel A Friess
- Department of Geography, National University of Singapore, Singapore 117570;
| | - Lucy G Gillis
- Leibniz-Zentrum für Marine Tropenforschung (ZMT), 28359 Bremen, Germany;
| | - Stacey M Trevathan-Tackett
- Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Burwood, Victoria 3125, Australia;
| | - Oliver M Terrett
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
| | - Joy E M Watts
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom;
| | - Daniel L Distel
- Ocean Genome Legacy Center of New England Biolabs, Marine Science Center, Northeastern University, Nahant, Massachusetts 01908, USA;
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom; ,
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14
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Houfani AA, Větrovský T, Navarrete OU, Štursová M, Tláskal V, Beiko RG, Boucherba N, Baldrian P, Benallaoua S, Jorquera MA. Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems. MICROBIAL ECOLOGY 2019; 77:713-725. [PMID: 30209585 DOI: 10.1007/s00248-018-1251-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.
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Affiliation(s)
- Aicha Asma Houfani
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tomáš Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Oscar U Navarrete
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile
| | - Martina Štursová
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - Nawel Boucherba
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Said Benallaoua
- Laboratoire de Microbiologie Appliquée (LMA), Département de Microbiologie, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000, Bejaia, Algérie
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departmento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
- Scientific and Biotechnological Bioresource Nucleus, Universidad de La Frontera, Ave. Franciosco Salazar, 01145, Temuco, Chile.
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15
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Ortega-Arbulú AS, Pichler M, Vuillemin A, Orsi WD. Effects of organic matter and low oxygen on the mycobenthos in a coastal lagoon. Environ Microbiol 2018; 21:374-388. [PMID: 30411473 PMCID: PMC7379666 DOI: 10.1111/1462-2920.14469] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 11/30/2022]
Abstract
Fungi living in sediments (‘mycobenthos’) are hypothesized to play a role in the degradation of organic matter deposited at the land‐sea interface, but the environmental factors influencing the mycobenthos are poorly understood. We used mock community calibrated Illumina sequencing to show that the mycobenthos community structure in a coastal lagoon was significantly changed after exposure to a lignocellulose extract and subsequent development of benthic anoxia over a relatively short (10 h) incubation. Saprotrophic taxa dominated and were selected for under benthic anoxia, specifically Aquamyces (Chytridiomycota) and Orbilia (Ascomycota), implicating these genera as important benthic saprotrophs. Protein encoding genes involved in energy and biomass production from Fungi and the fungal‐analogue group Labyrinthulomycetes had the highest increase in expression with the added organic matter compared with all other groups, indicating that lignocellulose stimulates metabolic activity in the mycobenthos. Flavobacteria dominated the active bacterial community that grew rapidly with the lignocellulose extract and crashed sharply upon O2 depletion. Our findings indicate that the diversity, activity and trophic potential of the mycobenthos changes rapidly in response to organic matter and decreasing O2 concentrations, which together with heterotrophic Flavobacteria, undergo ‘boom and bust’ dynamics during lignocellulose degradation in estuarine ecosystems.
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Affiliation(s)
- Ana-Sofia Ortega-Arbulú
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Monica Pichler
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Aurèle Vuillemin
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, 80333 Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
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16
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Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment. ISME JOURNAL 2018; 13:277-289. [PMID: 30206424 PMCID: PMC6331629 DOI: 10.1038/s41396-018-0269-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/11/2018] [Accepted: 07/26/2018] [Indexed: 11/08/2022]
Abstract
Coastal saltmarsh sediments represent an important source of natural methane emissions, much of which originates from quaternary and methylated amines, such as choline and trimethylamine. In this study, we combine DNA stable isotope probing with high throughput sequencing of 16S rRNA genes and 13C2-choline enriched metagenomes, followed by metagenome data assembly, to identify the key microbes responsible for methanogenesis from choline. Microcosm incubation with 13C2-choline leads to the formation of trimethylamine and subsequent methane production, suggesting that choline-dependent methanogenesis is a two-step process involving trimethylamine as the key intermediate. Amplicon sequencing analysis identifies Deltaproteobacteria of the genera Pelobacter as the major choline utilizers. Methanogenic Archaea of the genera Methanococcoides become enriched in choline-amended microcosms, indicating their role in methane formation from trimethylamine. The binning of metagenomic DNA results in the identification of bins classified as Pelobacter and Methanococcoides. Analyses of these bins reveal that Pelobacter have the genetic potential to degrade choline to trimethylamine using the choline-trimethylamine lyase pathway, whereas Methanococcoides are capable of methanogenesis using the pyrrolysine-containing trimethylamine methyltransferase pathway. Together, our data provide a new insight on the diversity of choline utilizing organisms in coastal sediments and support a syntrophic relationship between Bacteria and Archaea as the dominant route for methanogenesis from choline in this environment.
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17
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Pelve EA, Fontanez KM, DeLong EF. Bacterial Succession on Sinking Particles in the Ocean's Interior. Front Microbiol 2017; 8:2269. [PMID: 29225592 PMCID: PMC5706468 DOI: 10.3389/fmicb.2017.02269] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/03/2017] [Indexed: 11/13/2022] Open
Abstract
Sinking particles formed in the photic zone and moving vertically through the water column are a main mechanism for nutrient transport to the deep ocean, and a key component of the biological carbon pump. The particles appear to be processed by a microbial community substantially different from the surrounding waters. Single cell genomics and metagenomics were employed to describe the succession of dominant bacterial groups during particle processing. Sinking particles were extracted from sediment traps at Station Aloha in the North Pacific Subtropical Gyre (NPSG) during two different trap deployments conducted in July and August 2012. The microbial communities in poisoned vs. live sediment traps differed significantly from one another, consistent with prior observations by Fontanez et al. (2015). Partial genomes from these communities were sequenced from cells belonging to the genus Arcobacter (commensalists potentially associated with protists such as Radiolaria), and Vibrio campbellii (a group previously reported to be associated with crustacea). These bacteria were found in the particle-associated communities at specific depths in both trap deployments, presumably due to their specific host-associations. Partial genomes were also sequenced from cells belonging to Idiomarina and Kangiella that were enriched in live traps over a broad depth range, that represented a motile copiotroph and a putatively non-motile algicidal saprophyte, respectively. Planktonic bacterial cells most likely caught in the wake of the particles belonging to Actinomarina and the SAR11 clade were also sequenced. Our results suggest that similar groups of eukaryote-associated bacteria are consistently found on sinking particles at different times, and that particle remineralization involves specific, reproducible bacterial succession events in oligotrophic ocean waters.
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Affiliation(s)
- Erik A Pelve
- Department of Cell and Molecular Biology-Molecular Evolution, Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Kristina M Fontanez
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Edward F DeLong
- Daniel K. Inoue Center for Microbial Oceanograpy: Research and Education, Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, United States
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18
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Ziegler M, Roik A, Porter A, Zubier K, Mudarris MS, Ormond R, Voolstra CR. Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea. MARINE POLLUTION BULLETIN 2016; 105:629-40. [PMID: 26763316 DOI: 10.1016/j.marpolbul.2015.12.045] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/25/2015] [Accepted: 12/22/2015] [Indexed: 05/20/2023]
Abstract
Coral-associated bacteria play an increasingly recognized part in coral health. We investigated the effect of local anthropogenic impacts on coral microbial communities on reefs near Jeddah, the largest city on the Saudi Arabian coast of the central Red Sea. We analyzed the bacterial community structure of water and corals (Pocillopora verrucosa and Acropora hemprichii) at sites that were relatively unimpacted, exposed to sedimentation & local sewage, or in the discharge area of municipal wastewaters. Coral microbial communities were significantly different at impacted sites: in both corals the main symbiotic taxon decreased in abundance. In contrast, opportunistic bacterial families, such as e.g. Vibrionaceae and Rhodobacteraceae, were more abundant in corals at impacted sites. In conclusion, microbial community response revealed a measurable footprint of anthropogenic impacts to coral ecosystems close to Jeddah, even though the corals appeared visually healthy.
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Affiliation(s)
- Maren Ziegler
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, 4700 King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Anna Roik
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, 4700 King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia
| | - Adam Porter
- College of Life and Environmental Sciences: Biosciences, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Khalid Zubier
- Faculty of Marine Science, King Abdulaziz University, PO Box 80207, Jeddah 21589, Saudi Arabia
| | - Mohammed S Mudarris
- Faculty of Marine Science, King Abdulaziz University, PO Box 80207, Jeddah 21589, Saudi Arabia
| | - Rupert Ormond
- Faculty of Marine Science, King Abdulaziz University, PO Box 80207, Jeddah 21589, Saudi Arabia; Centre for Marine Biotechnology and Biodiversity, School of Life Sciences, Heriot-Watt University, Riccarton, Edinburgh EH14 4AS, Scotland, United Kingdom
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, 4700 King Abdullah University of Science and Technology (KAUST), 23955-6900 Thuwal, Saudi Arabia.
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19
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Occurrence of Priming in the Degradation of Lignocellulose in Marine Sediments. PLoS One 2015; 10:e0143917. [PMID: 26633175 PMCID: PMC4669084 DOI: 10.1371/journal.pone.0143917] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/11/2015] [Indexed: 11/23/2022] Open
Abstract
More than 50% of terrestrially-derived organic carbon (terrOC) flux from the continents to the ocean is remineralised in the coastal zone despite its perceived high refractivity. The efficient degradation of terrOC in the marine environment could be fuelled by labile marine-derived material, a phenomenon known as “priming effect”, but experimental data to confirm this mechanism are lacking. We tested this hypothesis by treating coastal sediments with 13C-lignocellulose, as a proxy for terrOC, with and without addition of unlabelled diatom detritus that served as the priming inducer. The occurrence of priming was assessed by the difference in lignocellulose mineralisation between diatom-amended treatments and controls in aerobic sediment slurries. Priming of lignocellulose degradation was observed only at the initial stages of the experiment (day 7) and coincided with overall high microbial activity as exemplified by total CO2 production. Lignocellulose mineralisation did not differ consistently between diatom treatments and control for the remaining experimental time (days 14–28). Based on this pattern, we hypothesize that the faster initiation of lignocellulose mineralisation in diatom-amended treatments is attributed to the decomposition of accessible polysaccharide components within the lignocellulose complex by activated diatom degraders. The fact that diatom-degraders contributed to lignocellulose degradation was also supported by the different patterns in 13C-enrichment of phospholipid fatty acids between treatments. Although we did not observe differences between treatments in the total quantity of respired lignocellulose at the end of the experiment, differences in timing could be important in natural ecosystems where the amount of time that a certain compound is subject to aerobic degradation before burial to deeper anoxic sediments may be limited.
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Quantitative microbial ecology through stable isotope probing. Appl Environ Microbiol 2015; 81:7570-81. [PMID: 26296731 DOI: 10.1128/aem.02280-15] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/17/2015] [Indexed: 12/26/2022] Open
Abstract
Bacteria grow and transform elements at different rates, and as yet, quantifying this variation in the environment is difficult. Determining isotope enrichment with fine taxonomic resolution after exposure to isotope tracers could help, but there are few suitable techniques. We propose a modification to stable isotope probing (SIP) that enables the isotopic composition of DNA from individual bacterial taxa after exposure to isotope tracers to be determined. In our modification, after isopycnic centrifugation, DNA is collected in multiple density fractions, and each fraction is sequenced separately. Taxon-specific density curves are produced for labeled and nonlabeled treatments, from which the shift in density for each individual taxon in response to isotope labeling is calculated. Expressing each taxon's density shift relative to that taxon's density measured without isotope enrichment accounts for the influence of nucleic acid composition on density and isolates the influence of isotope tracer assimilation. The shift in density translates quantitatively to isotopic enrichment. Because this revision to SIP allows quantitative measurements of isotope enrichment, we propose to call it quantitative stable isotope probing (qSIP). We demonstrated qSIP using soil incubations, in which soil bacteria exhibited strong taxonomic variations in (18)O and (13)C composition after exposure to [(18)O]water or [(13)C]glucose. The addition of glucose increased the assimilation of (18)O into DNA from [(18)O]water. However, the increase in (18)O assimilation was greater than expected based on utilization of glucose-derived carbon alone, because the addition of glucose indirectly stimulated bacteria to utilize other substrates for growth. This example illustrates the benefit of a quantitative approach to stable isotope probing.
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