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Carmichael MJ, Martinez M, Bräuer SL, Ardón M. Microbial Communities in Standing Dead Trees in Ghost Forests are Largely Aerobic, Saprophytic, and Methanotrophic. Curr Microbiol 2024; 81:229. [PMID: 38896154 PMCID: PMC11186919 DOI: 10.1007/s00284-024-03767-w] [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: 03/10/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Standing dead trees (snags) are recognized for their influence on methane (CH4) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH4 fluxes were highly variable (- 0.11-0.51 mg CH4 m-2 h-1). CH4 production was measured in three out of ten snags; whereas, CH4 consumption was measured in two out of ten snags. Potential CH4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH4 g-1 h-1, respectively. Four cores oxidized CH4 under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH4 g-1 h-1. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH4-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.
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Affiliation(s)
- Mary Jane Carmichael
- Departments of Biology and Environmental Studies, Hollins University, Roanoke, VA, 24020, USA.
| | - Melinda Martinez
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, 20708, USA
| | - Suzanna L Bräuer
- Department of Biology, Appalachian State University, Boone, NC, 28608, USA
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
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Bonilla-Espadas M, Zafrilla B, Lifante-Martínez I, Camacho M, Orgilés-Calpena E, Arán-Aís F, Bertazzo M, Bonete MJ. Selective Isolation and Identification of Microorganisms with Dual Capabilities: Leather Biodegradation and Heavy Metal Resistance for Industrial Applications. Microorganisms 2024; 12:1029. [PMID: 38792858 PMCID: PMC11124520 DOI: 10.3390/microorganisms12051029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/26/2024] Open
Abstract
Tanning, crucial for leather production, relies heavily on chromium yet poses risks due to chromium's oxidative conversion, leading to significant wastewater and solid waste generation. Physico-chemical methods are typically used for heavy metal removal, but they have drawbacks, prompting interest in eco-friendly biological remediation techniques like biosorption, bioaccumulation, and biotransformation. The EU Directive (2018/850) mandates alternatives to landfilling or incineration for industrial textile waste management, highlighting the importance of environmentally conscious practices for leather products' end-of-life management, with composting being the most researched and viable option. This study aimed to isolate microorganisms from tannery wastewater and identify those responsible for different types of tanned leather biodegradation. Bacterial shifts during leather biodegradation were observed using a leather biodegradation assay (ISO 20136) with tannery and municipal wastewater as the inoculum. Over 10,000 bacterial species were identified in all analysed samples, with 7 bacterial strains isolated from tannery wastewaters. Identification of bacterial genera like Acinetobacter, Brevundimonas, and Mycolicibacterium provides insights into potential microbial candidates for enhancing leather biodegradability, wastewater treatment, and heavy metal bioremediation in industrial applications.
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Affiliation(s)
- Manuela Bonilla-Espadas
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Basilio Zafrilla
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Irene Lifante-Martínez
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Mónica Camacho
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
| | - Elena Orgilés-Calpena
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Francisca Arán-Aís
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - Marcelo Bertazzo
- INESCOP-Footwear Technological Centre, 03600 Alicante, Spain; (M.B.-E.); (I.L.-M.); (E.O.-C.); (F.A.-A.); (M.B.)
| | - María-José Bonete
- Grupo Biotecnología de Extremófilos, Departamento de Bioquímica y Biología Molecular y Edafología y Química Agrícola, Universidad de Alicante, 03690 Alicante, Spain; (B.Z.); (M.C.)
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Yun W, Cho K, Jung J, Choi D. Aerobic and anoxic utilization of organic matter for flexible nitrite supply in nutrient conversion pathways based on anaerobic ammonium oxidation: Microbial interactive mechanism. BIORESOURCE TECHNOLOGY 2024; 397:130473. [PMID: 38387844 DOI: 10.1016/j.biortech.2024.130473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/18/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
This study investigated nutrient conversion pathways and corresponding interactive mechanisms in a mainstream partial-nitritation (PN)/anaerobic ammonium oxidation (anammox)/partial-denitrification-(PD)-enhanced biological phosphorus-removal (EBPR) (PN/A/PD-EBPR) process. A laboratory-scale sequencing batch reactor was operated for 301 days under different operational strategies. Mainstream PN/A/PD-EBPR was successfully operated with aerobic and anoxic utilization of organic matter. Aerobic utilization of organic matter was an effective strategy for conversion to denitrifying polyphosphate-accumulating organism-based phosphorus removal, referring to a biological reaction that outperformed nitrite-oxidizing bacteria. Aerobically adsorbed organic matter could be used as a carbon source for PD, which further enhanced nitrogen removal by PN/A. Ultimately, the interaction between complex nutrient conversion pathways served to achieve stable performance. High-throughput sequencing results elucidated the core microbe functioning in the mainstream PN/A/PD-EBPR process with respect to various nutrients. The outcomes of this study will be beneficial to those attempting to implement mainstream PN/A/PD-EBPR.
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Affiliation(s)
- Wonsang Yun
- Department of Environmental Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan-Si 38541 Gyeongbuk, South Korea
| | - Kyungjin Cho
- Center for Water Cycle Research, Korea Institute of Science and Technology, Seoul 02792, South Korea; Division of Energy & Environment Technology, KIST school, Korea University of Science and Technology (UST), Seoul 02792, South Korea
| | - Jinyoung Jung
- Department of Environmental Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan-Si 38541 Gyeongbuk, South Korea
| | - Daehee Choi
- Department of Environmental Engineering, Yeungnam University, 280 Daehak-Ro, Gyeongsan-Si 38541 Gyeongbuk, South Korea.
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Lazar CS, Schwab VF, Ueberschaar N, Pohnert G, Trumbore S, Küsel K. Microbial degradation and assimilation of veratric acid in oxic and anoxic groundwaters. Front Microbiol 2023; 14:1252498. [PMID: 37901809 PMCID: PMC10602745 DOI: 10.3389/fmicb.2023.1252498] [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: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, University of Quebec at Montreal (UQAM), Montreal, QC, Canada
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Valérie F. Schwab
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - Susan Trumbore
- Department Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Ecology, Friedrich Schiller University Jena, Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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Gagnon JC, Beauregard-Tousignant S, Marcil JS, Lazar CS. Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada. Genes (Basel) 2023; 14:1529. [PMID: 37628582 PMCID: PMC10454208 DOI: 10.3390/genes14081529] [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: 06/15/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.
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Affiliation(s)
- Jean-Christophe Gagnon
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
- Interuniversity Research Group in Limnology/Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Montréal, QC H3C 3P8, Canada
| | - Samuel Beauregard-Tousignant
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
| | - Jean-Sébastien Marcil
- Derena Geosciences, Quebec, QC G7A 3Y5, Canada;
- Ressources Utica Inc., Quebec, QC G1V 4M7, Canada
| | - Cassandre Sara Lazar
- Department of Biological Sciences, University of Québec at Montréal (UQAM), C.P. 8888, Succ. Centre-Ville, Montréal, QC H3C 3P8, Canada; (J.-C.G.); (S.B.-T.)
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Oren A, Garrity G. Notification of changes in taxonomic opinion previously published outside the IJSEM. List of changes in taxonomic opinion no. 36. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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