1
|
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.
Collapse
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
| |
Collapse
|
2
|
Purahong W, Ji L, Wu YT. Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing. MICROBIAL ECOLOGY 2024; 87:66. [PMID: 38700528 PMCID: PMC11068674 DOI: 10.1007/s00248-024-02372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/31/2024] [Indexed: 05/06/2024]
Abstract
Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.
Collapse
Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
| | - Li Ji
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle (Saale), Germany
- School of Forestry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Yu-Ting Wu
- Department of Forestry, National Pingtung University of Science and Technology, Pingtung, 91201, Taiwan.
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
| |
Collapse
|
3
|
Reiß F, Kiefer N, Purahong W, Borken W, Kalkhof S, Noll M. Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168689. [PMID: 38000743 DOI: 10.1016/j.scitotenv.2023.168689] [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: 08/19/2022] [Revised: 09/20/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and metabolically active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal internal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungal richness. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.
Collapse
Affiliation(s)
- Fabienne Reiß
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Nadine Kiefer
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Witoon Purahong
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
| | - Werner Borken
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Stefan Kalkhof
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany; Proteomics Unit, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Department of Applied Natural Sciences and Health, Coburg University of Applied Sciences and Arts, Coburg, Germany; Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany.
| |
Collapse
|
4
|
Groß C, Hossen S, Dittrich S, Knorr KH, Borken W, Noll M. Biological nitrogen fixation, diversity and community structure of diazotrophs in two mosses in 25 temperate forests. Environ Microbiol 2024; 26:e16555. [PMID: 38148519 DOI: 10.1111/1462-2920.16555] [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: 07/19/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
Many moss species are associated with nitrogen (N)-fixing bacteria (diazotrophs) that support the N supply of mosses. Our knowledge relates primarily to pristine ecosystems with low atmospheric N input, but knowledge of biological N fixation (BNF) and diazotrophic communities in mosses in temperate forests with high N deposition is limited. We measured BNF rates using the direct stable isotope method and studied the total and potentially active diazotrophic communities in two abundant mosses, Brachythecium rutabulum and Hypnum cupressiforme, both growing on lying deadwood trunks in 25 temperate forest sites. BNF rates in both mosses were similar to those observed in moss species of pristine ecosystems. H. cupressiforme fixed three times more N2 and exhibited lower diazotrophic richness than B. rutabulum. Frankia was the most prominent diazotroph followed by cyanobacteria Nostoc. Manganese, iron, and molybdenum contents in mosses were positively correlated with BNF and diazotrophic communities. Frankia maintained high BNF rates in H. cupressiforme and B. rutabulum even under high chronic N deposition in Central European forests. Moss N concentration and 15 N abundance indicate a rather minor contribution of BNF to the N nutrition of these mosses.
Collapse
Affiliation(s)
- Christina Groß
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Shakhawat Hossen
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| | - Sebastian Dittrich
- Biodiversity and Conservation, Technical University of Dresden, Tharandt, Germany
| | - Klaus-Holger Knorr
- Institute of Landscape Ecology, Ecohydrology and Biogeochemistry Group, University of Münster, Münster, Germany
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, Bayreuth, Germany
| | - Matthias Noll
- Institute for Bioanalysis, Coburg University of Applied Sciences and Arts, Coburg, Germany
| |
Collapse
|
5
|
Li Y, Ten MMZ, Tham CAT, Lim YX, Lu Y, Li D. Brassica rapa subsp. Chinensis juice enhances Bacillus subtilis selectively in leafy green production. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:229-238. [PMID: 36916773 PMCID: PMC10464693 DOI: 10.1111/1758-2229.13154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/03/2023] [Indexed: 05/06/2023]
Abstract
Bacillus subtilis (BS) is a well-known beneficial microorganism for plants but is not competitive in the plant rhizosphere microbiome. We report the selective support of Brassica rapa subsp. Chinensis (Xiao Bai Cai) juice (XBCJ) on BS both in hydroponic nutrient solution and the plant rhizosphere of lettuce. After 2 weeks of being inoculated in the lettuce rhizosphere, the Bacillus population was enumerated at 3.30 ± 0.07 log CFU/unit in the BS group and at 5.20 ± 0.39 log CFU/unit in the BS + XBCJ group (p < 0.05). Accordingly, lettuce crops from the BS + XBCJ group were significantly higher than the control group for all of the tested biomass-related parameters (p < 0.05). The treatment did not significantly affect the texture, colour, moisture contents, total phenolic contents, or antioxidant activities of the lettuce crops (p > 0.05). Non-target ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) suggested that phenolic compounds could be the key class of phytochemicals being responsible for the selectivity. High-throughput RNA-based 16S rRNA gene sequencing and analysis were performed to depict the influence of BS and XBCJ over the global microbiome compositions of plant rhizosphere.
Collapse
Affiliation(s)
- Yingyue Li
- Department of Food Science and TechnologyFaculty of Science, National University of SingaporeSingaporeSingapore
| | - Michelle Mei Zhen Ten
- Department of Food Science and TechnologyFaculty of Science, National University of SingaporeSingaporeSingapore
| | - Cliff An Ting Tham
- Department of Food Science and TechnologyFaculty of Science, National University of SingaporeSingaporeSingapore
| | - Yan Xi Lim
- Department of Food Science and TechnologyFaculty of Science, National University of SingaporeSingaporeSingapore
| | - Yuyun Lu
- Department of Food Science and TechnologyFaculty of Science, National University of SingaporeSingaporeSingapore
| | - Dan Li
- Department of Food Science and TechnologyFaculty of Science, National University of SingaporeSingaporeSingapore
| |
Collapse
|