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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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Lee J, Um S, Kim SH. Metabolomic analysis of halotolerant endophytic bacterium Salinivibrio costicola isolated from Suaeda maritima (L.) dumort. Front Mol Biosci 2022; 9:967945. [PMID: 36120548 PMCID: PMC9478568 DOI: 10.3389/fmolb.2022.967945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, the Salinivibrio costicola strain was isolated from Suaeda maritima (L.) Dumort. collected in Sinan, Republic of Korea. The endophytic characteristics of the Gram-negative bacterium S. costicola were verified with metagenomics sequencing of S. maritima. S. costicola was cultivated for 3 days in a liquid medium with 3.3% sea salt and analyzed the metabolites produced by the strain cultured in five different bacterial cultivation media. From the bacterial cultures, polyhydroxybutyrate derivatives were detected using high-resolution mass spectrometry, and three major compounds were isolated by high-performance liquid chromatography. The chemical structures of the compounds were elucidated using nuclear magnetic resonance and MS analyses. The relationship between the compounds was confirmed with Global Natural Product Social Molecular Networking, which showed clustering of the compounds. From the S. maritima extract, polyhydroxybutyrate derivatives produced by S. costicola were detected as being accumulated in the host plant.
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Favila N, Madrigal-Trejo D, Legorreta D, Sánchez-Pérez J, Espinosa-Asuar L, Eguiarte LE, Souza V. MicNet toolbox: Visualizing and unraveling a microbial network. PLoS One 2022; 17:e0259756. [PMID: 35749381 PMCID: PMC9231805 DOI: 10.1371/journal.pone.0259756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 04/05/2022] [Indexed: 11/19/2022] Open
Abstract
Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.
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Affiliation(s)
- Natalia Favila
- Laboratorio de Inteligencia Artificial, Ixulabs, Mexico City, Mexico
| | - David Madrigal-Trejo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Daniel Legorreta
- Laboratorio de Inteligencia Artificial, Ixulabs, Mexico City, Mexico
| | - Jazmín Sánchez-Pérez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Laura Espinosa-Asuar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Centro de Estudios del Cuaternario de Fuego-Patagonia y Antártica (CEQUA), Punta Arenas, Chile
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Wallenius AJ, Dalcin Martins P, Slomp CP, Jetten MSM. Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments. Front Microbiol 2021; 12:631621. [PMID: 33679659 PMCID: PMC7935538 DOI: 10.3389/fmicb.2021.631621] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/29/2021] [Indexed: 12/05/2022] Open
Abstract
Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.
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Affiliation(s)
- Anna J. Wallenius
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Paula Dalcin Martins
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Caroline P. Slomp
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, Netherlands
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Khalmuratova I, Choi DH, Woo JR, Jeong MJ, Oh Y, Kim YG, Lee IJ, Choo YS, Kim JG. Diversity and Plant Growth-Promoting Effects of Fungal Endophytes Isolated from Salt-Tolerant Plants. J Microbiol Biotechnol 2020; 30:1680-1687. [PMID: 32876070 PMCID: PMC9728227 DOI: 10.4014/jmb.2006.06050] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/15/2022]
Abstract
Fungal endophytes are symbiotic microorganisms that are often found in asymptomatic plants. This study describes the genetic diversity of the fungal endophytes isolated from the roots of plants sampled from the west coast of Korea. Five halophytic plant species, Limonium tetragonum, Suaeda australis, Suaeda maritima, Suaeda glauca Bunge, and Phragmites australis, were collected from a salt marsh in Gochang and used to isolate and identify culturable, root-associated endophytic fungi. The fungal internal transcribed spacer (ITS) region ITS1-5.8S-ITS2 was used as the DNA barcode for the classification of these specimens. In total, 156 isolates of the fungal strains were identified and categorized into 23 genera and two phyla (Ascomycota and Basidiomycota), with Dothideomycetes and Sordariomycetes as the predominant classes. The genus Alternaria accounted for the largest number of strains, followed by Cladosporium and Fusarium. The highest diversity index was obtained from the endophytic fungal group associated with the plant P. australis. Waito-C rice seedlings were treated with the fungal culture filtrates to analyze their plant growth-promoting capacity. A bioassay of the Sm-3-7-5 fungal strain isolated from S. maritima confirmed that it had the highest plant growth-promoting capacity. Molecular identification of the Sm-3-7-5 strain revealed that it belongs to Alternaria alternata and is a producer of gibberellins. These findings provided a fundamental basis for understanding the symbiotic interactions between plants and fungi.
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Affiliation(s)
- Irina Khalmuratova
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 4566, Republic of Korea
| | - Doo-Ho Choi
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 4566, Republic of Korea
| | - Ju-Ri Woo
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 4566, Republic of Korea
| | - Min-Ji Jeong
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 4566, Republic of Korea
| | - Yoosun Oh
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 4566, Republic of Korea
| | - Young-Guk Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 4566, Republic of Korea
| | - In-Jung Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeon-Sik Choo
- Department of Biology, College of National Sciences, Kyungpook National University, Daeagu 41566, Republic of Korea
| | - Jong-Guk Kim
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 4566, Republic of Korea,Corresponding author Phone: +82-53-950-5379 Fax: +82-53-955-5379 E-mail:
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Kolton M, Rolando JL, Kostka JE. Elucidation of the rhizosphere microbiome linked to Spartina alterniflora phenotype in a salt marsh on Skidaway Island, Georgia, USA. FEMS Microbiol Ecol 2020; 96:5813622. [PMID: 32227167 DOI: 10.1093/femsec/fiaa026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/23/2020] [Indexed: 01/04/2023] Open
Abstract
Smooth cordgrass, Spartina alterniflora, dominates salt marshes on the east coast of the United States. While the physicochemical cues affecting S. alterniflora productivity have been studied intensively, the role of plant-microbe interactions in ecosystem functioning remains poorly understood. Thus, in this study, the effects of S. alterniflora phenotype on the composition of archaeal, bacterial, diazotrophic and fungal communities were investigated. Overall, prokaryotic communities were more diverse and bacteria were more abundant in the areas colonized by the tall plant phenotype in comparison to those of short plant phenotype. Diazotrophic methanogens (Methanomicrobia) preferentially colonized the area of the short plant phenotype. Putative iron-oxidizing Zetaproteobacteria and sulfur-oxidizing Campylobacteria were identified as indicator species in the rhizosphere of tall and short plant phenotypes, respectively. Finally, while diazotrophic populations shaped microbial interactions in the areas colonized by the tall plant phenotype, fungal populations filled this role in the areas occupied by the short plant phenotype. The results here demonstrate that S. alterniflora phenotype and proximity to the root zone are selective forces dictating microbial community assembly. Results further reveal that reduction-oxidation chemistry is a major factor driving the selection of belowground microbial populations in salt marsh habitats.
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Affiliation(s)
- Max Kolton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - José L Rolando
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study. Genomics 2020; 112:4968-4979. [PMID: 32911024 DOI: 10.1016/j.ygeno.2020.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/15/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution.
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Mason LM, Eagar A, Patel P, Blackwood CB, DeForest JL. Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest. J Appl Microbiol 2020; 130:109-122. [PMID: 32619072 DOI: 10.1111/jam.14761] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 06/17/2020] [Accepted: 06/24/2020] [Indexed: 01/20/2023]
Abstract
AIMS The soil microbial community plays a critical role in increasing phosphorus (P) availability in low-P, weathered soils by "mining" recalcitrant organic P through the production of phosphatase enzymes. However, there is a lack of data on the fungal and bacterial taxa which are directly involved in P mining, which could also serve as potential microbial bioindicators of low P availability. METHODS AND RESULTS Leveraging a 5-year P enrichment experiment on low-P forest soils, high-throughput sequencing was used to profile the microbial community to determine which taxa associate closely with P availability. We hypothesized that there would be a specialized group of soil micro-organisms that could access recalcitrant P and whose presence could serve as a bioindicator of P mining. Community profiling revealed several candidate bioindicators of P mining (Russulales, Acidobacteria Subgroup 2, Acidobacteriales, Obscuribacterales and Solibacterales), whose relative abundance declined with elevated P and had a significant, positive association with phosphatase production. In addition, we identified candidate bioindicators of high P availability (Mytilinidales, Sebacinales, Chitinophagales, Cytophagales, Saccharimonadales, Opitulales and Gemmatales). CONCLUSIONS This research provides evidence that mitigating P limitation in this ecosystem may be a specialized trait and is mediated by a few microbial taxa. SIGNIFICANCE AND IMPACT OF THE STUDY Here, we characterize Orders of soil microbes associated with manipulated phosphorus availability in forest soils to determine bioindicator candidates for phosphorus. Likewise, we provide evidence that the microbial trait to utilize recalcitrant organic forms of P (e.g. P mining) is likely a specialized trait and not common to all members of the soil microbial community. This work further elucidates the role that a complex microbial community plays in the cycling of P in low-P soils, and provides evidence for future studies on microbial linkages to human-induced ecosystem changes.
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Affiliation(s)
- L M Mason
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
| | - A Eagar
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - P Patel
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - C B Blackwood
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - J L DeForest
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, USA
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