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Lemke M, DeSalle R. The Next Generation of Microbial Ecology and Its Importance in Environmental Sustainability. MICROBIAL ECOLOGY 2023; 85:781-795. [PMID: 36826587 PMCID: PMC10156817 DOI: 10.1007/s00248-023-02185-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/24/2023] [Indexed: 05/04/2023]
Abstract
Collectively, we have been reviewers for microbial ecology, genetics and genomics studies that include environmental DNA (eDNA), microbiome studies, and whole bacterial genome biology for Microbial Ecology and other journals for about three decades. Here, we wish to point out trends and point to areas of study that readers, especially those moving into the next generation of microbial ecology research, might learn and consider. In this communication, we are not saying the work currently being accomplished in microbial ecology and restoration biology is inadequate. What we are saying is that a significant milestone in microbial ecology has been reached, and approaches that may have been overlooked or were unable to be completed before should be reconsidered in moving forward into a new more ecological era where restoration of the ecological trajectory of systems has become critical. It is our hope that this introduction, along with the papers that make up this special issue, will address the sense of immediacy and focus needed to move into the next generation of microbial ecology study.
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Affiliation(s)
- Michael Lemke
- Department of Biology, University of Illinois at Springfield, Springfield, IL, USA.
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| | - Rob DeSalle
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
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Loera-Muro A, Caamal-Chan MG, Castellanos T, Luna-Camargo A, Aguilar-Díaz T, Barraza A. Growth effects in oregano plants ( Origanum vulgare L.) assessment through inoculation of bacteria isolated from crop fields located on desert soils. Can J Microbiol 2020; 67:381-395. [PMID: 33136463 DOI: 10.1139/cjm-2020-0352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacteria can establish beneficial interactions with plants by acting as growth promoters and enhancing stress tolerance during plant interactions. Likewise, bacteria can develop multispecies communities where multiple interactions are possible. In this work, we assessed the physiological effects of three bacteria isolated from an arid environment (Bacillus niacini, Bacillus megaterium, and Moraxella osloensis) applied as single species or as a consortium on oregano (Origanum vulgare L.) plants. Moreover, we assessed the quorum-sensing (QS) signaling activity to determine the molecular communication between plant-growth-promoting bacteria. The plant inoculation with B. megaterium showed a positive effect on morphometric and physiologic parameters. However, no synergistic effects were observed when a bacterial consortium was inoculated. Likewise, activation of QS signaling in biofilm assays was observed only for interspecies interaction within the Bacillus genus, not for either interaction with M. osloensis. These results suggest a neutral or antagonistic interaction for interspecific bacterial biofilm establishment, as well as for the interaction with oregano plants when bacteria were inoculated in a consortium. In conclusion, we were able to determine that the bacterial interactions are not always positive or synergistic, but they also might be neutral or antagonistic.
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Affiliation(s)
- Abraham Loera-Muro
- CONACYT - Centro de Investigaciones Biológicas del Noroeste, S.C., Instituto Politécnico Nacional, 195 Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, México
| | - María Goretty Caamal-Chan
- CONACYT - Centro de Investigaciones Biológicas del Noroeste, S.C., Instituto Politécnico Nacional, 195 Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, México
| | - Thelma Castellanos
- Centro de Investigaciones Biológicas del Noroeste, S.C., Instituto Politécnico Nacional, 195 Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
| | - Angélica Luna-Camargo
- Instituto Tecnológico de La Paz, 4720 Boulevard Forjadores de Baja California Sur, 8 de Octubre 2da Secc, La Paz, Baja California Sur, C.P. 23080, Mexico
| | - Trinidad Aguilar-Díaz
- Centro de Investigaciones Biológicas del Noroeste, S.C., Instituto Politécnico Nacional, 195 Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, Mexico
| | - Aarón Barraza
- CONACYT - Centro de Investigaciones Biológicas del Noroeste, S.C., Instituto Politécnico Nacional, 195 Playa Palo de Santa Rita Sur, La Paz, Baja California Sur, C.P. 23096, México
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Under-detection of endospore-forming Firmicutes in metagenomic data. Comput Struct Biotechnol J 2015; 13:299-306. [PMID: 25973144 PMCID: PMC4427659 DOI: 10.1016/j.csbj.2015.04.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/06/2015] [Accepted: 04/18/2015] [Indexed: 11/24/2022] Open
Abstract
Microbial diversity studies based on metagenomic sequencing have greatly enhanced our knowledge of the microbial world. However, one caveat is the fact that not all microorganisms are equally well detected, questioning the universality of this approach. Firmicutes are known to be a dominant bacterial group. Several Firmicutes species are endospore formers and this property makes them hardy in potentially harsh conditions, and thus likely to be present in a wide variety of environments, even as residents and not functional players. While metagenomic libraries can be expected to contain endospore formers, endospores are known to be resilient to many traditional methods of DNA isolation and thus potentially undetectable. In this study we evaluated the representation of endospore-forming Firmicutes in 73 published metagenomic datasets using two molecular markers unique to this bacterial group (spo0A and gpr). Both markers were notably absent in well-known habitats of Firmicutes such as soil, with spo0A found only in three mammalian gut microbiomes. A tailored DNA extraction method resulted in the detection of a large diversity of endospore-formers in amplicon sequencing of the 16S rRNA and spo0A genes. However, shotgun classification was still poor with only a minor fraction of the community assigned to Firmicutes. Thus, removing a specific bias in a molecular workflow improves detection in amplicon sequencing, but it was insufficient to overcome the limitations for detecting endospore-forming Firmicutes in whole-genome metagenomics. In conclusion, this study highlights the importance of understanding the specific methodological biases that can contribute to improve the universality of metagenomic approaches. Endospore formers were under-detected by profile analysis of sporulation genes in metagenomes. Endospore formers were absent even from those habitats known to harbor them. A tailored DNA extraction method improved detection in amplicon sequencing. Ameliorated DNA extraction did not improve shotgun classification. Endospore-formers represent an undetectable community fraction by metagenomic approaches.
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Draft Genome Sequence of the Nicotinate-Metabolizing Soil Bacterium Bacillus niacini DSM 2923. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01251-14. [PMID: 25477409 PMCID: PMC4256190 DOI: 10.1128/genomea.01251-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacillus niacini is a member of a small yet diverse group of bacteria able to catabolize nicotinic acid. We report here the availability of a draft genome for B. niacini, which we will use to understand the evolution of its namesake phenotype, which appears to be unique among the species in its phylogenetic neighborhood.
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Jones CM, Welsh A, Throbäck IN, Dörsch P, Bakken LR, Hallin S. Phenotypic and genotypic heterogeneity among closely related soil-borne N2- and N2O-producing Bacillus isolates harboring the nosZ gene. FEMS Microbiol Ecol 2011; 76:541-52. [DOI: 10.1111/j.1574-6941.2011.01071.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Mandic-Mulec I, Prosser JI. Diversity of Endospore-forming Bacteria in Soil: Characterization and Driving Mechanisms. SOIL BIOLOGY 2011. [DOI: 10.1007/978-3-642-19577-8_2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Tzeneva VA, Li Y, Felske ADM, de Vos WM, Akkermans ADL, Vaughan EE, Smidt H. Development and application of a selective PCR-denaturing gradient gel electrophoresis approach to detect a recently cultivated Bacillus group predominant in soil. Appl Environ Microbiol 2004; 70:5801-9. [PMID: 15466517 PMCID: PMC522134 DOI: 10.1128/aem.70.10.5801-5809.2004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The worldwide presence of a hitherto-nondescribed group of predominant soil microorganisms related to Bacillus benzoevorans was analyzed after development of two sets of selective primers targeting 16S rRNA genes in combination with denaturing gradient gel electrophoresis (DGGE). The high abundance and cultivability of at least some of these microorganisms makes them an appropriate subject for studies on their biogeographical dissemination and diversity. Since cultivability can vary significantly with the physiological state and even between closely related strains, we developed a culture-independent 16S rRNA gene-targeted DGGE fingerprinting protocol for the detection of these bacteria from soil samples. The composition of the B. benzoevorans relatives in the soil samples from The Netherlands, Bulgaria, Russia, Pakistan, and Portugal showed remarkable differences between the different countries. Differences in the DGGE profiles of these communities in archived soil samples from the Dutch Wieringermeer polder were observed over time during which a shift from anaerobic to aerobic and from saline to freshwater conditions occurred. To complement the molecular methods, we additionally cultivated B. benzoevorans-related strains from all of the soil samples. The highest number of B. benzoevorans relatives was found in the soils from the northern part of The Netherlands. The present study contributes to our knowledge of the diversity and abundance of this interesting group of microbes in soils throughout the world.
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Affiliation(s)
- Vesela A Tzeneva
- Laboratory of Microbiology, Wageningen University, Hesselink van Suchtelenweg 4, NL-6703 CT Wageningen, The Netherlands.
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