Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information

Barberán, Albert; Velazquez, Hildamarie Caceres; Jones, Stuart; Fierer, Noah

doi:10.1128/msphere.00237-17

Cited by 76 publications

(104 citation statements)

References 62 publications

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“…In most studies, the questions of interest correspond to function, so we propose that functional diversity receive attention. Microbial functional ecology is at a key moment of its structuring, novel tools are being continuously developed (Langille et al, ; Takami, ), data are made available (Barberán et al, ; Huse et al, ; Meyer et al., ), and pioneers are paving the way for a rapidly advancing field (Fierer et al, ; Louca et al, ; Raguideau et al, ). In order to fulfill its promises, the field of microbial functional ecology will require solid foundations and we hope the synthesis and perspectives presented here will stimulate the thought and discussions toward this goal.…”

Section: Discussionmentioning

confidence: 99%

Microbial functional diversity: From concepts to applications

Escalas

Hale

Voordeckers

et al. 2019

Ecology and Evolution

162

110

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Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

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Section: Discussionmentioning

confidence: 99%

Microbial functional diversity: From concepts to applications

Escalas

Hale

Voordeckers

et al. 2019

Ecology and Evolution

162

110

View full text Add to dashboard Cite

show abstract

“…Representative partial 16S rRNA gene sequences from each phylotype were matched against full length 16S rRNA gene sequences from the IJSEM phenotypic database (Barberán et al. ) and from the Integrated Microbial Genomes (IMG) database (Markowitz et al. ).…”

Section: Methodsmentioning

confidence: 99%

“…However, the selected traits typically show a strong phylogenetic signal and are generally conserved across broader taxa and lineages (Barberán et al. ).…”

Section: Methodsmentioning

confidence: 99%

“…We were able to match a total of 1,461 16S rRNA gene sequences of dust phylotypes (including 518 Proteobacteria, 428 Actinobacteria, 293 Firmicutes, and 222 Bacteroidetes) to 2,487 unique full‐length 16S rRNA gene sequences in the IJSEM phenotypic database (Barberán et al. ). We assessed how the AOO varied in relation to the following phenotypic traits: oxygen tolerance, sporulation, pigmentation, Gram stain reaction, and source habitat.…”

Section: Methodsmentioning

confidence: 99%

“…Here, source habitat refers to the reported isolation source of a given strain from the IJSEM phenotypic database (Barberán et al. ). We selected these traits because we expected that these traits may influence dispersal and colonization capabilities.…”

Section: Methodsmentioning

confidence: 99%

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Variation in range size and dispersal capabilities of microbial taxa

Choudoir

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Menninger

et al. 2018

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Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes. However, contrary to expectations, those microbial taxa that were locally abundant did not necessarily have larger range sizes. The observed differences in microbial range sizes were generally predictable from taxonomic identity, phenotypic traits, genomic attributes, and habitat preferences, findings that provide insight into the factors shaping patterns of microbial biogeography.

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Development of a microbe domestication pod (MD Pod) for in situ cultivation of micro‐encapsulated marine bacteria

Alkayyali

Pope

Wheatley

et al. 2020

Biotech & Bioengineering

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Microbial marine natural products hold significant potential for the discovery of new bioactive therapeutics such as antibiotics. Unfortunately, this discovery is hindered by the inability to culture the majority of microbes using traditional laboratory approaches. While many new methods have been developed to increase cultivability, a high‐throughput in situ incubation chamber capable of simultaneously isolating individual microbes while allowing cellular communication has not previously been reported. Development of such a device would expedite the discovery of new microbial taxa and, thus, facilitate access to their associated natural products. In this study, this concept is achieved by the development of a new device termed by the authors as the microbe domestication (MD) Pod. The MD Pod enables single‐cell cultivation by isolating marine bacterial cells in agarose microbeads produced using microfluidics, while allowing potential transmission of chemical signals between cells during in situ incubation in a chamber, or “Pod,” that is deployed in the environment. The design of the MD Pod was optimized to ensure the use of biocompatible materials, allow for simple assembly in a field setting, and maintain sterility throughout incubation. The encapsulation process was designed to ensure that the viability of marine sediment bacteria was not adversely impacted by the encapsulation process. The process was validated using representative bacteria isolated from temperate marine sediment samples: Marinomonas polaris, Psychrobacter aquimaris, and Bacillus licheniformis. The overall process appeared to promote metabolic activity of most representative species. Thus, microfluidic encapsulation of marine bacteria and subsequent in situ incubation in the MD Pod is expected to accelerate marine natural products discovery by increasing the cultivability of marine bacteria.

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Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information

Cited by 76 publications

References 62 publications

Microbial functional diversity: From concepts to applications

Microbial functional diversity: From concepts to applications

Variation in range size and dispersal capabilities of microbial taxa

Development of a microbe domestication pod (MD Pod) for in situ cultivation of micro‐encapsulated marine bacteria

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