Exploring the diversity of extremely halophilic archaea in food-grade salts

Henriet, Olivier; Fourmentin, Jeanne; Delincé, Bruno; Mahillon, Jacques

doi:10.1016/j.ijfoodmicro.2014.08.019

Cited by 43 publications

(32 citation statements)

References 43 publications

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“…Despite this, Haloquadratum has been detected globally in hypersaline brines (Di Meglio et al, ; Oh, Porter, Russ, Burns, & Dyall‐Smith, ; Podell et al, ). A previous study of halite‐associated Archaea found Haloquadratum to be a very small component of the halite‐associated community, despite being highly abundant in the hypersaline brine that was the source of the halite (Henriet et al, ). Furthermore, Gramain et al () demonstrated that Haloquadratum resumed growth slowly after halite entombment compared with other haloarchaea, inferring that it is a relatively poor survivor in halite.…”

Section: Discussionmentioning

confidence: 99%

“…The halite-associated Archaea fulfil these criteria. These Archaea typically belong to the class Halobacteria (more commonly referred to as haloarchaea) and are a major component of halite endolith communities (Henriet, Fourmentin, Delinc e, & Mahillon, 2014). Their entombment into the brine inclusions of halite crystals is believed to be an escape mechanism from desiccation and the increasingly chaotropic conditions present in evaporating brines (Hallsworth et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

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Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization?

Clark

Mathieu²,

Mourot³

et al. 2017

Global Ecol. Biogeogr.

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Aim: Biogeographical regions are the fundamental geographical units for grouping Earth's biodiversity.Biogeographical regionalization has been demonstrated for many higher taxa, such as terrestrial plants and vertebrates, but not in microbial communities. Therefore, we sought to test empirically whether microbial communities, or taxa, show patterns consistent with biogeographical regionalization.Location: Within halite (NaCl) crystals from coastal solar salterns of western Europe, the Mediterranean and east Africa. Major taxa studied: Archaea.Methods: Using high-throughput Illumina amplicon sequencing, we generated the most highresolution characterization of halite-associated archaeal communities to date, using samples from 17 locations. We grouped communities into biogeographical clusters based on community turnover to test whether these communities show biogeographical regionalization. To examine whether individual taxa, rather than communities, show biogeographical patterns, we also tested whether the relative abundance of individual genera may be indicative of a community's biogeographical origins using machine learning methods, specifically random forest classification.Results: We found that the rate of community turnover was greatest over subregional spatial scales (< 500 km), whereas at regional spatial scales the turnover was independent of geographical distance. Biogeographical clusters of communities were either not statistically robust or lacked spatial coherence, inconsistent with biogeographical regionalization. However, we identified several archaeal genera that were good indicators of biogeographical origin, providing classification error rates of < 10%.Main conclusions: Overall, our results provide little support for the concept of biogeographical regions in these extremophilic microbial communities, despite the fact that some taxa do show biogeographical patterns. We suggest that variable dispersal ability among the halite-associated Archaea may disrupt biogeographical patterns at the community level, preventing the formation of biogeographical regions. This means that the processes that lead to the formation of biogeographical regions operate differentially on individual microbial taxa rather than on entire communities.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization?

Clark

Mathieu²,

Mourot³

et al. 2017

Global Ecol. Biogeogr.

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“…Microbial DNA extraction from salt samples was carried out using a slightly modified method as described in Henriet et al (2014). Afdera salt was used as a model.…”

Section: Methodsmentioning

confidence: 99%

“…However, some studies revealed that salt itself contains a wide range of halophilic organisms, including bacteria and archaea that are unique to these environments (Henriet et al, 2014) as well as salted and fermented foods (Park et al, 2009; Roh et al, 2010). In recent years, novel halophilic archaea namely Halopiger thermotololerans (Minegishi et al, 2016), Haloparvum alkalitolerans (Kondo et al, 2016), and Halarchaeum grantii (Shimane et al, 2015) were isolated from commercial salts using culture-based methods.…”

Section: Introductionmentioning

confidence: 99%

Diversity of Extremely Halophilic Archaeal and Bacterial Communities from Commercial Salts

et al. 2017

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Salting is one of the oldest food preservation techniques. However, salt is also the source of living halophilic microorganisms that may affect human health. In order to determine the microbial communities of commercial salts, an investigation were done using amplicon sequencing approach in four commercial salts: Ethiopian Afdera salt (EAS), Ethiopian rock salt (ERS), Korean Jangpan salt (KJS), and Korean Topan salt (KTS). Using domain-specific primers, a region of the 16S rRNA gene was amplified and sequenced using a Roche 454 instrument. The results indicated that these microbial communities contained 48.22–61.4% Bacteria, 37.72–51.26% Archaea, 0.51–0.86% Eukarya, and 0.005–0.009% unclassified reads. Among bacteria, the communities in these salts were dominated by the phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. Of the archaea, 91.58% belonged to the class Halobacteria, whereas the remaining 7.58, 0.83, and 0.01% were Nanoarchaea, Methanobacteria, and Thermococci, respectively. This comparison of microbial diversity in salts from two countries showed the presence of many archaeal and bacterial genera that occurred in salt samples from one country but not the other. The bacterial genera Enterobacter and Halovibrio were found only in Korean and Ethiopian salts, respectively. This study indicated the occurrence and diversity of halophilic bacteria and archaea in commercial salts that could be important in the gastrointestinal tract after ingestion.

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“…They are widely distributed in various hypersaline environments, from which they have been isolated. Solar salterns are one of the hypersaline environments inhabited by halophilic archaea and remain one of the primary sources of novel strains (Henriet et al, 2014;Viver et al, 2015). There are many solar salterns worldwide and natural salt is produced by slightly different methods at each site on a large or small scale.…”

mentioning

confidence: 99%

Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern

Mori

Nurcahyanto

Kawasaki

et al. 2016

International Journal of Systematic and Evolutionary Microbiology

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Exploring the diversity of extremely halophilic archaea in food-grade salts

Cited by 43 publications

References 43 publications

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization?

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization?

Diversity of Extremely Halophilic Archaeal and Bacterial Communities from Commercial Salts

Halobium palmae gen. nov., sp. nov., an extremely halophilic archaeon isolated from a solar saltern

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