Microbial biogeography of 1,000 geothermal springs in New Zealand

Power, Jean F.; Carere, Carlo R.; Lee, Charles K.; Wakerley, Georgia L.J.; Evans, David W.; Button, Mathew; White, Duncan; Climo, Melissa; Hinze, Annika; Morgan, Xochitl C.; McDonald, Ian R.; Cary, S. Craig; Stott, Matthew B.

doi:10.1101/247759

Cited by 7 publications

(10 citation statements)

References 82 publications

(101 reference statements)

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“…Several studies have analyzed the impact of pH on community composition in hot springs. The most extensive ones are Inskeep, Jay, Tringe, Herrgård, and Rusch () who studied 20 samples from YNP, Sharp et al () who analyzed 36 samples from the Taupo hydrothermal field in New Zealand and in western Canada, and Power et al () who analyzed 925 hot springs from the Taupo field. In all these cases springs could be classified as acid (pH = 2–4) or circum‐neutral (pH = 6–8).…”

Section: Results and Discusionmentioning

confidence: 99%

“…It seems than in their case the differences in pH were so large that its importance was obvious, while in our case we had to resort to statistical analysis to show the same effect. Power et al () had the largest data set ever studied. Once more, their samples fit in two pH clusters, those with acid pH (1–3) and those with neutral or alkaline pH (5–9).…”

Section: Results and Discusionmentioning

confidence: 99%

“…In effect, microorganisms must be adapted to live at high temperatures in order to thrive in such environments and the main groups of Bacteria and Archaea living at different temperature ranges are usually the same in very distant springs. Usually Cyanobacteria , Chloroflexi , Deinococcus‐Thermus , and Aquificae are found as temperature increases in springs in North America, New Zealand, or Tibet (Jiménez et al, ; Power et al, ; Sharp et al, ; Wang et al, ). The genera involved are many times the same ones and they show preference for growth at temperatures close to (or slightly below) those in situ (Zeikus & Brock, ).…”

Section: Introductionmentioning

confidence: 99%

“…However, these authors also found that richness increased with increasing pH, indicating that this variable also had an influence on the diversity. Power et al () analyzed around 1,000 samples from hot springs in New Zealand and concluded that temperature only had an impact above 70°C, while pH was the main factor determining diversity in the temperature range between 20 and 70 degrees. In both studies samples grouped in two distinct clusters with pH values around 3–4 on the one hand and around 7 on the other.…”

Section: Introductionmentioning

confidence: 99%

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The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica

et al. 2019

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We used the 16S rRNA gene pyrosequencing approach to investigate the microbial diversity and community composition in several Costa Rican hot springs alongside the latitudinal axis of the country, with a range of temperatures (37–63°C), pH (6–7.5) and other geochemical conditions. A principal component analyses of the physicochemical parameters showed the samples were separated into three geochemically distinct habitats associated with the location (North, Central, and South). Cyanobacteria and Chloroflexi comprised 93% of the classified community, the former being the most abundant phylum in all samples except for Rocas Calientes 1, (63°C, pH 6), where Chloroflexi and Deinococcus‐Thermus represented 84% of the OTUs. Chloroflexi were more abundant as temperature increased. Proteobacteria, Bacteriodetes and Deinococcus‐Thermus comprised 5% of the OTUs represented. Other Phyla were present in very small percentages (<1%). A LINKTREE analysis showed that the community structure of the mats was shaped primarily by pH, separating samples with pH > 6.6 from samples with pH < 6.4. Thus, both pH and temperature were relevant for community composition even within the moderate ranges of variables studied. These results provide a basis for an understanding of the physicochemical influences in moderately thermophilic microbial mats.

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Section: Results and Discusionmentioning

confidence: 99%

Section: Results and Discusionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica

et al. 2019

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“…In part, this is due to the fact that the samples and lakes included in this analysis are limited in number and are geographically close to each other [22, 24, 25, 36]. Therefore, for a more thorough analysis, larger datasets from more variable sites would be neccessary, as currently only available from large-scale environmental sequencing efforts such as the Earth Microbiome Project [37] or the 1000 Springs Project [28, 38]. Nevertheless, on the basis of the results presented here, experiments can be designed in order to illuminate the mechanistic and causal relationships between environmental features and microbial biodiversity.…”

Section: Discussionmentioning

confidence: 99%

SEDE-GPS: socio-economic data enrichment based on GPS information

Sperlea¹,

Füser²,

Boenigk³

et al. 2018

BMC Bioinformatics

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BackgroundMicrobes are essentail components of all ecosystems because they drive many biochemical processes and act as primary producers. In freshwater ecosystems, the biodiversity in and the composition of microbial communities can be used as indicators for environmental quality. Recently, some environmental features have been identified that influence microbial ecosystems. However, the impact of human action on lake microbiomes is not well understood. This is, in part, due to the fact that environmental data is, albeit theoretically accessible, not easily available.ResultsIn this work, we present SEDE-GPS, a tool that gathers data that are relevant to the environment of an user-provided GPS coordinate. To this end, it accesses a list of public and corporate databases and aggregates the information in a single file, which can be used for further analysis. To showcase the use of SEDE-GPS, we enriched a lake microbial ecology sequencing dataset with around 18,000 socio-economic, climate, and geographic features. The sources of SEDE-GPS are public databases such as Eurostat, the Climate Data Center, and OpenStreetMap, as well as corporate sources such as Twitter. Using machine learning and feature selection methods, we were able to identify features in the data provided by SEDE-GPS that can be used to predict lake microbiome alpha diversity.ConclusionThe results presented in this study show that SEDE-GPS is a handy and easy-to-use tool for comprehensive data enrichment for studies of ecology and other processes that are affected by environmental features. Furthermore, we present lists of environmental, socio-economic, and climate features that are predictive for microbial biodiversity in lake ecosystems. These lists indicate that human action has a major impact on lake microbiomes. SEDE-GPS and its source code is available for download at http://SEDE-GPS.heiderlab.deElectronic supplementary materialThe online version of this article (10.1186/s12859-018-2419-4) contains supplementary material, which is available to authorized users.

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Cultivation strategies for prokaryotes from extreme environments

Yang

Lian

Liu

et al. 2023

iMeta

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The great majority of microorganisms are as‐yet‐uncultivated, mostly found in extreme environments. High‐throughput sequencing provides data‐rich genomes from single‐cell and metagenomic techniques, which has enabled researchers to obtain a glimpse of the unexpected genetic diversity of “microbial dark matter.” However, cultivating microorganisms from extreme environments remains essential for dissecting and utilizing the functions of extremophiles. Here, we provide a straightforward protocol for efficiently isolating prokaryotic microorganisms from different extreme habitats (thermal, xeric, saline, alkaline, acidic, and cryogenic environments), which was established through previous successful work and our long‐term experience in extremophile resource mining. We propose common processes for extremophile isolation at first and then summarize multiple cultivation strategies for recovering prokaryotic microorganisms from extreme environments and meanwhile provide specific isolation tips that are always overlooked but important. Furthermore, we propose the use of multi‐omics‐guided microbial cultivation approaches for culturing these as‐yet‐uncultivated microorganisms and two examples are provided to introduce how these approaches work. In summary, the protocol allows researchers to significantly improve the isolation efficiency of pure cultures and novel taxa, which therefore paves the way for the protection and utilization of microbial resources from extreme environments.

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Microbial biogeography of 1,000 geothermal springs in New Zealand

Cited by 7 publications

References 82 publications

The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica

The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica

SEDE-GPS: socio-economic data enrichment based on GPS information

Cultivation strategies for prokaryotes from extreme environments

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