Microbial Community Analysis of Colored Snow from an Alpine Snowfield in Northern Japan Reveals the Prevalence of Betaproteobacteria with Snow Algae

Terashima, Masanao; Umezawa, Kazuhiro; Mori, Shoichi; Kojima, Hisaya; Fukui, Manabu

doi:10.3389/fmicb.2017.01481

Cited by 45 publications

(47 citation statements)

References 100 publications

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“…and Sphingobacteriaceae spp. (34,35) (see Table S1 in the supplemental material). We also observed several fungal phylotypes belonging to the Mucorales and Mortierellales orders that clustered in module 4 (Table S1).…”

Section: Resultsmentioning

confidence: 99%

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Carini

Delgado‐Baquerizo

Hinckley

et al. 2020

mBio

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Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes. IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.

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Section: Resultsmentioning

confidence: 99%

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Carini

Delgado‐Baquerizo

Hinckley

et al. 2020

mBio

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“…Explorations of the bacterial community structure on differently colored snowfields revealed Solitalea koreensi ( Sphingobacteriaceae ) and other common inhabitants of polar and alpine environments. They are typical indicators for a highly specialized community in psychrophilic environments [ 46 , 54 – 56 ]. The two prevalent bacterial phyla Proteobacteria and Bacteroidetes share the ability to rapidly degrade organic matter which may underpin a potential direct transfer of organic carbon from algae to bacteria [ 57 ].…”

Section: Discussionmentioning

confidence: 99%

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities

et al. 2020

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Mutualistic interactions within microbial assemblages provide a survival strategy under extreme conditions; however, little is known about the complexity of interaction networks in multipartite, free-living communities. In the present study, the interplay within algae-dominated microbial communities exposed to harsh environmental influences in the Austrian Alps was assessed in order to reveal the interconnectivity of eukaryotic and prokaryotic inhabitants. All analyzed snowfields harbored distinct microbial communities. Network analyses revealed that mutual exclusion prevailed among microalgae in the alpine environment, while bacteria were mainly positively embedded in the interaction networks. Especially members of Proteobacteria , with a high prevalence of Oxalobacteraceae , Pseudomonadaceae , and Sphingomonadaceae showed genus-specific co-occurrences with distinct microalgae. Co-cultivation experiments with algal and bacterial isolates confirmed beneficial interactions that were predicted based on the bioinformatic analyses; they resulted in up to 2.6-fold more biomass for the industrially relevant microalga Chlorella vulgaris , and up to 4.6-fold increase in biomass for the cryophilic Chloromonas typhlos . Our findings support the initial hypothesis that microbial communities exposed to adverse environmental conditions in alpine systems harbor inter-kingdom supportive capacities. The insights into mutualistic inter-kingdom interactions and the ecology of microalgae within complex microbial communities provide explanations for the prevalence and resilience of such assemblages in alpine environments.

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“…and Sphingobacteriaceae spp. (32, 33) (Supplementary Table 1). We also observed several fungal phylotypes belonging to the Mucorales and Mortierellales orders that clustered in module 4 (Supplementary Table 1).…”

Section: Resultsmentioning

confidence: 99%

Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities

Carini

Delgado‐Baquerizo

Hinckley

et al. 2018

Preprint

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32Few studies have comprehensively investigated the temporal variability in soil microbial 33 communities despite widespread recognition that the belowground environment is 34 dynamic. In part, this stems from the challenges associated with the high degree of 35 spatial heterogeneity in soil microbial communities and because the presence of relic 36 DNA (DNA from non-living cells) may dampen temporal signals. Here we disentangle 37 the relationships among spatial, temporal, and relic DNA effects on bacterial, archaeal, 38 and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. 39 We intensively sampled plots on each hillslope over six months to discriminate between 40 temporal variability, intra-plot spatial heterogeneity, and relic DNA effects on the soil 41 prokaryotic and fungal communities. We show that the intra-plot spatial variability in 42 microbial community composition was strong and independent of relic DNA effects with 43 these spatial patterns persisting throughout the study. When controlling for intra-plot 44 2 spatial variability, we identified significant temporal variability in both plots over the six-45 month study. These microbial communities were more dissimilar over time after relic 46 DNA was removed, suggesting that relic DNA hinders the detection of important 47 temporal dynamics in belowground microbial communities. We identified microbial taxa 48 that exhibited shared temporal responses and show these responses were often 49 predictable from temporal changes in soil conditions. Our findings highlight approaches 50 that can be used to better characterize temporal shifts in soil microbial communities, 51 information that is critical for predicting the environmental preferences of individual soil 52 microbial taxa and identifying linkages between soil microbial community composition 53 and belowground processes. 55Importance: Nearly all microbial communities are dynamic in time. Understanding how 56 temporal dynamics in microbial community structure affect soil biogeochemistry and 57 fertility are key to being able to predict the responses of the soil microbiome to 58 environmental perturbations. Here we explain the effects of soil spatial structure and 59 relic DNA on the determination of microbial community fluctuations over time. We found 60 that intensive spatial sampling is required to identify temporal effects in microbial 61 communities because of the high degree of spatial heterogeneity in soil and that DNA 62 from non-living microbial cells masks important temporal patterns. We identified groups 63 of microbes that display correlated behavior over time and show that these patterns are 64 predictable from soil characteristics. These results provide insight into the 65 environmental preferences and temporal relationships between individual microbial taxa 66 and highlight the importance of considering relic DNA when trying to detect temporal 67 dynamics in belowground communities. 68 69 Introduction: 70 Information on the temporal dynamics of m...

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Microbial Community Analysis of Colored Snow from an Alpine Snowfield in Northern Japan Reveals the Prevalence of Betaproteobacteria with Snow Algae

Cited by 45 publications

References 100 publications

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities

Unraveling the effects of spatial variability and relic DNA on the temporal dynamics of soil microbial communities

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