Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic

Coelho, Lígia F.; Couceiro, Joana Fernandes; Keller‐Costa, Tina; Valente, Sara; Ramalho, Tiago Pereirinha; Carneiro, Joana; Comte, Jérôme; Blais, Marie-Amélie; Vincent, Warwick F.; Martins, Zita; Canário, João; Costa, Rodrigo

doi:10.1016/j.scitotenv.2022.154286

Cited by 6 publications

(9 citation statements)

References 65 publications

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“…No colony forming units (CFUs) were registered on the processing control plates, during the 30 days of the experiment (Table 1 -A). The interface water samples had notable more culturable bacteria than the sea ice samples, an expected result since usually winter sea ice has relatively low biomass 28 . This suggests that the culture methodologies adopted were appropriate for the environmental samples used, validating the results of the processing control.…”

Section: Resultsmentioning

confidence: 75%

“…TC-DNA extractions were performed on the filters of both the environmental samples (Ice1, Ice2, Water1, Water2, Water3) the background controls (processing control and DNA-extraction control) at iBB in Portugal. The TC-DNA extraction was carried out as described previously 28 , 77 . The bench was previously cleaned with both ethanol (70%) and HCl (0.1 M).…”

Section: Methodsmentioning

confidence: 99%

“…The TC-DNA extracts were subjected to 16S rRNA gene-based high-throughput sequencing on an Illumina MiSeq platform at MR DNA following the company’s protocol ( www.mrdnalab.com , Shallowater, TX, USA) and using prokaryotic universal primers (for both bacterial and archaeal identification) 515F (5′ -GTG YCA GCM GCC GCG GTAA-3′) and 806RB (5′-GGA CTA CNV GGG TWT CTA AT-3′) 78 , 79 . During sequencing, an average of around 300 bp (base-pairs) sequences were generated for all samples as described in Coelho et al 28 . An average quantity of 23,000, 21,000, and 9000 paired-end sequences were generated per environmental interface water sample, background control sample, and environmental ice sample, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…The 16S rRNA gene amplicon libraries generated in this study were processed within the framework of a previous microbial ecology study on the Hudson Bay coastal ice 28 and deposited in the open-source online metagenomic repositorium European Nucleotide Archive (ENA) under the study accession number [PRJEB44116]. Briefly, raw sequences with less than 150 bp and with ambiguous base calls as well as chimeric sequences and singletons, were removed as described earlier 80 .…”

Section: Methodsmentioning

confidence: 99%

“…For example, ethanol is an effective disinfectant to decrease contamination for culture-dependent analysis, however, it does not destroy DNA molecules 20 . While excising the external layers of the ice cores has proved effective in removing most contaminating cells 20 , 23 , 26 , 27 , without compromising the interior native biota, no known protocol can completely prevent contamination, which leads us to the last possible resource for an ethical sampling and processing methodology: contamination monitoring through the use of background controls 27 that have proved to be very effective 27 , 28 . Culture-dependent and -independent analyses 9 , 27 , 29 – 39 have been used in background controls and in the planetary protection context.…”

Section: Introductionmentioning

confidence: 99%

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Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus

Coelho

Blais

Matveev

et al. 2022

Sci Rep

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Missions to detect extraterrestrial life are being designed to visit Europa and Enceladus in the next decades. The contact between the mission payload and the habitable subsurface of these satellites involves significant risk of forward contamination. The standardization of protocols to decontaminate ice cores from planetary field analogs of icy moons, and monitor the contamination in downstream analysis, has a direct application for developing clean approaches crucial to life detection missions in these satellites. Here we developed a comprehensive protocol that can be used to monitor and minimize the contamination of Arctic ice cores in processing and downstream analysis. We physically removed the exterior layers of ice cores to minimize bioburden from sampling. To monitor contamination, we constructed artificial controls and applied culture-dependent and culture-independent techniques such as 16S rRNA amplicon sequencing. We identified 13 bacterial contaminants, including a radioresistant species. This protocol decreases the contamination risk, provides quantitative and qualitative information about contamination agents, and allows validation of the results obtained. This study highlights the importance of decreasing and evaluating prokaryotic contamination in the processing of polar ice cores, including in their use as analogs of Europa and Enceladus.

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Section: Resultsmentioning

confidence: 75%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus

Coelho

Blais

Matveev

et al. 2022

Sci Rep

Self Cite

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Assessing the Impact of Recreational Activities on Streams: A Colorado Case Study

Hamdan,

Villaruel,

Newmeyer

et al. 2024

ACS EST Water

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Water-based recreational activities can impact freshwater systems, but the resulting anthropogenic alterations to the chemical and microbial composition of natural streams remain poorly understood. Utilizing state-of-the-art analytical approaches, including liquid chromatography-high-resolution mass spectrometry (LC-HRMS), inductively coupled plasma mass spectrometry (ICP-MS), and 16S rRNA gene sequencing, we investigated changes in stream chemistry and microbiology resulting from recreational activities in Clear Creek (Golden, Colorado). Spatial and temporal sampling was conducted for 3 days over a summer holiday weekend when a large influx of recreational float tubing activity occurred. Nontarget LC-HRMS analysis demonstrated substantial differences in the organic fingerprint on days and locations with high recreational use compared to that of low use. Similarly, increases in the total suspended solids were correlated with suspended particulate metal concentrations (Al, Cu, Ti, Pb, and Zn). Element ratios suggest recreation-induced resuspension of streambed sediments as the metal source rather than other anthropogenic inputs (e.g., Ti/Zn-containing sunscreens). Gene sequencing revealed significant shifts in the stream microbial community, supporting an input of human-associated enteric microbiota during high recreation periods. However, the overall results indicate that recreational activities have a short-lived effect on the stream. In this work, we established a first-of-its-kind holistic assessment of the impact of anthropogenic activity on a natural stream by simultaneously considering changes in the organic, inorganic, and microbial fingerprints.

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Evolution and adaptation of terrestrial plant‐associated Plantibacter species into remote marine environments

Liao,

Qin,

et al. 2024

Molecular Ecology

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Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant‐related bacteria in plant‐free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant‐associated relatives shared over 98% whole‐genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant‐related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non‐Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant‐associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth‐promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth‐promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant‐associated and plant‐free environments at the genome level.

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Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic

Cited by 6 publications

References 65 publications

Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus

Contamination analysis of Arctic ice samples as planetary field analogs and implications for future life-detection missions to Europa and Enceladus

Assessing the Impact of Recreational Activities on Streams: A Colorado Case Study

Evolution and adaptation of terrestrial plant‐associated Plantibacter species into remote marine environments

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